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Liu W, Tian X, Huang X, Malit JJL, Wu C, Guo Z, Tang JW, Qian PY. Discovery of P450-Modified Sesquiterpenoids Levinoids A-D through Global Genome Mining. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38377956 DOI: 10.1021/acs.jnatprod.3c01136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Cytochrome P450-modified bacterial terpenoids remain in a vast chemical space to be explored. In the present study, we conducted global genome mining of 223,829 bacterial genomes and identified 2892 bacterial terpenoid biosynthetic gene clusters (BGCs) with cytochrome P450 genes. Among these, we selected 562 with multiple P450 enzymes, which were further clustered as 355 gene cluster families by sequence similarity analysis. We then chose lev, a BGC from Streptomyces levis MCCC1A01616, for heterologous expression and discovered four new α-amorphene-type sesquiterpenoids, levinoids A-D (1-4). The structures and absolute configurations of these four new compounds were determined by employing extensive NMR analysis, NMR chemical shift calculations with DP4+, and ECD calculations. Furthermore, levinoid C (3) exhibited a moderate level of neuroprotective activity (EC50 = 21 μM) in the glutamate-induced excitotoxicity cell model. Our findings highlight the untapped chemical diversity of P450-modified bacterial terpenoids, opening new avenues for further exploration and discovery.
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Affiliation(s)
- Wenchao Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Xueying Tian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xin Huang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | | | - Chuanhai Wu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhihong Guo
- Department of Chemistry, Department of Physics, and Bioengineering Program, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wei Tang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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Miyamoto N, Nishigami A, Hosoda N, Hayashi K, Yamada N, Tsuge K. A Novel Method for Creating Heterologous Lethal Antibiotic Producers by Screening from Combi-OGAB Library with Various Promoters in a Biosynthetic Gene Cluster. ACS OMEGA 2024; 9:6873-6879. [PMID: 38371756 PMCID: PMC10870263 DOI: 10.1021/acsomega.3c08240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/20/2024]
Abstract
In this study, we devised a novel method to create heterologous producers of lethal antibiotics against host bacteria. Heterologous producers cannot be created when antibiotics are toxic to host bacteria. To overcome this challenge, we developed a novel method involving construction of a combinatorial library with various promoters and screening based on the production. To realize this, we utilized Combi-OGAB (Combinatorial Ordered Gene Assembly in Bacillus subtilis), which technology can effectively construct diverse combinatorial library and accelerate screening procedures. B. subtilis and Gramicidin S were selected as the host bacterium and the targeted antibiotic, respectively. The screened producer from Combi-OGAB screening cycles achieved >30-fold productivity over the lethal level. These results suggest that our strategy has the potential to maximize the phenotypic resistance of host bacteria to create heterologous lethal antibiotic producers.
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Affiliation(s)
| | | | - Nao Hosoda
- Synplogen Co., Ltd., Kobe, Hyogo 6500047, Japan
| | | | | | - Kenji Tsuge
- Synplogen Co., Ltd., Kobe, Hyogo 6500047, Japan
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Gu B, Kim DG, Kim DK, Kim M, Kim HU, Oh MK. Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor. Microb Cell Fact 2023; 22:212. [PMID: 37838667 PMCID: PMC10576301 DOI: 10.1186/s12934-023-02218-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Oviedomycin is one among several polyketides known for their potential as anticancer agents. The biosynthetic gene cluster (BGC) for oviedomycin is primarily found in Streptomyces antibioticus. However, because this BGC is usually inactive under normal laboratory conditions, it is necessary to employ systematic metabolic engineering methods, such as heterologous expression, refactoring of BGCs, and optimization of precursor biosynthesis, to allow efficient production of these compounds. RESULTS Oviedomycin BGC was captured from the genome of Streptomyces antibioticus by a newly constructed plasmid, pCBA, and conjugated into the heterologous strain, S. coelicolor M1152. To increase the production of oviedomycin, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system was utilized in an in vitro setting to refactor the native promoters within the ovm BGC. The target promoters of refactoring were selected based on examination of factors such as transcription levels and metabolite profiling. Furthermore, genome-scale metabolic simulation was applied to find overexpression targets that could enhance the biosynthesis of precursors or cofactors related to oviedomycin production. The combined approach led to a significant increase in oviedomycin production, reaching up to 670 mg/L, which is the highest titer reported to date. This demonstrates the potential of the approach undertaken in this study. CONCLUSIONS The metabolic engineering approach used in this study led to the successful production of a valuable polyketide, oviedomycin, via BGC cloning, promoter refactoring, and gene manipulation of host metabolism aided by genome-scale metabolic simulation. This approach can be also useful for the efficient production of other secondary molecules encoded by 'silent' BGCs.
