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Klumbys E, Xu W, Koduru L, Heng E, Wei Y, Wong FT, Zhao H, Ang EL. Discovery, characterization, and engineering of an advantageous Streptomyces host for heterologous expression of natural product biosynthetic gene clusters. Microb Cell Fact 2024; 23:149. [PMID: 38790014 PMCID: PMC11127301 DOI: 10.1186/s12934-024-02416-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Streptomyces is renowned for its robust biosynthetic capacity in producing medically relevant natural products. However, the majority of natural products biosynthetic gene clusters (BGCs) either yield low amounts of natural products or remain cryptic under standard laboratory conditions. Various heterologous production hosts have been engineered to address these challenges, and yet the successful activation of BGCs has still been limited. In our search for a valuable addition to the heterologous host panel, we identified the strain Streptomyces sp. A4420, which exhibited rapid initial growth and a high metabolic capacity, prompting further exploration of its potential. RESULTS We engineered a polyketide-focused chassis strain based on Streptomyces sp. A4420 (CH strain) by deleting 9 native polyketide BGCs. The resulting metabolically simplified organism exhibited consistent sporulation and growth, surpassing the performance of most existing Streptomyces based chassis strains in standard liquid growth media. Four distinct polyketide BGCs were chosen and expressed in various heterologous hosts, including the Streptomyces sp. A4420 wild-type and CH strains, alongside Streptomyces coelicolor M1152, Streptomyces lividans TK24, Streptomyces albus J1074, and Streptomyces venezuelae NRRL B-65442. Remarkably, only the Streptomyces sp. A4420 CH strain demonstrated the capability to produce all metabolites under every condition outperforming its parental strain and other tested organisms. To enhance visualization and comparison of the tested strains, we developed a matrix-like analysis involving 15 parameters. This comprehensive analysis unequivocally illustrated the significant potential of the new strain to become a popular heterologous host. CONCLUSION Our engineered Streptomyces sp. A4420 CH strain exhibits promising attributes for the heterologous expression of natural products with a focus on polyketides, offering an alternative choice in the arsenal of heterologous production strains. As genomics and cloning strategies progress, establishment of a diverse panel of heterologous production hosts will be crucial for expediting the discovery and production of medically relevant natural products derived from Streptomyces.
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Affiliation(s)
- Evaldas Klumbys
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore
| | - Wei Xu
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore.
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore.
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Zhuang Z, Kong W, Wen Z, Tong N, Lin J, Zhang F, Fan Z, Yi L, Huang Y, Duan Y, Yan X, Zhu X. Combinatorial metabolic engineering of Streptomyces sp. CB03234-S for the enhanced production of anthraquinone-fused enediyne tiancimycins. Microb Cell Fact 2024; 23:128. [PMID: 38704580 PMCID: PMC11069151 DOI: 10.1186/s12934-024-02399-w] [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: 02/19/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Anthraquinone-fused enediynes (AFEs) are excellent payloads for antibody-drug conjugates (ADCs). The yields of AFEs in the original bacterial hosts are extremely low. Multiple traditional methods had been adopted to enhance the production of the AFEs. Despite these efforts, the production titers of these compounds are still low, presenting a practical challenge for their development. Tiancimycins (TNMs) are a class of AFEs produced by Streptomyces sp. CB03234. One of their salient features is that they exhibit rapid and complete cell killing ability against various cancer cell lines. RESULTS In this study, a combinatorial metabolic engineering strategy guided by the CB03234-S genome and transcriptome was employed to improve the titers of TNMs. First, re-sequencing of CB03234-S (Ribosome engineered mutant strains) genome revealed the deletion of a 583-kb DNA fragment, accounting for about 7.5% of its genome. Second, by individual or combined inactivation of seven potential precursor competitive biosynthetic gene clusters (BGCs) in CB03234-S, a double-BGC inactivation mutant, S1009, was identified with an improved TNMs titer of 28.2 ± 0.8 mg/L. Third, overexpression of five essential biosynthetic genes, including two post-modification genes, and three self-resistance auxiliary genes, was also conducted, through which we discovered that mutants carrying the core genes, tnmE or tnmE10, exhibited enhanced TNMs production. The average TNMs yield reached 43.5 ± 2.4 mg/L in a 30-L fermenter, representing an approximately 360% increase over CB03234-S and the highest titer among all AFEs to date. Moreover, the resulting mutant produced TNM-W, a unique TNM derivative with a double bond instead of a common ethylene oxide moiety. Preliminary studies suggested that TNM-W was probably converted from TNM-A by both TnmE and TnmE10. CONCLUSIONS Based on the genome and transcriptome analyses, we adopted a combined metabolic engineering strategy for precursor enrichment and biosynthetic pathway reorganization to construct a high-yield strain of TNMs based on CB03234-S. Our study establishes a solid basis for the clinical development of AFE-based ADCs.
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Affiliation(s)
- Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Wenping Kong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Zhongqing Wen
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Nian Tong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Jing Lin
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Fan Zhang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Zhiying Fan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
- The Affiliated Nanhua Hospital, Department of Pharmacy, Institute of Clinical Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421002, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, China.
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China.
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, China.
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Lee SQE, Ma GL, Candra H, Khandelwal S, Pang LM, Low ZJ, Cheang QW, Liang ZX. Streptomyces sungeiensis SD3 as a Microbial Chassis for the Heterologous Production of Secondary Metabolites. ACS Synth Biol 2024; 13:1259-1272. [PMID: 38513222 DOI: 10.1021/acssynbio.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
We present the newly isolated Streptomyces sungeiensis SD3 strain as a promising microbial chassis for heterologous production of secondary metabolites. S. sungeiensis SD3 exhibits several advantageous traits as a microbial chassis, including genetic tractability, rapid growth, susceptibility to antibiotics, and metabolic capability supporting secondary metabolism. Genomic and transcriptomic sequencing unveiled the primary metabolic capabilities and secondary biosynthetic pathways of S. sungeiensis SD3, including a previously unknown pathway responsible for the biosynthesis of streptazone B1. The unique placement of S. sungeiensis SD3 in the phylogenetic tree designates it as a type strain, setting it apart from other frequently employed Streptomyces chassis. This distinction makes it the preferred chassis for expressing biosynthetic gene clusters (BGCs) derived from strains within the same phylogenetic or neighboring phylogenetic clade. The successful expression of secondary biosynthetic pathways from a closely related yet slow-growing strain underscores the utility of S. sungeiensis SD3 as a heterologous expression chassis. Validation of CRISPR/Cas9-assisted genetic tools for chromosomal deletion and insertion paved the way for further strain improvement and BGC refactoring through rational genome editing. The addition of S. sungeiensis SD3 to the heterologous chassis toolkit will facilitate the discovery and production of secondary metabolites.
