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Du G, Yang X, Wu Z, Pan M, Dong Z, Zhang Y, Xiang W, Li S. Influence of Cluster-Situated Regulator PteF in Filipin Biosynthetic Cluster on Avermectin Biosynthesis in Streptomyces avermitilis. BIOLOGY 2024; 13:344. [PMID: 38785828 PMCID: PMC11118972 DOI: 10.3390/biology13050344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of filipin, which competes for building blocks with avermectins in Streptomyces avermitilis. However, little is known about the effects of PteF and PteR on avermectin biosynthesis. In this study, we investigated their impact on avermectin biosynthesis and global cell metabolism. The deletion of pteF resulted in a 55.49% avermectin titer improvement, which was 23.08% higher than that observed from pteR deletion, suggesting that PteF plays a more significant role in regulating avermectin biosynthesis, while PteF hardly influences the transcription level of genes in avermectin and other polyketide BGCs. Transcriptome data revealed that PteF exhibited a global regulatory effect. Avermectin production enhancement could be attributed to the repression of the tricarboxylic acid cycle and fatty acid biosynthetic pathway, as well as the enhancement of pathways supplying acyl-CoA precursors. These findings provide new insights into the role of PteF on avermectin biosynthesis and cell metabolism, offering important clues for designing and building efficient metabolic pathways to develop high-yield avermectin-producing strains.
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Affiliation(s)
- Guozhong Du
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Xue Yang
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Zhengxiong Wu
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Minghui Pan
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, China
| | - Zhuoxu Dong
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, China
| | - Yanyan Zhang
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, China
| | - Shanshan Li
- 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; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
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Wan M, Gan L, Li Z, Wang M, Chen J, Chen S, Hu J, Li J. Enhancement of fungichromin production of Streptomyces sp. WP-1 by genetic engineering. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12672-4. [PMID: 37417973 DOI: 10.1007/s00253-023-12672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Fungichromin is a polyene macrolide antibiotic with potent killing activity against a broad range of agricultural pathogens and filamentous fungi and a wide range of potential applications. The production of fungichromin is still hampered by poor fermentation yield and high cost. In this study, the whole genome sequencing of fungichromin-producing Streptomyces sp. WP-1 was conducted, and the fungichromin biosynthetic gene cluster was identified. Comparative analysis revealed that the fungichromin biosynthetic gene cluster contains two regulatory genes, ptnF, and ptnR. The roles of ptnF and ptnR were determined through knockout and complementation. The yield of fungichromin was increased by overexpressing these two regulatory genes, as well as the crotonyl CoA reductase/carboxylase gene ptnB in Streptomyces sp. WP-1. The yield of fungichromin was increased to 8.5 g/L using a combination of genetic engineering and a medium optimization strategy, which is the highest fermentation titer recorded. KEY POINTS: • Confirmation of the positive regulation of ptnF and ptnR on fungichromin. • Improvement of fungichromin production by the construction of ptnF, ptnR, and ptnB overexpression strains. • Improvement of fungichromin production by the addition of soybean oil and copper ions at optimal concentration.
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Affiliation(s)
- Miyang Wan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Lu Gan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhenxin Li
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Mengran Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jingtao Chen
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Shaoxin Chen
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Jinfeng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiyang Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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Babczyk A, Menche D. Total Synthesis of Pentamycin by a Conformationally Biased Double Stille Ring Closure with a Trienyl-bis-stannane. J Am Chem Soc 2023; 145:10974-10979. [PMID: 37162233 DOI: 10.1021/jacs.3c03011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The total synthesis of the potent polyene macrolide antibiotic pentamycin was accomplished by an expedient strategy involving a highly stereoselective assembly of the polyol segment in combination with an adventurous double Stille cross-coupling with a trienyl-bis-stannane closing the macrolactone and installing the sensitive pentaene fragment. Presumably, this remarkable linchpin insertion is enhanced by the linear hydrogen bonding skeleton of the polyol substrate. Further key features include a tailored Rychnovsky alkylation of cyanohydrin acetonides and elaborate Krische couplings to set the characteristic hydroxyl and hydroxymethyl bearing centers with excellent selectivity and yield. The total synthesis unequivocally confirms the full relative and absolute stereochemistry of this polyketide, including a previously uncertain hydroxyl bearing center.