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Affiliation(s)
- Boncheol Gu
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Duck Gyun Kim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Do-Kyung Kim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minji Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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4
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Induja DK, Jesmina ARS, Joseph MM, Shamjith S, Ingaladal N, Maiti KK, Kumar BSD, Lankalapalli RS. Isolation of two new stereochemical variants of streptophenazine by cocultivation of Streptomyces NIIST-D31, Streptomyces NIIST-D47, and Streptomyces NIIST-D63 strains in 3C 2 combinations. J Antibiot (Tokyo) 2023; 76:567-578. [PMID: 37308605 DOI: 10.1038/s41429-023-00638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/14/2023]
Abstract
Cocultivation of combinations of Streptomyces species isolated from the same soil was explored to isolate novel secondary metabolites. Recently, we reported the isolation of a novel vicinal diepoxide of alloaureothin along with three carboxamides, 4-aminobenzoic acid, and 1,6-dimethoxyphenazine from the individual culture of Streptomyces luteireticuli NIIST-D31. Herein, cocultivation of NIIST-D31 with Streptomyces luteoverticillatus NIIST-D47 afforded two new stereochemical variants of streptophenazine (S1 and S2), and 1-N-methylalbonoursin, where the individual culture of NIIST-D47 primarily produced carbazomycins A, D, and E. The new streptophenazines and 1-N-methylalbonoursin were also observed during cocultivation of NIIST-D31 with Streptomyces thioluteus NIIST-D63, where the individual culture of NIIST-D63 strain afforded for the first time 2,2'-bipyridines (caerulomycinamide and dipyrimicin B), picolinamide, 2,3-dimethoxybenzamide, 2-hydroxy-3-methoxybenzamide, and 6-amino-2-pyridone along with known natural products aureothin and 1,6-dimethoxyphenazine. Finally, cocultivation of NIIST-D47 and NIIST-D63 strains produced carbazomycins B and C, alloaureothin, cyclo-(Leu-Pro), investiamide, and 4-aminobenzoic acid. Some of the compounds observed in the individual cultures were also produced in cocultivations. Improvement in the yield of secondary metabolites during cocultivation compared to individual culturing is well-known, which is noted here for vicinal diepoxide of alloaureothin. The production of new streptophenazines by cocultivation combinations with NIIST-D31 suggests that NIIST-D47 and NIIST-D63 may function as inducers in activating cryptic secondary metabolite-biosynthetic gene clusters. Cytotoxicity of the new streptophenazines in cancerous (MCF7 and MDA-MB-231) or non-cancerous (WI-38) cells were tested, however, they exhibited no significant activity.
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Affiliation(s)
- D K Induja
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - A R S Jesmina
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
| | - Manu M Joseph
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
| | - Shanmughan Shamjith
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nagaraja Ingaladal
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kaustabh Kumar Maiti
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - B S Dileep Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India
| | - Ravi S Lankalapalli
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness. Microbiol Spectr 2023; 11:e0317622. [PMID: 36472430 PMCID: PMC9927498 DOI: 10.1128/spectrum.03176-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. IMPORTANCE Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.