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Affiliation(s)
- Sean Qiu En Lee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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Rill A, Zhao L, Bode HB. Genetic toolbox for Photorhabdus and Xenorhabdus: pSEVA based heterologous expression systems and CRISPR/Cpf1 based genome editing for rapid natural product profiling. Microb Cell Fact 2024; 23:98. [PMID: 38561780 PMCID: PMC10983751 DOI: 10.1186/s12934-024-02363-8] [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: 12/17/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Bacteria of the genus Photorhabdus and Xenorhabdus are motile, Gram-negative bacteria that live in symbiosis with entomopathogenic nematodes. Due to their complex life cycle, they produce a large number of specialized metabolites (natural products) encoded in biosynthetic gene clusters (BGC). Genetic tools for Photorhabdus and Xenorhabdus have been rare and applicable to only a few strains. In the past, several tools have been developed for the activation of BGCs and the deletion of individual genes. However, these often have limited efficiency or are time consuming. Among the limitations, it is essential to have versatile expression systems and genome editing tools that could facilitate the practical work. RESULTS In the present study, we developed several expression vectors and a CRISPR-Cpf1 genome editing vector for genetic manipulations in Photorhabdus and Xenorhabdus using SEVA plasmids. The SEVA collection is based on modular vectors that allow exchangeability of different elements (e.g. origin of replication and antibiotic selection markers with the ability to insert desired sequences for different end applications). Initially, we tested different SEVA vectors containing the broad host range origins and three different resistance genes for kanamycin, gentamycin and chloramphenicol, respectively. We demonstrated that these vectors are replicative not only in well-known representatives, e.g. Photorhabdus laumondii TTO1, but also in other rarely described strains like Xenorhabdus sp. TS4. For our CRISPR/Cpf1-based system, we used the pSEVA231 backbone to delete not only small genes but also large parts of BGCs. Furthermore, we were able to activate and refactor BGCs to obtain high production titers of high value compounds such as safracin B, a semisynthetic precursor for the anti-cancer drug ET-743. CONCLUSIONS The results of this study provide new inducible expression vectors and a CRISPR/CPf1 encoding vector all based on the SEVA (Standard European Vector Architecture) collection, which can improve genetic manipulation and genome editing processes in Photorhabdus and Xenorhabdus.
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Affiliation(s)
- Alexander Rill
- Department of Natural Products in Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Chemical Biology, Phillips University Marburg, 35043, Marburg, Germany
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Chemical Biology, Phillips University Marburg, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043, Marburg, Germany.
- Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany.
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Ravagnan G, Lesemann J, Müller MF, Poehlein A, Daniel R, Noack S, Kabisch J, Schmid J. Genome reduction in Paenibacillus polymyxa DSM 365 for chassis development. Front Bioeng Biotechnol 2024; 12:1378873. [PMID: 38605990 PMCID: PMC11007031 DOI: 10.3389/fbioe.2024.1378873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
The demand for highly robust and metabolically versatile microbes is of utmost importance for replacing fossil-based processes with biotechnological ones. Such an example is the implementation of Paenibacillus polymyxa DSM 365 as a novel platform organism for the production of value-added products such as 2,3-butanediol or exopolysaccharides. For this, a complete genome sequence is the first requirement towards further developing this host towards a microbial chassis. A genome sequencing project has just been reported for P. polymyxa DSM 365 showing a size of 5,788,318 bp with a total of 47 contigs. Herein, we report the first complete genome sequence of P. polymyxa DSM 365, which consists of 5,889,536 bp with 45 RNAs, 106 tRNAs, 5,370 coding sequences and an average GC content of 45.6%, resulting in a closed genome of P. polymyxa 365. The additional nucleotide data revealed a novel NRPS synthetase that may contribute to the production of tridecaptin. Building on these findings, we initiated the top-down construction of a chassis variant of P. polymyxa. In the first stage, single knock-out mutants of non-essential genomic regions were created and evaluated for their biological fitness. As a result, two out of 18 variants showed impaired growth. The remaining deletion mutants were combined in two genome-reduced P. polymyxa variants which either lack the production of endogenous biosynthetic gene clusters (GR1) or non-essential genomic regions including the insertion sequence ISPap1 (GR2), with a decrease of the native genome of 3.0% and 0.6%, respectively. Both variants, GR1 and GR2, showed identical growth characteristics to the wild-type. Endpoint titers of 2,3-butanediol and EPS production were also unaffected, validating these genome-reduced strains as suitable for further genetic engineering.
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Affiliation(s)
- Giulia Ravagnan
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Janne Lesemann
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Moritz-Fabian Müller
- Institute of Bio-and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Stephan Noack
- Institute of Bio-and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Johannes Kabisch
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Kim K, Choe D, Cho S, Palsson B, Cho BK. Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology. Trends Biotechnol 2024:S0167-7799(24)00037-4. [PMID: 38423803 DOI: 10.1016/j.tibtech.2024.02.008] [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: 12/14/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Advances in systems and synthetic biology have propelled the construction of reduced bacterial genomes. Genome reduction was initially focused on exploring properties of minimal genomes, but more recently it has been deployed as an engineering strategy to enhance strain performance. This review provides the latest updates on reduced genomes, focusing on dual-track approaches of top-down reduction and bottom-up synthesis for their construction. Using cases from studies that are based on established industrial workhorse strains, we discuss the construction of a series of synthetic phenotypes that are candidates for biotechnological applications. Finally, we address the possible uses of reduced genomes for biotechnological applications and the needed future research directions that may ultimately lead to the total synthesis of rationally designed genomes.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Suhyung Cho
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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8
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Augustijn HE, Roseboom AM, Medema MH, van Wezel GP. Harnessing regulatory networks in Actinobacteria for natural product discovery. J Ind Microbiol Biotechnol 2024; 51:kuae011. [PMID: 38569653 PMCID: PMC10996143 DOI: 10.1093/jimb/kuae011] [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: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Anna M Roseboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Hamed MB, Busche T, Simoens K, Carpentier S, Kormanec J, Van Mellaert L, Anné J, Kalinowski J, Bernaerts K, Karamanou S, Economou A. Enhanced protein secretion in reduced genome strains of Streptomyces lividans. Microb Cell Fact 2024; 23:13. [PMID: 38183102 PMCID: PMC10768272 DOI: 10.1186/s12934-023-02269-x] [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: 07/26/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND S. lividans TK24 is a popular host for the production of small molecules and the secretion of heterologous protein. Within its large genome, twenty-nine non-essential clusters direct the biosynthesis of secondary metabolites. We had previously constructed ten chassis strains, carrying deletions in various combinations of specialized metabolites biosynthetic clusters, such as those of the blue actinorhodin (act), the calcium-dependent antibiotic (cda), the undecylprodigiosin (red), the coelimycin A (cpk) and the melanin (mel) clusters, as well as the genes hrdD, encoding a non-essential sigma factor, and matAB, a locus affecting mycelial aggregation. Genome reduction was aimed at reducing carbon flow toward specialized metabolite biosynthesis to optimize the production of secreted heterologous protein. RESULTS Two of these S. lividans TK24 derived chassis strains showed ~ 15% reduction in biomass yield, 2-fold increase of their total native secretome mass yield and enhanced abundance of several secreted proteins compared to the parental strain. RNAseq and proteomic analysis of the secretome suggested that genome reduction led to cell wall and oxidative stresses and was accompanied by the up-regulation of secretory chaperones and of secDF, a Sec-pathway component. Interestingly, the amount of the secreted heterologous proteins mRFP and mTNFα, by one of these strains, was 12 and 70% higher, respectively, than that secreted by the parental strain. CONCLUSION The current study described a strategy to construct chassis strains with enhanced secretory abilities and proposed a model linking the deletion of specialized metabolite biosynthetic clusters to improved production of secreted heterologous proteins.