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Affiliation(s)
- Alexander Babczyk
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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Li H, Hu Y, Zhang Y, Ma Z, Bechthold A, Yu X. Identification of RimR2 as a positive pathway-specific regulator of rimocidin biosynthesis in Streptomyces rimosus M527. Microb Cell Fact 2023; 22:32. [PMID: 36810073 PMCID: PMC9942304 DOI: 10.1186/s12934-023-02039-9] [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: 10/23/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Streoptomyces rimosus M527 is a producer of the polyene macrolide rimocidin which shows activity against various plant pathogenic fungi. Notably, the regulatory mechanisms underlying rimocidin biosynthesis are yet to be elucidated. RESULTS In this study, using domain structure and amino acid alignment and phylogenetic tree construction, rimR2, which located in the rimocidin biosynthetic gene cluster, was first found and identified as a larger ATP-binding regulators of the LuxR family (LAL) subfamily regulator. The rimR2 deletion and complementation assays were conducted to explore its role. Mutant M527-ΔrimR2 lost its ability to produce rimocidin. Complementation of M527-ΔrimR2 restored rimocidin production. The five recombinant strains, M527-ER, M527-KR, M527-21R, M527-57R, and M527-NR, were constructed by overexpressing rimR2 gene using the promoters permE*, kasOp*, SPL21, SPL57, and its native promoter, respectively, to improve rimocidin production. M527-KR, M527-NR, and M527-ER exhibited 81.8%, 68.1%, and 54.5% more rimocidin production, respectively, than the wild-type (WT) strain, while recombinant strains M527-21R and M527-57R exhibited no obvious differences in rimocidin production compared with the WT strain. RT-PCR assays revealed that the transcriptional levels of the rim genes were consistent with the changes in rimocidin production in the recombinant strains. Using electrophoretic mobility shift assays, we confirmed that RimR2 can bind to the promoter regions of rimA and rimC. CONCLUSION A LAL regulator RimR2 was identified as a positive specific-pathway regulator of rimocidin biosynthesis in M527. RimR2 regulates the rimocidin biosynthesis by influencing the transcriptional levels of rim genes and binding to the promoter regions of rimA and rimC.
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Affiliation(s)
- Huijie Li
- grid.411485.d0000 0004 1755 1108Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Yefeng Hu
- grid.411485.d0000 0004 1755 1108Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Yongyong Zhang
- grid.411485.d0000 0004 1755 1108Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang, People's Republic of China.
| | - Andreas Bechthold
- grid.5963.9Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104 Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang, People's Republic of China.
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Zhang N, Dong Y, Zhou H, Cui H. Effect of PAS-LuxR Family Regulators on the Secondary Metabolism of Streptomyces. Antibiotics (Basel) 2022; 11:antibiotics11121783. [PMID: 36551440 PMCID: PMC9774167 DOI: 10.3390/antibiotics11121783] [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: 11/06/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
With the development of sequencing technology and further scientific research, an increasing number of biosynthetic gene clusters associated with secondary Streptomyces metabolites have been identified and characterized. The encoded genes of a family of regulators designated as PAS-LuxR are gradually being discovered in some biosynthetic gene clusters of polyene macrolide, aminoglycoside, and amino acid analogues. PAS-LuxR family regulators affect secondary Streptomyces metabolites by interacting with other family regulators to regulate the transcription of the target genes in the gene cluster. This paper provides a review of the structure, function, regulatory mechanism, and application of these regulators to provide more information on the regulation of secondary metabolite biosynthesis in Streptomyces, and promote the application of PAS-LuxR family regulators in industrial breeding and other directions.
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Affiliation(s)
- Naifan Zhang
- College of Chemistry and Pharmaceutical Engineering, Jilin Institute of Chemical Technology, Jilin 132022, China
| | - Yao Dong
- College of Biology & Food Engineering, Jilin Institute of Chemical Technology, Jilin 132022, China
| | - Hongli Zhou
- College of Chemistry and Pharmaceutical Engineering, Jilin Institute of Chemical Technology, Jilin 132022, China
- Engineering Research Center for Agricultural Resources and Comprehensive Utilization of Jilin Province, Jilin Institute of Chemical Technology, Jilin 132022, China
- Correspondence: (H.Z.); (H.C.); Tel.: +86-432-62185246 (H.Z. & H.C.)
| | - Hao Cui
- College of Chemistry and Pharmaceutical Engineering, Jilin Institute of Chemical Technology, Jilin 132022, China
- Engineering Research Center for Agricultural Resources and Comprehensive Utilization of Jilin Province, Jilin Institute of Chemical Technology, Jilin 132022, China
- Correspondence: (H.Z.); (H.C.); Tel.: +86-432-62185246 (H.Z. & H.C.)