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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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7
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Randall JR, Davies BW. Mining for novel antibiotics. Curr Opin Microbiol 2021; 63:66-69. [PMID: 34217916 PMCID: PMC8463434 DOI: 10.1016/j.mib.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Justin R Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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Li X, Hu X, Sheng Y, Wang H, Tao M, Ou Y, Deng Z, Bai L, Kang Q. Adaptive Optimization Boosted the Production of Moenomycin A in the Microbial Chassis Streptomyces albus J1074. ACS Synth Biol 2021; 10:2210-2221. [PMID: 34470207 DOI: 10.1021/acssynbio.1c00094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Great efforts have been made to improve Streptomyces chassis for efficient production of targeted natural products. Moenomycin family antibiotics, represented by moenomycin (Moe) and nosokomycin, are phosphoglycolipid antibiotics that display extraordinary inhibition against Gram-positive bacteria. Herein, we assembled a completed 34 kb hybrid biosynthetic gene cluster (BGC) of moenomycin A (moe-BGC) based on a 24 kb nosokomycin analogue biosynthetic gene cluster (noso-BGC). The heterologous expression of the hybrid moe-BGC in Streptomyces albus J1074 achieved the production of moenomycin A in the recombinant strain LX01 with a yield of 12.1 ± 2 mg/L. Further strong promoter refactoring to improve the transcriptional levels of all of the functional genes in strain LX02 enhanced the production of moenomycin A by 58%. However, the yield improvement of moenomycin A resulted in a dramatic 38% decrease in the chassis biomass compared with the control strain. To improve the weak physiological tolerance to moenomycin A of the chassis, another copy of the gene salb-PBP2 (P238N&F200D), encoding peptidoglycan biosynthetic protein PBP2, was introduced into the chassis strain, producing strain LX03. Cell growth was restored, and the fermentation titer of moenomycin A was 130% higher than that of LX01. Additionally, the production of moenomycin A in strain LX03 was further elevated by 45% to 40.0 ± 3 mg/L after media optimization. These results suggested that the adaptive optimization strategy of strong promoter refactoring in the BGC plus physiological tolerance in the chassis was an efficient approach for obtaining the desired natural products with high titers.
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Affiliation(s)
- Xing Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaojing Hu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Sheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hengyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yixin Ou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Gencbay T, Saygin H, Guven K, Topkara AR, Saricaoglu S, Sahin N, Isik K. Streptomyces scabichelini sp. nov., isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33470928 DOI: 10.1099/ijsem.0.004639] [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: 12/29/2022] Open
Abstract
A novel actinomycete, designated strain HC44T, was isolated from a soil sample collected from Hacibektaş, Turkey, and characterized using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that HC44T clustered with members of the genus Streptomyces and the highest 16S rRNA gene sequence similarity values were obtained with Streptomyces vastus NBRC 13094T (97.6 %) and Streptomyces kalpinensis TRM 46509T (96.9 %). Multi-locus sequence analysis (MLSA) based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that the MLSA evolutionary distance value was 0.043 between strain HC44T and S. vastus NBRC 13094T. Whole-cell hydrolysates contained ll-diaminopimelic acid, glucose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content of the draft genome sequence, consisting of 11.2 Mbp, was 69.8 mol%. On the basis of polyphasic taxonomic evidence, strain HC44T represents a novel species of the genus Streptomyces, for which the name Streptomyces scabichelini sp. nov. is proposed. The type strain is HC44T (=DSM 106874T=KCTC 39872T).
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Affiliation(s)
- Talha Gencbay
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Hayrettin Saygin
- Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Kiymet Guven
- Department of Biology, Faculty of Science, Eskisehir Technical University, Eskisehir 26555, Turkey
| | - Ahmet Ridvan Topkara
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Salih Saricaoglu
- Department of Therapy and Rehabilitation, Health Services Vocational College, Kirsehir Ahi Evran University, Kirsehir 44200, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Kamil Isik
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
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10
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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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11
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Lopatniuk M, Myronovskyi M, Nottebrock A, Busche T, Kalinowski J, Ostash B, Fedorenko V, Luzhetskyy A. Effect of “ribosome engineering” on the transcription level and production of S. albus indigenous secondary metabolites. Appl Microbiol Biotechnol 2019; 103:7097-7110. [DOI: 10.1007/s00253-019-10005-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/11/2019] [Accepted: 06/30/2019] [Indexed: 01/31/2023]
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12
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Davy AM, Kildegaard HF, Andersen MR. Cell Factory Engineering. Cell Syst 2019; 4:262-275. [PMID: 28334575 DOI: 10.1016/j.cels.2017.02.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/11/2016] [Accepted: 02/15/2017] [Indexed: 11/30/2022]
Abstract
Rational approaches to modifying cells to make molecules of interest are of substantial economic and scientific interest. Most of these efforts aim at the production of native metabolites, expression of heterologous biosynthetic pathways, or protein expression. Reviews of these topics have largely focused on individual strategies or cell types, but collectively they fall under the broad umbrella of a growing field known as cell factory engineering. Here we condense >130 reviews and key studies in the art into a meta-review of cell factory engineering. We identified 33 generic strategies in the field, all applicable to multiple types of cells and products, and proven successful in multiple major cell types. These apply to three major categories: production of native metabolites and/or bioactives, heterologous expression of biosynthetic pathways, and protein expression. This meta-review provides general strategy guides for the broad range of applications of rational engineering of cell factories.