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Affiliation(s)
- Mohamed Belal Hamed
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, B-3000, Belgium
- Molecular Biology Depart, National Research Centre, Dokii, Cairo, Egypt
- Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Kenneth Simoens
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, Leuven, B-3001, Belgium
| | - Sebastien Carpentier
- SYBIOMA, KU Leuven facility for Systems Biology Based Mass Spectrometry, Leuven, B-3000, Belgium
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, Bratislava, 84551, Slovakia
| | - Lieve Van Mellaert
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, B-3000, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, B-3000, Belgium
| | - Joern Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, Leuven, B-3001, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, B-3000, Belgium.
| | - Anastassios Economou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, B-3000, Belgium
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10
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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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11
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Qiu S, Yang B, Li Z, Li S, Yan H, Xin Z, Liu J, Zhao X, Zhang L, Xiang W, Wang W. Building a highly efficient Streptomyces super-chassis for secondary metabolite production by reprogramming naturally-evolved multifaceted shifts. Metab Eng 2024; 81:210-226. [PMID: 38142854 DOI: 10.1016/j.ymben.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Streptomyces has an extensive array of bioactive secondary metabolites (SMs). Nevertheless, devising a framework for the heterologous production of these SMs remains challenging. We here reprogrammed a versatile plug-and-play Streptomyces super-chassis and established a universal pipeline for production of diverse SMs via understanding of the inherent pleiotropic effects of ethanol shock on jadomycin production in Streptomyces venezuelae. We initially identified and characterized a set of multiplex targets (afsQ1, bldD, bldA, and miaA) that contribute to SM (jadomycin) production when subjected to ethanol shock. Subsequently, we developed an ethanol-induced orthogonal amplification system (EOAS), enabling dynamic and precise control over targets. Ultimately, we integrated these multiplex targets into functional units governed by the EOAS, generating a universal and plug-and-play Streptomyces super-chassis. In addition to achieving the unprecedented titer and yield of jadomycin B, we also evidenced the potential of this super-chassis for production of diverse heterologous SMs, including antibiotic oxytetracycline, anticancer drug doxorubicins, agricultural herbicide thaxtomin A, and plant growth regulator guvermectin, all with the yields of >10 mg/g glucose in a simple mineral medium. Given that the production of SMs all required complexed medium and the cognate yields were usually much lower, our achievement of using a universal super-chassis and engineering pipeline in a simple mineral medium is promising for convenient heterologous production of SMs.
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Affiliation(s)
- Shiwen Qiu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bowen Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, 200237, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingfang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuejin Zhao
- State Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, 200237, China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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12
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Seo K, Shu W, Rückert-Reed C, Gerlinger P, Erb TJ, Kalinowski J, Wittmann C. From waste to health-supporting molecules: biosynthesis of natural products from lignin-, plastic- and seaweed-based monomers using metabolically engineered Streptomyces lividans. Microb Cell Fact 2023; 22:262. [PMID: 38114944 PMCID: PMC10731712 DOI: 10.1186/s12934-023-02266-0] [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: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Transforming waste and nonfood materials into bulk biofuels and chemicals represents a major stride in creating a sustainable bioindustry to optimize the use of resources while reducing environmental footprint. However, despite these advancements, the production of high-value natural products often continues to depend on the use of first-generation substrates, underscoring the intricate processes and specific requirements of their biosyntheses. This is also true for Streptomyces lividans, a renowned host organism celebrated for its capacity to produce a wide array of natural products, which is attributed to its genetic versatility and potent secondary metabolic activity. Given this context, it becomes imperative to assess and optimize this microorganism for the synthesis of natural products specifically from waste and nonfood substrates. RESULTS We metabolically engineered S. lividans to heterologously produce the ribosomally synthesized and posttranslationally modified peptide bottromycin, as well as the polyketide pamamycin. The modified strains successfully produced these compounds using waste and nonfood model substrates such as protocatechuate (derived from lignin), 4-hydroxybenzoate (sourced from plastic waste), and mannitol (from seaweed). Comprehensive transcriptomic and metabolomic analyses offered insights into how these substrates influenced the cellular metabolism of S. lividans. In terms of production efficiency, S. lividans showed remarkable tolerance, especially in a fed-batch process using a mineral medium containing the toxic aromatic 4-hydroxybenzoate, which led to enhanced and highly selective bottromycin production. Additionally, the strain generated a unique spectrum of pamamycins when cultured in mannitol-rich seaweed extract with no additional nutrients. CONCLUSION Our study showcases the successful production of high-value natural products based on the use of varied waste and nonfood raw materials, circumventing the reliance on costly, food-competing resources. S. lividans exhibited remarkable adaptability and resilience when grown on these diverse substrates. When cultured on aromatic compounds, it displayed a distinct array of intracellular CoA esters, presenting promising avenues for polyketide production. Future research could be focused on enhancing S. lividans substrate utilization pathways to process the intricate mixtures commonly found in waste and nonfood sources more efficiently.
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Affiliation(s)
- Kyoyoung Seo
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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13
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Geistodt-Kiener A, Totozafy JC, Le Goff G, Vergne J, Sakai K, Ouazzani J, Mouille G, Viaud M, O'Connell RJ, Dallery JF. Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites. Metab Eng 2023; 80:216-231. [PMID: 37863177 DOI: 10.1016/j.ymben.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Transcriptomic studies have revealed that fungal pathogens of plants activate the expression of numerous biosynthetic gene clusters (BGC) exclusively when in presence of a living host plant. The identification and structural elucidation of the corresponding secondary metabolites remain challenging. The aim was to develop a polycistronic system for heterologous expression of fungal BGCs in Saccharomyces cerevisiae. Here we adapted a polycistronic vector for efficient, seamless and cost-effective cloning of biosynthetic genes using in vivo assembly (also called transformation-assisted recombination) directly in Escherichia coli followed by heterologous expression in S. cerevisiae. Two vectors were generated with different auto-inducible yeast promoters and selection markers. The effectiveness of these vectors was validated with fluorescent proteins. As a proof-of-principle, we applied our approach to the Colletochlorin family of molecules. These polyketide secondary metabolites were known from the phytopathogenic fungus Colletotrichum higginsianum but had never been linked to their biosynthetic genes. Considering the requirement for a halogenase, and by applying comparative genomics, we identified a BGC putatively involved in the biosynthesis of Colletochlorins in C. higginsianum. Following the expression of those genes in S. cerevisiae, we could identify the presence of the precursor Orsellinic acid, Colletochlorins and their non-chlorinated counterparts, the Colletorins. In conclusion, the polycistronic vectors described herein were adapted for the host S. cerevisiae and allowed to link the Colletochlorin compound family to their corresponding biosynthetic genes. This system will now enable the production and purification of infection-specific secondary metabolites of fungal phytopathogens. More widely, this system could be applied to any fungal BGC of interest.
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Affiliation(s)
| | - Jean Chrisologue Totozafy
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, 78000, Versailles, France
| | - Géraldine Le Goff
- Centre National de La Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, 91190, Gif-sur-Yvette, France
| | - Justine Vergne
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Kaori Sakai
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jamal Ouazzani
- Centre National de La Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, 91190, Gif-sur-Yvette, France
| | - Grégory Mouille
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, 78000, Versailles, France
| | - Muriel Viaud
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
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14
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Beganovic S, Rückert-Reed C, Sucipto H, Shu W, Gläser L, Patschkowski T, Struck B, Kalinowski J, Luzhetskyy A, Wittmann C. Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer. Microb Cell Fact 2023; 22:222. [PMID: 37898787 PMCID: PMC10612213 DOI: 10.1186/s12934-023-02215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Oxytetracycline which is derived from Streptomyces rimosus, inhibits a wide range of bacteria and is industrially important. The underlying biosynthetic processes are complex and hinder rational engineering, so industrial manufacturing currently relies on classical mutants for production. While the biochemistry underlying oxytetracycline synthesis is known to involve polyketide synthase, hyperproducing strains of S. rimosus have not been extensively studied, limiting our knowledge on fundamental mechanisms that drive production. RESULTS In this study, a multiomics analysis of S. rimosus is performed and wild-type and hyperproducing strains are compared. Insights into the metabolic and regulatory networks driving oxytetracycline formation were obtained. The overproducer exhibited increased acetyl-CoA and malonyl CoA supply, upregulated oxytetracycline biosynthesis, reduced competing byproduct formation, and streamlined morphology. These features were used to synthesize bhimamycin, an antibiotic, and a novel microbial chassis strain was created. A cluster deletion derivative showed enhanced bhimamycin production. CONCLUSIONS This study suggests that the precursor supply should be globally increased to further increase the expression of the oxytetracycline cluster while maintaining the natural cluster sequence. The mutagenized hyperproducer S. rimosus HP126 exhibited numerous mutations, including large genomic rearrangements, due to natural genetic instability, and single nucleotide changes. More complex mutations were found than those typically observed in mutagenized bacteria, impacting gene expression, and complicating rational engineering. Overall, the approach revealed key traits influencing oxytetracycline production in S. rimosus, suggesting that similar studies for other antibiotics could uncover general mechanisms to improve production.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Hilda Sucipto
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Ben Struck
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany. *
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15
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Lopatniuk M, Riedel F, Wildfeuer J, Stierhof M, Dahlem C, Kiemer AK, Luzhetskyy A. Development of a Streptomyces-based system for facile thioholgamide library generation and analysis. Metab Eng 2023; 78:48-60. [PMID: 37142115 DOI: 10.1016/j.ymben.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide - a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.
