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Abstract
The Streptomyces clavuligerus genome consists in a linear chromosome of about 6.7 Mb and four plasmids (pSCL1 to pSCL4), the latter one of 1.8 Mb. Deletion of pSCL4, results in viable mutants with high instability in the chromosome arms, which may lead to chromosome circularisation. Transcriptomic and proteomic studies comparing different mutants with the wild-type strain improved our knowledge on the biosynthesis and regulation of clavulanic acid, cephamycin C and holomycin. Additional knowledge has been obtained on the SARP-type CcaR activator and the network of connections with other regulators (Brp, AreB, AdpA, BldG, RelA) controlling ccaR expression. The transcriptional pattern of the cephamycin and clavulanic acid clusters is supported by the binding of CcaR to different promoters and confirmed that ClaR is a CcaR-dependent activator that controls the late steps of clavulanic biosynthesis. Metabolomic studies allowed the detection of new metabolites produced by S. clavuligerus such as naringenin, desferroxamines, several N-acyl tunicamycins, the terpenes carveol and cuminyl alcohol or bafilomycin J. Heterologous expression of S. clavuligerus terpene synthases resulted in the formation of no less than 15 different terpenes, although none of them was detected in S. clavuligerus culture broth. In summary, application of the Omic tools results in a better understanding of the molecular biology of S. clavuligerus, that allows the use of this strain as an industrial actinobacterial platform and helps to improve CA production.
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Affiliation(s)
- Paloma Liras
- Microbiology Section. Department of Molecular Biology University of León, León 24071. Spain
| | - Juan F Martín
- Microbiology Section. Department of Molecular Biology University of León, León 24071. Spain
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Ordóñez-Robles M, Santos-Beneit F, Martín JF. Unraveling Nutritional Regulation of Tacrolimus Biosynthesis in Streptomyces tsukubaensis through omic Approaches. Antibiotics (Basel) 2018; 7:antibiotics7020039. [PMID: 29724001 PMCID: PMC6022917 DOI: 10.3390/antibiotics7020039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022] Open
Abstract
Streptomyces tsukubaensis stands out among actinomycetes by its ability to produce the immunosuppressant tacrolimus. Discovered about 30 years ago, this macrolide is widely used as immunosuppressant in current clinics. Other potential applications for the treatment of cancer and as neuroprotective agent have been proposed in the last years. In this review we introduce the discovery of S. tsukubaensis and tacrolimus, its biosynthetic pathway and gene cluster (fkb) regulation. We have focused this work on the omic studies performed in this species in order to understand tacrolimus production. Transcriptomics, proteomics and metabolomics have improved our knowledge about the fkb transcriptional regulation and have given important clues about nutritional regulation of tacrolimus production that can be applied to improve production yields. Finally, we address some points of S. tsukubaensis biology that deserve more attention.
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Affiliation(s)
- María Ordóñez-Robles
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León 24071, Spain.
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, León 24006, Spain.
| | - Fernando Santos-Beneit
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, León 24006, Spain.
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo 33006, Spain.
| | - Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León 24071, Spain.
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3
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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Park OK, Choi HY, Kim GW, Kim WG. Generation of New Complestatin Analogues by Heterologous Expression of the Complestatin Biosynthetic Gene Cluster from Streptomyces chartreusis AN1542. Chembiochem 2016; 17:1725-31. [PMID: 27383040 DOI: 10.1002/cbic.201600241] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 01/19/2023]
Abstract
The heterologous expression of the biosynthetic gene cluster (BGC) of natural products enables the production of complex metabolites in a well-characterized host, and facilitates the generation of novel analogues by the manipulation of the genes. However, the BGCs of glycopeptides such as vancomycin, teicoplanin, and complestatin are usually too large to be directly cloned into a single cosmid. Here, we describe the heterologous expression of the complestatin BGC. The 54.5 kb cluster was fully reconstituted from two overlapping cosmids into one cosmid by λ-RED recombination-mediated assembly. Heterologous expression of the assembled gene cluster in Streptomyces lividans TK24 resulted in the production of complestatin. Deletion of cytochrome P450 monooxygenase genes (open reading frames 10 and 11) and heterologous expression of the modified clusters led to the production of two new monocyclic and linear derivatives, complestatins M55 and S56.