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Affiliation(s)
- Anne Mathilde Davy
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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13
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Recent achievements in the generation of stable genome alterations/mutations in species of the genus Streptomyces. Appl Microbiol Biotechnol 2019; 103:5463-5482. [DOI: 10.1007/s00253-019-09901-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022]
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14
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Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes. Curr Microbiol 2019; 77:645-656. [PMID: 31069462 DOI: 10.1007/s00284-019-01698-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Abstract
Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.
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15
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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16
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019; 36:1412-1436. [DOI: 10.1039/c8np00091c] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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17
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Nepal KK, Wang G. Streptomycetes: Surrogate hosts for the genetic manipulation of biosynthetic gene clusters and production of natural products. Biotechnol Adv 2019; 37:1-20. [PMID: 30312648 PMCID: PMC6343487 DOI: 10.1016/j.biotechadv.2018.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022]
Abstract
Due to the worldwide prevalence of multidrug-resistant pathogens and high incidence of diseases such as cancer, there is an urgent need for the discovery and development of new drugs. Nearly half of the FDA-approved drugs are derived from natural products that are produced by living organisms, mainly bacteria, fungi, and plants. Commercial development is often limited by the low yield of the desired compounds expressed by the native producers. In addition, recent advances in whole genome sequencing and bioinformatics have revealed an abundance of cryptic biosynthetic gene clusters within microbial genomes. Genetic manipulation of clusters in the native host is commonly used to awaken poorly expressed or silent gene clusters, however, the lack of feasible genetic manipulation systems in many strains often hinders our ability to engineer the native producers. The transfer of gene clusters into heterologous hosts for expression of partial or entire biosynthetic pathways is an approach that can be used to overcome this limitation. Heterologous expression also facilitates the chimeric fusion of different biosynthetic pathways, leading to the generation of "unnatural" natural products. The genus Streptomyces is especially known to be a prolific source of drugs/antibiotics, its members are often used as heterologous expression hosts. In this review, we summarize recent applications of Streptomyces species, S. coelicolor, S. lividans, S. albus, S. venezuelae and S. avermitilis, as heterologous expression systems.
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Affiliation(s)
- Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA.
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18
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Rigali S, Anderssen S, Naômé A, van Wezel GP. Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery. Biochem Pharmacol 2018; 153:24-34. [DOI: 10.1016/j.bcp.2018.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
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19
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Li S, Wang J, Xiang W, Yang K, Li Z, Wang W. An Autoregulated Fine-Tuning Strategy for Titer Improvement of Secondary Metabolites Using Native Promoters in Streptomyces. ACS Synth Biol 2018; 7:522-530. [PMID: 29087698 DOI: 10.1021/acssynbio.7b00318] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Streptomycetes are well-known producers of biologically active secondary metabolites. Various efforts have been made to increase productions of these metabolites, while few approaches could well coordinate the biosynthesis of secondary metabolites and other physiological events of their hosts. Here we develop a universal autoregulated strategy for fine-tuning the expression of secondary metabolites biosynthetic gene clusters (BGCs) in Streptomyces species. First, inducible promoters were used to control the expression of secondary metabolites BGCs. Then, the optimal induction condition was determined by response surface model in both dimensions of time and strength. Finally, native promoters with similar transcription profile to the inducible promoter under the optimal condition were identified based on time-course transcriptome analyses, and used to replace the inducible promoter following an elaborate replacement approach. The expression of actinorhodin (Act) and heterogeneous oxytetracycline (OTC) BGCs were optimized in Streptomyces coelicolor using this strategy. Compared to modulating the expression via constitutive promoters, our strategy could dramatically improve the titers of Act and OTC by 1.3- and 9.1-fold, respectively. The autoregulated fine-tuning strategy developed here opens a novel route for titer improvement of desired secondary metabolites in Streptomyces.