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Affiliation(s)
- Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Florian Riedel
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Julia Wildfeuer
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Marc Stierhof
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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16
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Cuervo L, Malmierca MG, García-Salcedo R, Méndez C, Salas JA, Olano C, Ceniceros A. Co-Expression of Transcriptional Regulators and Housekeeping Genes in Streptomyces spp.: A Strategy to Optimize Metabolite Production. Microorganisms 2023; 11:1585. [PMID: 37375086 DOI: 10.3390/microorganisms11061585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The search for novel bioactive compounds to overcome resistance to current therapeutics has become of utmost importance. Streptomyces spp. are one of the main sources of bioactive compounds currently used in medicine. In this work, five different global transcriptional regulators and five housekeeping genes, known to induce the activation or overproduction of secondary metabolites in Streptomyces coelicolor, were cloned in two separated constructs and expressed in 12 different strains of Streptomyces spp. from the in-house CS collection. These recombinant plasmids were also inserted into streptomycin and rifampicin resistant Streptomyces strains (mutations known to enhance secondary metabolism in Streptomyces). Different media with diverse carbon and nitrogen sources were selected to assess the strains' metabolite production. Cultures were then extracted with different organic solvents and analysed to search for changes in their production profiles. An overproduction of metabolites already known to be produced by the biosynthesis wild-type strains was observed such as germicidin by CS113, collismycins by CS149 and CS014, or colibrimycins by CS147. Additionally, the activation of some compounds such as alteramides in CS090a pSETxkBMRRH and CS065a pSETxkDCABA or inhibition of the biosynthesis of chromomycins in CS065a in pSETxkDCABA when grown in SM10 was demonstrated. Therefore, these genetic constructs are a relatively simple tool to manipulate Streptomyces metabolism and explore their wide secondary metabolites production potential.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Mónica G Malmierca
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Raúl García-Salcedo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - José A Salas
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Ana Ceniceros
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
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17
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 DOI: 10.3390/ph16060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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18
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Ye JJ, Zou RJ, Zhou DD, Deng XL, Wu NL, Chen DD, Xu J. Insights into the phylogenetic diversity, biological activities, and biosynthetic potential of mangrove rhizosphere Actinobacteria from Hainan Island. Front Microbiol 2023; 14:1157601. [PMID: 37323895 PMCID: PMC10264631 DOI: 10.3389/fmicb.2023.1157601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Mangrove rhizosphere soils host diverse Actinobacteria tolerant to numerous stresses and are inevitably capable of exhibiting excellent biological activity by producing impressive numbers of bioactive natural products, including those with potential medicinal applications. In this study, we applied an integrated strategy of combining phylogenetic diversity, biological activities, and biosynthetic gene clusters (BGCs) screening approach to investigate the biotechnological importance of Actinobacteria isolated from mangrove rhizosphere soils from Hainan Island. The actinobacterial isolates were identifified using a combination of colony morphological characteristics and 16S rRNA gene sequence analysis. Based on the results of PCR-detected BGCs screening, type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes were detected. Crude extracts of 87 representative isolates were subjected to antimicrobial evaluation by determining the minimum inhibitory concentration of each strain against six indicator microorganisms, anticancer activities were determined on human cancer cell lines HepG2, HeLa, and HCT-116 using an MTT colorimetric assay, and immunosuppressive activities against the proliferation of Con A-induced T murine splenic lymphocytes in vitro. A total of 287 actinobacterial isolates affiliated to 10 genera in eight families of six orders were isolated from five different mangrove rhizosphere soil samples, specififically, Streptomyces (68.29%) and Micromonospora (16.03%), of which 87 representative strains were selected for phylogenetic analysis. The crude extracts of 39 isolates (44.83%) showed antimicrobial activity against at least one of the six tested indicator pathogens, especially ethyl acetate extracts of A-30 (Streptomyces parvulus), which could inhibit the growth of six microbes with MIC values reaching 7.8 μg/mL against Staphylococcus aureus and its resistant strain, compared to the clinical antibiotic ciproflfloxacin. Furthermore, 79 crude extracts (90.80%) and 48 (55.17%) of the isolates displayed anticancer and immunosuppressive activities, respectively. Besides, four rare strains exhibited potent immunosuppressive activity against the proliferation of Con A-induced T murine splenic lymphocyte in vitro with an inhibition rate over 60% at 10 μg/mL. Type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes were detected in 49.43, 66.67, and 88.51% of the 87 Actinobacteria, respectively. Signifificantly, these strains (26 isolates, 29.89%) harbored PKS I, PKS II, and NRPS genes in their genomes. Nevertheless, their bioactivity is independent of BGCs in this study. Our findings highlighted the antimicrobial, immunosuppressive, and anticancer potential of mangrove rhizosphere Actinobacteria from Hainan Island and the biosynthetic prospects of exploiting the corresponding bioactive natural product.
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Affiliation(s)
| | | | | | | | | | | | - Jing Xu
- Collaborative Innovation Center of Ecological Civilization, School of Chemical Engineering and Technology, Hainan University, Haikou, China
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19
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Moore SJ, Lai HE, Li J, Freemont PS. Streptomyces cell-free systems for natural product discovery and engineering. Nat Prod Rep 2023; 40:228-236. [PMID: 36341536 PMCID: PMC9945932 DOI: 10.1039/d2np00057a] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces bacteria are a major microbial source of natural products, which are encoded within so-called biosynthetic gene clusters (BGCs). This highlight discusses the emergence of native Streptomyces cell-free systems as a new tool to accelerate the study of the fundamental chemistry and biology of natural product biosynthesis from these bacteria. Cell-free systems provide a prototyping platform to study plug-and-play reactions in microscale reactions. So far, Streptomyces cell-free systems have been used to rapidly characterise gene expression regulation, access secondary metabolite biosynthetic enzymes, and catalyse cell-free transcription, translation, and biosynthesis of example natural products. With further progress, we anticipate the development of more complex systems to complement existing experimental tools for the discovery and engineering of natural product biosynthesis from Streptomyces and related high G + C (%) bacteria.