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Affiliation(s)
- Ok-Kyung Park
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon, 34141, Republic of Korea
| | - Ha-Young Choi
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon, 34141, Republic of Korea
| | - Geon-Woo Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon, 34141, Republic of Korea
| | - Won-Gon Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon, 34141, Republic of Korea.
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Trends in the biosynthesis and production of the immunosuppressant tacrolimus (FK506). Appl Microbiol Biotechnol 2013; 98:497-507. [PMID: 24272367 DOI: 10.1007/s00253-013-5362-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 01/03/2023]
Abstract
The current off-patent state of tacrolimus (FK506) has opened the hunting season for new generic pharmaceutical formulations of this immunosuppressant. This fact has boosted the scientific and industrial research on tacrolimus for the last 5 years in order to improve its production. The fast discovery of tacrolimus producer strains has generated a huge number of producers, which presents the biosynthetic cluster of FK506 as a high promiscuous genetic region. For the first time, the current state-of-the-art on the tacrolimus biosynthesis, production improvements and drug purification is reviewed. On one hand, all the genes involved in the tacrolimus biosynthesis, in addition to the traditional PKS/NRPS, as well as their regulation are analysed. On the other hand, tacrolimus direct and indirect precursors are reviewed as a straight manner to improve the final yield, which is a current trend in the field. Twenty years of industrial and scientific improvements on tacrolimus production are summarised, whereas future trends are also drafted.
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Ban YH, Lee JH, Gu GR, Lee B, Mo S, Kwon HJ, Yoon YJ. Mutational biosynthesis of a FK506 analogue containing a non-natural starter unit. MOLECULAR BIOSYSTEMS 2013; 9:944-7. [PMID: 23223556 DOI: 10.1039/c2mb25419k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A FK506 analogue containing a non-natural starter unit was obtained through mutasynthesis by feeding cultures of Streptomyces sp. KCTC 11604BP fkbO deletion mutant with 3-cyclohexene-1-carboxylic acid. The structure of the new compound, 32-dehydroxy-FK506, and its biological activities were determined.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea
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Lechner A, Wilson MC, Ban YH, Hwang JY, Yoon YJ, Moore BS. Designed biosynthesis of 36-methyl-FK506 by polyketide precursor pathway engineering. ACS Synth Biol 2013; 2:379-83. [PMID: 23654255 DOI: 10.1021/sb3001062] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The polyketide synthase (PKS) biosynthetic code has recently expanded to include a newly recognized group of extender unit substrates derived from α,β-unsaturated acyl-CoA molecules that deliver diverse side chain chemistry to polyketide backbones. Herein we report the identification of a three-gene operon responsible for the biosynthesis of the PKS building block isobutyrylmalonyl-CoA associated with the macrolide ansalactam A from the marine bacterium Streptomyces sp. CNH189. Using a synthetic biology approach, we engineered the production of unnatural 36-methyl-FK506 in Streptomyces sp. KCTC 11604BP by incorporating the branched extender unit into FK506 biosynthesis in place of its natural C-21 allyl side chain, which has been shown to be critical for FK506's potent immunosuppressant and neurite outgrowth activities.
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Affiliation(s)
| | | | - Yeon Hee Ban
- Department of Chemistry and Nano
Science, Ewha Womans University, Seoul
120-750, Republic of Korea
| | - Jae-yeon Hwang
- Department of Chemistry and Nano
Science, Ewha Womans University, Seoul
120-750, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nano
Science, Ewha Womans University, Seoul
120-750, Republic of Korea
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Ban YH, Shinde PB, Hwang JY, Song MC, Kim DH, Lim SK, Sohng JK, Yoon YJ. Characterization of FK506 biosynthetic intermediates involved in post-PKS elaboration. JOURNAL OF NATURAL PRODUCTS 2013; 76:1091-1098. [PMID: 23706030 DOI: 10.1021/np4001224] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The post-PKS modification steps of FK506 biosynthesis include C9-oxidation and 31-O-methylation, but the sequence of these reactions and the exact route have remained unclear. This study details the post-PKS modification pathways in FK506 biosynthesis through the identification of all intermediates and in vitro enzymatic reactions of the cytochrome P450 hydroxylase FkbD and the methyltransferase FkbM. These results complete our understanding of post-PKS modification steps to FK506 showing the substrate flexibility of two enzymes involved and the existence of two parallel biosynthetic routes to FK506.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea
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Moss SJ, Stanley-Smith AE, Schell U, Coates NJ, Foster TA, Gaisser S, Gregory MA, Martin CJ, Nur-e-Alam M, Piraee M, Radzom M, Suthar D, Thexton DG, Warneck TD, Zhang MQ, Wilkinson B. Novel FK506 and FK520 analogues via mutasynthesis: mutasynthon scope and product characteristics. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20266b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel FK506 and FK520 analogues were generated via biosynthetic engineering in order to generate analogue compounds with equal potency but improved pharmacological profiles compared to FK506.