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Affiliation(s)
- Shanshan Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute
of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District,
Beijing 100193, China
| | - Junyang Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Wensheng Xiang
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute
of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District,
Beijing 100193, China
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Zilong Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Weishan Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
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20
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Ding H, Wang JN, Zhang DS, Ma ZJ. Derivatives of Holomycin and Cyclopropaneacetic Acid fromStreptomycessp. DT-A37. Chem Biodivers 2017. [DOI: 10.1002/cbdv.201700140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hui Ding
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
| | - Jia-Nan Wang
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
| | - Da-Shan Zhang
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
| | - Zhong-Jun Ma
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
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21
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Improvement of oxytetracycline production mediated via cooperation of resistance genes in Streptomyces rimosus. SCIENCE CHINA-LIFE SCIENCES 2017; 60:992-999. [PMID: 28755296 DOI: 10.1007/s11427-017-9121-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/12/2017] [Indexed: 01/15/2023]
Abstract
Increasing the self-resistance levels of Streptomyces is an effective strategy to improve the production of antibiotics. To increase the oxytetracycline (OTC) production in Streptomyces rimosus, we investigated the cooperative effect of three co-overexpressing OTC resistance genes: one gene encodes a ribosomal protection protein (otrA) and the other two express efflux proteins (otrB and otrC). Results indicated that combinational overexpression of otrA, otrB, and otrC (MKABC) exerted a synergetic effect. OTC production increased by 179% in the recombinant strain compared with that of the wild-type strain M4018. The resistance level to OTC was increased by approximately two-fold relative to the parental strain, thereby indicating that applying the cooperative effect of self-resistance genes is useful to improve OTC production. Furthermore, the previously identified cluster-situated activator OtcR was overexpressed in MKABC in constructing the recombinant strain MKRABC; such strain can produce OTC of approximately 7.49 g L-1, which represents an increase of 19% in comparison with that of the OtcR-overexpressing strain alone. Our work showed that the cooperative overexpression of self-resistance genes is a promising strategy to enhance the antibiotics production in Streptomyces.
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22
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Basitta P, Westrich L, Rösch M, Kulik A, Gust B, Apel AK. AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters. ACS Synth Biol 2017; 6:817-825. [PMID: 28182401 DOI: 10.1021/acssynbio.6b00319] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The generation of novel secondary metabolites by reengineering or refactoring biochemical pathways is a rewarding but also challenging goal of synthetic biology. For this, the development of tools for the reconstruction of secondary metabolite gene clusters as well as the challenge of understanding the obstacles in this process is of great interest. The artificial gene operon assembly system (AGOS) is a plug-and-play method developed as a tool to consecutively assemble artificial gene operons into a destination vector and subsequently express them under the control of a de-repressed promoter in a Streptomyces host strain. AGOS was designed as a set of entry plasmids for the construction of artificial gene operons and a SuperCos1 based destination vector, into which the constructed operons can be assembled by Red/ET-mediated recombination. To provide a proof-of-concept of this method, we disassembled the well-known novobiocin biosynthetic gene cluster into four gene operons, encoding for the different moieties of novobiocin. We then genetically reorganized these gene operons with the help of AGOS to finally obtain the complete novobiocin gene cluster again. The production of novobiocin precursors and of novobiocin could successfully be detected by LC-MS and LC-MS/MS. Furthermore, we demonstrated that the omission of terminator sequences only had a minor impact on product formation in our system.
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Affiliation(s)
- Patrick Basitta
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | - Lucia Westrich
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | - Manuela Rösch
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | | | - Bertolt Gust
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | - Alexander Kristian Apel
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
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23
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Stark H. Further Developments. Arch Pharm (Weinheim) 2017; 350. [DOI: 10.1002/ardp.201770010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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