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Affiliation(s)
- Simon J Moore
- School of Biosciences, University of Kent, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, UK.
| | - Hung-En Lai
- School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, China
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20
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Palermo A. Metabolomics- and systems-biology-guided discovery of metabolite lead compounds and druggable targets. Drug Discov Today 2023; 28:103460. [PMID: 36427778 DOI: 10.1016/j.drudis.2022.103460] [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: 08/31/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Metabolomics enables the comprehensive and unbiased analysis of metabolites and lipids in biological systems. In conjunction with high-throughput activity screening, big data and synthetic biology, metabolomics can guide the discovery of lead compounds with pharmacological activity from natural sources and the gut microbiome. In combination with other omics, metabolomics can further unlock the elucidation of compound toxicity, the mode of action and novel druggable targets of disease. Here, we discuss the workflows, limitations and future opportunities to leverage metabolomics and big data in conjunction with systems and synthetic biology for streamlining the discovery and development of molecules of pharmaceutical interest.
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Affiliation(s)
- Amelia Palermo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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21
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Genomics-Driven Discovery of Benzoxazole Alkaloids from the Marine-Derived Micromonospora sp. SCSIO 07395. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020821. [PMID: 36677886 PMCID: PMC9864271 DOI: 10.3390/molecules28020821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/02/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023]
Abstract
Benzoxazole alkaloids exhibit a diverse array of structures and interesting biological activities. Herein we report the identification of a benzoxazole alkaloid-encoding biosynthetic gene cluster (mich BGC) in the marine-derived actinomycete Micromonospora sp. SCSIO 07395 and the heterologous expression of this BGC in Streptomyces albus. This approach led to the discovery of five new benzoxazole alkaloids microechmycin A-E (1-5), and a previously synthesized compound 6. Their structures were elucidated by HRESIMS and 1D and 2D NMR data. Microechmycin A (1) showed moderate antibacterial activity against Micrococcus luteus SCSIO ML01 with the minimal inhibitory concentration (MIC) value of 8 μg mL-1.
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22
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Rebets Y, Kormanec J, Lutzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production. Methods Mol Biol 2023; 2555:213-260. [PMID: 36306090 DOI: 10.1007/978-1-0716-2795-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.
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Affiliation(s)
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Lutzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety Division, KU Leuven, Leuven, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, lab. Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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23
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Hegemann JD, Birkelbach J, Walesch S, Müller R. Current developments in antibiotic discovery: Global microbial diversity as a source for evolutionary optimized anti-bacterials: Global microbial diversity as a source for evolutionary optimized anti-bacterials. EMBO Rep 2022; 24:e56184. [PMID: 36541849 PMCID: PMC9827545 DOI: 10.15252/embr.202256184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
In light of the pending antibiotic resistance crisis, we need to go back to nature and search for novel anti-bacterial compounds.
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Affiliation(s)
- Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany
| | - Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
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24
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Walesch S, Birkelbach J, Jézéquel G, Haeckl FPJ, Hegemann JD, Hesterkamp T, Hirsch AKH, Hammann P, Müller R. Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials. EMBO Rep 2022; 24:e56033. [PMID: 36533629 PMCID: PMC9827564 DOI: 10.15252/embr.202256033] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Thomas Hesterkamp
- Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
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25
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Shelton KE, Mitchell DA. Bioinformatic prediction and experimental validation of RiPP recognition elements. Methods Enzymol 2022; 679:191-233. [PMID: 36682862 PMCID: PMC9871372 DOI: 10.1016/bs.mie.2022.08.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products for which discovery efforts have rapidly grown over the past decade. There are currently 38 known RiPP classes encoded by prokaryotes. Half of the prokaryotic RiPP classes include a protein domain called the RiPP Recognition Element (RRE) for successful installation of post-translational modifications on a RiPP precursor peptide. In most cases, the RRE domain binds to the N-terminal "leader" region of the precursor peptide, facilitating enzymatic modification of the C-terminal "core" region. The prevalence of the RRE domain renders it a theoretically useful bioinformatic handle for class-independent RiPP discovery; however, first-in-class RiPPs have yet to be isolated and experimentally characterized using an RRE-centric strategy. Moreover, with most known RRE domains engaging their cognate precursor peptide(s) with high specificity and nanomolar affinity, evaluation of the residue-specific interactions that govern RRE:substrate complexation is a necessary first step to leveraging the RRE domain for various bioengineering applications. This chapter details protocols for developing custom bioinformatic models to predict and annotate RRE domains in a class-specific manner. Next, we outline methods for experimental validation of precursor peptide binding using fluorescence polarization binding assays and in vitro enzyme activity assays. We anticipate the methods herein will guide and enhance future critical analyses of the RRE domain, eventually enabling its future use as a customizable tool for molecular biology.
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Affiliation(s)
- Kyle E Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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26
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Yang Z, Liu C, Wang Y, Chen Y, Li Q, Zhang Y, Chen Q, Ju J, Ma J. MGCEP 1.0: A Genetic-Engineered Marine-Derived Chassis Cell for a Scaled Heterologous Expression Platform of Microbial Bioactive Metabolites. ACS Synth Biol 2022; 11:3772-3784. [PMID: 36241611 DOI: 10.1021/acssynbio.2c00362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Marine microorganisms produce a variety of bioactive secondary metabolites, which represent a significant source of novel antibiotics. Heterologous expression is a valuable tool for discovering marine microbial secondary metabolites; however, marine-derived chassis cell is very scarce. Here, we build an efficient plug-and-play marine-derived gene clusters expression platform 1.0 (MGCEP 1.0) by the systematic engineering of the deep-sea-derived Streptomyces atratus SCSIO ZH16. For a proof of concept, four families of microbial bioactive metabolite biosynthetic gene clusters (BGCs), including alkaloids, aminonucleosides, nonribosomal peptides, and polyketides, were efficiently expressed in this platform. Moreover, 19 compounds, including two new angucycline antibiotics, were produced in MGCEP 1.0. Dynamic patterns of global biosynthetic gene expression in MGCEP 1.0 with or without a heterologous gene cluster were revealed at the transcriptome level. The platform MGCEP 1.0 provides new possibilities for expressing microbial secondary metabolites, especially of marine origin.
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Affiliation(s)
- Zhijie Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Chunyu Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China
| | - Yuyang Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Yingying Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Yun Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Qi Chen
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
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27
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Paulus C, Myronovskyi M, Zapp J, Rodríguez Estévez M, Lopatniuk M, Rosenkränzer B, Palusczak A, Luzhetskyy A. Miramides A–D: Identification of Detoxin-like Depsipeptides after Heterologous Expression of a Hybrid NRPS-PKS Gene Cluster from Streptomyces mirabilis Lu17588. Microorganisms 2022; 10:microorganisms10091752. [PMID: 36144353 PMCID: PMC9503745 DOI: 10.3390/microorganisms10091752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Natural products derived from plants, fungi or bacteria have been used for years in the medicine, agriculture and food industries as they exhibit a variety of beneficial properties, such as antibiotic, antifungal, anticancer, herbicidal and immunosuppressive activities. Compared to synthetic compounds, natural products possess a greater chemical diversity, which is a reason why they are profitable templates for developing pharmaceutical drug candidates and ongoing research on them is inevitable. Performing heterologous expression with unknown gene clusters is the preferred method to activate gene clusters that are not expressed in the wild-type strain under laboratory conditions; thus, this method offers a way to discover new interesting metabolites. Here, we report the gene cluster assembly of a hybrid NRPS-PKS gene cluster from Streptomyces mirabilis Lu17588, which was heterologously expressed in Streptomyces albus Del14. Four new compounds were produced by the obtained strain, which were named miramides A–D. Isolation and structure elucidation revealed similarity of the isolated compounds to the known depsipeptides rimosamides/detoxins.