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Kosec G, Goranovič D, Mrak P, Fujs S, Kuščer E, Horvat J, Kopitar G, Petković H. Novel chemobiosynthetic approach for exclusive production of FK506. Metab Eng 2011; 14:39-46. [PMID: 22100790 DOI: 10.1016/j.ymben.2011.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 10/17/2011] [Accepted: 11/02/2011] [Indexed: 11/15/2022]
Abstract
FK506, a widely used immunosuppressant, is produced by industrial fermentation processes using various Streptomyces species. Independently of the strain, structurally related compound FK520 is co-produced, resulting in complex and costly isolation procedures. In this paper, we report a chemobiosynthetic approach for exclusive biosynthesis of FK506. This approach is based on the Streptomyces tsukubaensis strain with inactivated allR gene, a homologue of crotonyl-CoA carboxylase/reductase, encoded in the FK506 biosynthetic cluster. This strain produces neither FK506 nor FK520; however, if allylmalonyl-S-N-acetylcysteamine precursor is added to cultivation broth, the production of FK506 is reestablished without FK506-related by-products. Using a combination of metabolic engineering and chemobiosynthetic approach, we achieved exclusive production of FK506, representing a significant step towards development of an advanced industrial bioprocess.
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Affiliation(s)
- Gregor Kosec
- Acies Bio d.o.o., Tehnološki Park 21, SI-1000 Ljubljana, Slovenia
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Characterization and identification of pradimicin analogs from Actinomadura hibisca using liquid chromatography–tandem mass spectrometry. J Chromatogr A 2011; 1218:2284-91. [DOI: 10.1016/j.chroma.2011.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 02/11/2011] [Accepted: 02/14/2011] [Indexed: 11/21/2022]
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Ham YB, Koo YM. Identification of an 18-Methyl Derivative of Tacrolimus API in Streptomyces clavuligerus CKD-1119. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.1.109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mo S, Kim DH, Lee JH, Park JW, Basnet DB, Ban YH, Yoo YJ, Chen SW, Park SR, Choi EA, Kim E, Jin YY, Lee SK, Park JY, Liu Y, Lee MO, Lee KS, Kim SJ, Kim D, Park BC, Lee SG, Kwon HJ, Suh JW, Moore BS, Lim SK, Yoon YJ. Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues. J Am Chem Soc 2010; 133:976-85. [PMID: 21175203 DOI: 10.1021/ja108399b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The allyl moiety of the immunosuppressive agent FK506 is structurally unique among polyketides and critical for its potent biological activity. Here, we detail the biosynthetic pathway to allylmalonyl-coenzyme A (CoA), from which the FK506 allyl group is derived, based on a comprehensive chemical, biochemical, and genetic interrogation of three FK506 gene clusters. A discrete polyketide synthase (PKS) with noncanonical domain architecture presumably in coordination with the fatty acid synthase pathway of the host catalyzes a multistep enzymatic reaction to allylmalonyl-CoA via trans-2-pentenyl-acyl carrier protein. Characterization of this discrete pathway facilitated the engineered biosynthesis of novel allyl group-modified FK506 analogues, 36-fluoro-FK520 and 36-methyl-FK506, the latter of which exhibits improved neurite outgrowth activity. This unique feature of FK506 biosynthesis, in which a dedicated PKS provides an atypical extender unit for the main modular PKS, illuminates a new strategy for the combinatorial biosynthesis of designer macrolide scaffolds as well as FK506 analogues.
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Affiliation(s)
- SangJoon Mo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea
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