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Affiliation(s)
- Constanze Paulus
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Marta Rodríguez Estévez
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maria Lopatniuk
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Birgit Rosenkränzer
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Anja Palusczak
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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28
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Abstract
Actinomycetes are natural architects of numerous secondary metabolites including antibiotics. With increased multidrug-resistant (MDR) pathogens, antibiotics that can combat such pathogens are urgently required to improve the health care system globally. The characterization of actinomycetes available in Nepal is still very much untouched which is the reason why this paper showcases the characterization of actinomycetes from Nepal based on their morphology, 16S rRNA gene sequencing, and metabolic profiling. Additionally, antimicrobial assays and liquid chromatography-high resolution mass spectrometry (LC-HRMS) of ethyl acetate extracts were performed. In this study, we employed a computational-based dereplication strategy for annotating molecules which is also time-efficient. Molecular annotation was performed through the GNPS server, the SIRIUS platform, and the available databases to predict the secondary metabolites. The sequencing of the 16S rRNA gene revealed that the isolates BN6 and BN14 are closely related to Streptomyces species. BN14 showed broad-spectrum antibacterial activity with the zone of inhibition up to 30 mm against Staphylococcus aureus (MIC: 0.3051 µg/mL and MBC: 9.7656 µg/mL) and Shigella sonnei (MIC: 0.3051 µg/mL and MBC: 4.882 µg/mL). Likewise, BN14 also displayed significant inhibition to Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella typhi. GNPS approach suggested that the extracts of BN6 and BN14 consisted of diketopiperazines ((cyclo(D-Trp-L-Pro), cyclo(L-Leu-L-4-hydroxy-Pro), cyclo(L-Phe-D-Pro), cyclo(L-Trp-L-Pro), cyclo(L-Val-L-Pro)), and polypeptide antibiotics (actinomycin D and X2). Additional chemical scaffolds such as bacterial alkaloids (bohemamine, venezueline B, and G), anthramycin-type antibiotics (abbeymycin), lipase inhibitor (ebelactone B), cytocidal (oxopropaline D), antifungal and antitumor antibiotics (reductiomycin, streptimidone, deoxynybomycin), alaremycin, fumaramidmycin, anisomycin, and others were also annotated, which were further confirmed by using the SIRIUS platform, and literature survey. Thus, the bioprospecting of natural products from Streptomyces species from Nepal could be a potential source for the discovery of clinically significant and new antimicrobial agents in the future.
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29
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Grapevine Xylem Sap Is a Potent Elicitor of Antibiotic Production in Streptomyces spp. Antibiotics (Basel) 2022; 11:antibiotics11050672. [PMID: 35625316 PMCID: PMC9137808 DOI: 10.3390/antibiotics11050672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 02/06/2023] Open
Abstract
Streptomyces bacteria produce a wide number of antibiotics and antitumor compounds that have attracted the attention of pharmaceutical and biotech companies. In this study, we provide evidence showing that the xylem sap from grapevines has a positive effect on the production of different antibiotics by several Streptomyces species, including S. ambofaciens ATCC 23877 and S. argillaceus ATCC 12596 among others. The production of several already known compounds was induced: actinomycin D, chromomycin A3, fungichromin B, mithramycin A, etc., and four compounds with molecular formulas not included in the Dictionary of Natural Products (DNP v28.2) were also produced. The molecules present in the xylem sap that acts as elicitors were smaller than 3 kDa and soluble in water and insoluble in ether, ethyl acetate, or methanol. A combination of potassium citrate and di-D-fructose dianhydrides (related to levanbiose or inulobiose) seemed to be the main effectors identified from the active fraction. However, the level of induction obtained in the presence of these compounds mix was weaker and delayed with respect to the one got when using the whole xylem sap or the 3 kDa sap fraction, suggesting that another, not identified, elicitor must be also implied in this induction.
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30
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Mungan MD, Harbig TA, Perez NH, Edenhart S, Stegmann E, Nieselt K, Ziemert N. Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. Nucleic Acids Res 2022; 50:W682-W689. [PMID: 35580059 PMCID: PMC9252823 DOI: 10.1093/nar/gkac371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
For decades, natural products have been used as a primary resource in drug discovery pipelines to find new antibiotics, which are mainly produced as secondary metabolites by bacteria. The biosynthesis of these compounds is encoded in co-localized genes termed biosynthetic gene clusters (BGCs). However, BGCs are often not expressed under laboratory conditions. Several genetic manipulation strategies have been developed in order to activate or overexpress silent BGCs. Significant increases in production levels of secondary metabolites were indeed achieved by modifying the expression of genes encoding regulators and transporters, as well as genes involved in resistance or precursor biosynthesis. However, the abundance of genes encoding such functions within bacterial genomes requires prioritization of the most promising ones for genetic manipulation strategies. Here, we introduce the ‘Secondary Metabolite Transcriptomic Pipeline’ (SeMa-Trap), a user-friendly web-server, available at https://sema-trap.ziemertlab.com. SeMa-Trap facilitates RNA-Seq based transcriptome analyses, finds co-expression patterns between certain genes and BGCs of interest, and helps optimize the design of comparative transcriptomic analyses. Finally, SeMa-Trap provides interactive result pages for each BGC, allowing the easy exploration and comparison of expression patterns. In summary, SeMa-Trap allows a straightforward prioritization of genes that could be targeted via genetic engineering approaches to (over)express BGCs of interest.
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Affiliation(s)
- Mehmet Direnç Mungan
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
| | - Theresa Anisja Harbig
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Naybel Hernandez Perez
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Simone Edenhart
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
| | - Kay Nieselt
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 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, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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32
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Hwang S, Lee Y, Kim JH, Kim G, Kim H, Kim W, Cho S, Palsson BO, Cho BK. Streptomyces as Microbial Chassis for Heterologous Protein Expression. Front Bioeng Biotechnol 2022; 9:804295. [PMID: 34993191 PMCID: PMC8724576 DOI: 10.3389/fbioe.2021.804295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Heterologous production of recombinant proteins is gaining increasing interest in biotechnology with respect to productivity, scalability, and wide applicability. The members of genus Streptomyces have been proposed as remarkable hosts for heterologous production due to their versatile nature of expressing various secondary metabolite biosynthetic gene clusters and secretory enzymes. However, there are several issues that limit their use, including low yield, difficulty in genetic manipulation, and their complex cellular features. In this review, we summarize rational engineering approaches to optimizing the heterologous production of secondary metabolites and recombinant proteins in Streptomyces species in terms of genetic tool development and chassis construction. Further perspectives on the development of optimal Streptomyces chassis by the design-build-test-learn cycle in systems are suggested, which may increase the availability of secondary metabolites and recombinant proteins.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gahyeon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hyeseong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Innovative Biomaterials Research Center, KAIST Institutes, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Gren T, Whitford CM, Mohite OS, Jørgensen TS, Kontou EE, Nielsen JB, Lee SY, Weber T. Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters. Sci Rep 2021; 11:18301. [PMID: 34526549 PMCID: PMC8443760 DOI: 10.1038/s41598-021-97571-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/19/2021] [Indexed: 12/20/2022] Open
Abstract
Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S. griseofuscus, followed by the detailed exploration of its phenotype, including the production of native secondary metabolites and ability to utilise carbon, nitrogen, sulphur and phosphorus sources. Furthermore, several routes for genetic engineering of S. griseofuscus were explored, including use of GusA-based vectors, CRISPR-Cas9 and CRISPR-cBEST-mediated knockouts. Two out of the three native plasmids were cured using CRISPR-Cas9 technology, leading to the generation of strain S. griseofuscus DEL1. DEL1 was further modified by the full deletion of a pentamycin BGC and an unknown NRPS BGC, leading to the generation of strain DEL2, lacking approx. 500 kbp of the genome, which corresponds to a 5.19% genome reduction. DEL2 can be characterized by faster growth and inability to produce three main native metabolites: lankacidin, lankamycin, pentamycin and their derivatives. To test the ability of DEL2 to heterologously produce secondary metabolites, the actinorhodin BGC was used. We were able to observe a formation of a blue halo, indicating a potential production of actinorhodin by both DEL2 and a wild type.
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Affiliation(s)
- Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Tue S Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Eftychia E Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Julie B Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark.
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34
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 37118182 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 369] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations. ![]()
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J V Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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Zhang C, Sultan SA, T R, Chen X. Biotechnological applications of S-adenosyl-methionine-dependent methyltransferases for natural products biosynthesis and diversification. BIORESOUR BIOPROCESS 2021; 8:72. [PMID: 38650197 PMCID: PMC10992897 DOI: 10.1186/s40643-021-00425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/31/2021] [Indexed: 12/28/2022] Open
Abstract
In the biosynthesis of natural products, methylation is a common and essential transformation to alter molecules' bioavailability and bioactivity. The main methylation reaction is performed by S-adenosylmethionine (SAM)-dependent methyltransferases (MTs). With advancements in genomic and chemical profiling technologies, novel MTs have been discovered to accept complex substrates and synthesize industrially valuable natural products. However, to achieve a high yield of small molecules in microbial hosts, many methyltransferase activities have been reported to be insufficient. Moreover, inadequate co-factor supplies and feedback inhibition of the by-product, S-adenosylhomocysteine (SAH), further limit MTs' activities. Here, we review recent advances in SAM-dependent MTs to produce and diversify natural products. First, we surveyed recently identified novel methyltransferases in natural product biosynthesis. Second, we summarized enzyme engineering strategies to improve methyltransferase activity, with a particular focus on high-throughput assay design and application. Finally, we reviewed innovations in co-factor regeneration and diversification, both in vitro and in vivo. Noteworthily, many MTs are able to accept multiple structurally similar substrates. Such promiscuous methyltransferases are versatile and can be tailored to design de novo pathways to produce molecules whose biosynthetic pathway is unknown or non-existent in nature, thus broadening the scope of biosynthesized functional molecules.
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Affiliation(s)
- Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stella Amelia Sultan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Rehka T
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
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36
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Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria. Nat Commun 2021; 12:4347. [PMID: 34301933 PMCID: PMC8302735 DOI: 10.1038/s41467-021-24645-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for heterologous BGC expression, but its cells undergo early autolysis, hindering further applications. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chitinimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression.
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37
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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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van Staden ADP, van Zyl WF, Trindade M, Dicks LMT, Smith C. Therapeutic Application of Lantibiotics and Other Lanthipeptides: Old and New Findings. Appl Environ Microbiol 2021; 87:e0018621. [PMID: 33962984 PMCID: PMC8231447 DOI: 10.1128/aem.00186-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and posttranslationally modified peptides, with modifications that are incorporated during biosynthesis by dedicated enzymes. Various modifications of the peptides are possible, resulting in a highly diverse group of bioactive peptides that offer a potential reservoir for use in the fight against a plethora of diseases. Their activities range from the antimicrobial properties of lantibiotics, especially against antibiotic-resistant strains, to antiviral activity, immunomodulatory properties, antiallodynic effects, and the potential to alleviate cystic fibrosis symptoms. Lanthipeptide biosynthetic genes are widespread within bacterial genomes, providing a substantial repository for novel bioactive peptides. Using genome mining tools, novel bioactive lanthipeptides can be identified, and coupled with rapid screening and heterologous expression technologies, the lanthipeptide drug discovery pipeline can be significantly sped up. Lanthipeptides represent a group of bioactive peptides that hold great potential as biotherapeutics, especially at a time when novel and more effective therapies are required. With this review, we provide insight into the latest developments made toward the therapeutic applications and production of lanthipeptides, specifically looking at heterologous expression systems.
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Affiliation(s)
- Anton Du Preez van Staden
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
- Division of Clinical Pharmacology, Department Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Winschau F. van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Carine Smith
- Division of Clinical Pharmacology, Department Medicine, Stellenbosch University, Stellenbosch, South Africa
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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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Kuhl M, Rückert C, Gläser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann C. Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development. Biotechnol Bioeng 2021; 118:3076-3093. [PMID: 33974270 DOI: 10.1002/bit.27818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/17/2021] [Accepted: 04/30/2021] [Indexed: 11/09/2022]
Abstract
Actinobacteria provide a rich spectrum of bioactive natural products and therefore display an invaluable source towards commercially valuable pharmaceuticals and agrochemicals. Here, we studied the use of inorganic talc microparticles (hydrous magnesium silicate, 3MgO·4SiO2 ·H2 O, 10 µm) as a general supplement to enhance natural product formation in this important class of bacteria. Added to cultures of recombinant Streptomyces lividans, talc enhanced production of the macrocyclic peptide antibiotic bottromycin A2 and its methylated derivative Met-bottromycin A2 up to 109 mg L-1 , the highest titer reported so far. Hereby, the microparticles fundamentally affected metabolism. With 10 g L-1 talc, S. lividans grew to 40% smaller pellets and, using RNA sequencing, revealed accelerated morphogenesis and aging, indicated by early upregulation of developmental regulator genes such as ssgA, ssgB, wblA, sigN, and bldN. Furthermore, the microparticles re-balanced the expression of individual bottromycin cluster genes, resulting in a higher macrocyclization efficiency at the level of BotAH and correspondingly lower levels of non-cyclized shunt by-products, driving the production of mature bottromycin. Testing a variety of Streptomyces species, talc addition resulted in up to 13-fold higher titers for the RiPPs bottromycin and cinnamycin, the alkaloid undecylprodigiosin, the polyketide pamamycin, the tetracycline-type oxytetracycline, and the anthramycin-analogs usabamycins. Moreover, talc addition boosted production in other actinobacteria, outside of the genus of Streptomyces: vancomycin (Amycolatopsis japonicum DSM 44213), teicoplanin (Actinoplanes teichomyceticus ATCC 31121), and the angucyclinone-type antibiotic simocyclinone (Kitasatospora sp.). For teicoplanin, the microparticles were even crucial to activate production. Taken together, the use of talc was beneficial in 75% of all tested cases and optimized natural and heterologous hosts forming the substance of interest with clusters under native and synthetic control. Given its simplicity and broad benefits, microparticle-supplementation appears as an enabling technology in natural product research of these most important microbes.
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Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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41
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Zhang Y, Yun K, Huang H, Tu R, Hua E, Wang M. Antisense RNA Interference-Enhanced CRISPR/Cas9 Base Editing Method for Improving Base Editing Efficiency in Streptomyces lividans 66. ACS Synth Biol 2021; 10:1053-1063. [PMID: 33720688 DOI: 10.1021/acssynbio.0c00563] [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: 01/01/2023]
Abstract
CRISPR/Cas9-mediated base editors, based on cytidine deaminase or adenosine deaminase, are emerging genetic technologies that facilitate genomic manipulation in many organisms. Since base editing is free from DNA double-strand breaks (DSBs), it has certain advantages, such as a lower toxicity, compared to the traditional DSB-based genome engineering technologies. In terms of Streptomyces, a base editing method has been successfully applied in several model and non-model species, such as Streptomyces coelicolor and Streptomyces griseofuscus. In this study, we first proved that BE2 (rAPOBEC1-dCas9-UGI) and BE3 (rAPOBEC1-nCas9-UGI) were functional base editing tools in Streptomyces lividans 66, albeit with a much lower editing efficiency compared to that of S. coelicolor. Uracil generated in deamination is a key intermediate in the base editing process, and it can be hydrolyzed by uracil DNA glycosidase (UDG) involved in the intracellular base excision repair, resulting in a low base editing efficiency. By knocking out two endogenous UDGs (UDG1 and UDG2), we managed to improve the base editing efficiency by 3.4-67.4-fold among different loci. However, the inactivation of UDG is detrimental to the genome stability and future application of engineered strains. Therefore, we finally developed antisense RNA interference-enhanced CRISPR/Cas9 Base Editing method (asRNA-BE) to transiently disrupt the expression of uracil DNA glycosidases during base editing, leading to a 2.8-65.8-fold enhanced editing efficiency and better genome stability. Our results demonstrate that asRNA-BE is a much better editing tool for base editing in S. lividans 66 and might be beneficial for improving the base editing efficiency and genome stability in other Streptomyces strains.
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Affiliation(s)
- Yue Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Kaiyue Yun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Huamei Huang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ran Tu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Erbing Hua
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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42
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The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes. Essays Biochem 2021; 65:261-275. [PMID: 33956071 DOI: 10.1042/ebc20200132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Streptomycetes are producers of a wide range of specialized metabolites of great medicinal and industrial importance, such as antibiotics, antifungals, or pesticides. Having been the drivers of the golden age of antibiotics in the 1950s and 1960s, technological advancements over the last two decades have revealed that very little of their biosynthetic potential has been exploited so far. Given the great need for new antibiotics due to the emerging antimicrobial resistance crisis, as well as the urgent need for sustainable biobased production of complex molecules, there is a great renewed interest in exploring and engineering the biosynthetic potential of streptomycetes. Here, we describe the Design-Build-Test-Learn (DBTL) cycle for metabolic engineering experiments in streptomycetes and how it can be used for the discovery and production of novel specialized metabolites.
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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Liu Z, Zhao Y, Huang C, Luo Y. Recent Advances in Silent Gene Cluster Activation in Streptomyces. Front Bioeng Biotechnol 2021; 9:632230. [PMID: 33681170 PMCID: PMC7930741 DOI: 10.3389/fbioe.2021.632230] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) are critical sources of drug molecules for decades. About two-thirds of natural antibiotics are produced by Streptomyces. Streptomyces have a large number of secondary metabolite biosynthetic gene clusters (SM-BGCs) that may encode NPs. However, most of these BGCs are silent under standard laboratory conditions. Hence, activation of these silent BGCs is essential to current natural products discovery research. In this review, we described the commonly used strategies for silent BGC activation in Streptomyces from two aspects. One focused on the strategies applied in heterologous host, including methods to clone and reconstruct BGCs along with advances in chassis engineering; the other focused on methods applied in native host which includes engineering of promoters, regulatory factors, and ribosomes. With the metabolic network being elucidated more comprehensively and methods optimized more high-thoroughly, the discovery of NPs will be greatly accelerated.
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Affiliation(s)
- Zhenyu Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yatong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chaoqun Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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45
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Recent Advances in the Heterologous Biosynthesis of Natural Products from Streptomyces. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Streptomyces is a significant source of natural products that are used as therapeutic antibiotics, anticancer and antitumor agents, pesticides, and dyes. Recently, with the advances in metabolite analysis, many new secondary metabolites have been characterized. Moreover, genome mining approaches demonstrate that many silent and cryptic biosynthetic gene clusters (BGCs) and many secondary metabolites are produced in very low amounts under laboratory conditions. One strain many compounds (OSMAC), overexpression/deletion of regulatory genes, ribosome engineering, and promoter replacement have been utilized to activate or enhance the production titer of target compounds. Hence, the heterologous expression of BGCs by transferring to a suitable production platform has been successfully employed for the detection, characterization, and yield quantity production of many secondary metabolites. In this review, we introduce the systematic approach for the heterologous production of secondary metabolites from Streptomyces in Streptomyces and other hosts, the genome analysis tools, the host selection, and the development of genetic control elements for heterologous expression and the production of secondary metabolites.
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46
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Jose PA, Maharshi A, Jha B. Actinobacteria in natural products research: Progress and prospects. Microbiol Res 2021; 246:126708. [PMID: 33529791 DOI: 10.1016/j.micres.2021.126708] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 12/15/2022]
Abstract
Actinobacteria are well-recognised biosynthetic factories that produce an extensive spectrum of secondary metabolites. Recent genomic insights seem to impact the exploitation of these metabolically versatile bacteria in several aspects. Notably, from the isolation of novel taxa to the discovery of new compounds, different approaches evolve at a steady pace. Here, we systematically discuss the enduring importance of Actinobacteria in the field of drug discovery, the current focus of isolation efforts targeting bioactive Actinobacteria from diverse sources, recent discoveries of novel compounds with different bioactivities, and the relative employment of different strategies in the search for novel compounds. Ultimately, we highlight notable progress that will have profound impacts on future quests for secondary metabolites of Actinobacteria.
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Affiliation(s)
- Polpass Arul Jose
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India.
| | - Anjisha Maharshi
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, India.
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47
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Kang HS, Kim ES. Recent advances in heterologous expression of natural product biosynthetic gene clusters in Streptomyces hosts. Curr Opin Biotechnol 2021; 69:118-127. [PMID: 33445072 DOI: 10.1016/j.copbio.2020.12.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 01/09/2023]
Abstract
The heterologous expression of natural product biosynthetic gene clusters (BGCs) has traditionally been used as a genetic platform to link various natural product chemotypes to their corresponding genotypes. In recent years, heterologous expression has played an increasing role in natural products research with the advances in sequencing technologies and bioinformatics tools that allow for the rapid and systematic identification of known and cryptic BGCs from a large number of microbial genome sequences. The advances in synthetic biology have also facilitated the process of heterologous expression by providing tools for rapid cloning and engineering of BGCs to improve production yield or to activate silent BGCs. This paper summarizes the recent progress in the cloning and engineering of natural product BGCs and highlights recent examples of the heterologous expression of both known and cryptic BGCs in Streptomyces hosts, which will continue to play a pivotal role in genomics-driven natural product research.
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Affiliation(s)
- Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea.
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48
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Engineering Heterologous Hosts for the Enhanced Production of Non-ribosomal Peptides. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0080-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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49
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Shi J, Xu X, Liu PY, Hu YL, Zhang B, Jiao RH, Bashiri G, Tan RX, Ge HM. Discovery and biosynthesis of guanipiperazine from a NRPS-like pathway. Chem Sci 2021; 12:2925-2930. [PMID: 34164059 PMCID: PMC8179380 DOI: 10.1039/d0sc06135b] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are modular enzymes that use a thiotemplate mechanism to assemble the peptide backbones of structurally diverse and biologically active natural products in bacteria and fungi. Unlike these canonical multi-modular NRPSs, single-module NRPS-like enzymes, which lack the key condensation (C) domain, are rare in bacteria, and have been largely unexplored to date. Here, we report the discovery of a gene cluster (gup) encoding a NRPS-like megasynthetase through genome mining. Heterologous expression of the gup cluster led to the production of two unprecedented alkaloids, guanipiperazines A and B. The NRPS-like enzyme activates two l-tyrosine molecules, reduces them to the corresponding amino aldehydes, and forms an unstable imine product. The subsequent enzymatic reduction affords piperazine, which can be morphed by a P450 monooxygenase into a highly strained compound through C–O bond formation. Further intermolecular oxidative coupling forming the C–C or C–O bond is catalyzed by another P450 enzyme. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products. Genome mining of a NRPS-like gene cluster led to the identification of two novel alkaloids with antimicrobial activity. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products.![]()
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Xiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Pei Yi Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Ghader Bashiri
- Laboratory of Structural Biology, Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland Auckland 1010 New Zealand
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
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50
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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