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Li Z, Li X, Xia H. Roles of LuxR-family regulators in the biosynthesis of secondary metabolites in Actinobacteria. World J Microbiol Biotechnol 2022; 38:250. [DOI: 10.1007/s11274-022-03414-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/11/2022] [Indexed: 10/31/2022]
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7
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Li X, Ren W, Li Y, Shi Y, Sun H, Wang L, Wu L, Xie Y, Du Y, Jiang Z, Hong B. Production of chain-extended cinnamoyl compounds by overexpressing two adjacent cluster-situated LuxR regulators in Streptomyces globisporus C-1027. Front Microbiol 2022; 13:931180. [PMID: 35992673 PMCID: PMC9381841 DOI: 10.3389/fmicb.2022.931180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products from microorganisms are important sources for drug discovery. With the development of high-throughput sequencing technology and bioinformatics, a large amount of uncharacterized biosynthetic gene clusters (BGCs) in microorganisms have been found, which show the potential for novel natural product production. Nine BGCs containing PKS and/or NRPS in Streptomyces globisporus C-1027 were transcriptionally low/silent under the experimental fermentation conditions, and the products of these clusters are unknown. Thus, we tried to activate these BGCs to explore cryptic products of this strain. We constructed the cluster-situated regulator overexpressing strains which contained regulator gene(s) under the control of the constitutive promoter ermE*p in S. globisporus C-1027. Overexpression of regulators in cluster 26 resulted in significant transcriptional upregulation of biosynthetic genes. With the separation and identification of products from the overexpressing strain OELuxR1R2, three ortho-methyl phenyl alkenoic acids (compounds 1-3) were obtained. Gene disruption showed that compounds 1 and 2 were completely abolished in the mutant GlaEKO, but were hardly affected by deletion of the genes orf3 or echA in cluster 26. The type II PKS biosynthetic pathway of chain-extended cinnamoyl compounds was deduced by bioinformatics analysis. This study showed that overexpression of the two adjacent cluster-situated LuxR regulator(s) is an effective strategy to connect the orphan BGC to its products.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Modulation of Multiple Gene Clusters’ Expression by the PAS-LuxR Transcriptional Regulator PteF. Antibiotics (Basel) 2022; 11:antibiotics11080994. [PMID: 35892384 PMCID: PMC9394381 DOI: 10.3390/antibiotics11080994] [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: 06/28/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
PAS-LuxR transcriptional regulators are conserved proteins governing polyene antifungal biosynthesis. PteF is the regulator of filipin biosynthesis from Streptomyces avermitilis. Its mutation drastically abates filipin, but also oligomycin production, a macrolide ATP-synthase inhibitor, and delays sporulation; thus, it has been considered a transcriptional activator. Transcriptomic analyses were performed in S. avermitilis DpteF and its parental strain. Both strains were grown in a YEME medium without sucrose, and the samples were taken at exponential and stationary growth phases. A total of 257 genes showed an altered expression in the mutant, most of them at the exponential growth phase. Surprisingly, despite PteF being considered an activator, most of the genes affected showed overexpression, thereby suggesting a negative modulation. The affected genes were related to various metabolic processes, including genetic information processing; DNA, energy, carbohydrate, and lipid metabolism; morphological differentiation; and transcriptional regulation, among others, but were particularly related to secondary metabolite biosynthesis. Notably, 10 secondary metabolite gene clusters out of the 38 encoded by the genome showed altered expression profiles in the mutant, suggesting a regulatory role for PteF that is wider than expected. The transcriptomic results were validated by quantitative reverse-transcription polymerase chain reaction. These findings provide important clues to understanding the intertwined regulatory machinery that modulates antibiotic biosynthesis in Streptomyces.
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Zinc-Responsive Regulator Zur Regulates Zinc Homeostasis, Secondary Metabolism, and Morphological Differentiation in Streptomyces avermitilis. Appl Environ Microbiol 2022; 88:e0027822. [PMID: 35323024 DOI: 10.1128/aem.00278-22] [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] [Indexed: 12/15/2022] Open
Abstract
Zinc is an essential cofactor for many metal enzymes and transcription regulators. Zn2+ availability has long been known to affect antibiotic production and morphological differentiation of Streptomyces species. However, the molecular mechanism whereby zinc regulates these processes remains unclear. We investigated the regulatory roles of the zinc-sensing regulator Zur in Streptomyces avermitilis. Our findings demonstrate that Zur plays an essential role in maintaining zinc homeostasis by repressing the expression of the zinc uptake system ZnuACB and alternative non-zinc-binding ribosomal proteins and promoting the expression of zinc exporter ZitB. Deletion of the zur gene resulted in decreased production of avermectin and oligomycin and delayed morphological differentiation, and these parameters were restored close to wild-type levels in a zur-complemented strain. Zur bound specifically to Zur box in the promoter regions of avermectin pathway-specific activator gene aveR, oligomycin polyketide synthase gene olmA1, and filipin biosynthetic pathway-specific regulatory genes pteR and pteF. Analyses by reverse transcription quantitative PCR and luciferase reporter systems indicated that Zur directly activates the transcription of these genes, i.e., that Zur directly activates biosynthesis of avermectin and oligomycin. Zur positively regulated morphological development by repressing the transcription of differentiation-related genes ssgB and minD2. Our findings, taken together, demonstrate that Zur in S. avermitilis directly controls zinc homeostasis, biosynthesis of avermectin and oligomycin, and morphological differentiation. IMPORTANCE Biosynthesis of secondary metabolites and morphological differentiation in bacteria are affected by environmental signals. The molecular mechanisms whereby zinc availability affects secondary metabolism and morphological differentiation remain poorly understood. We identified several new target genes of the zinc response regulator Zur in Streptomyces avermitilis, the industrial producer of avermectin. Zur was found to directly and positively control avermectin production, oligomycin production, and morphological differentiation in response to extracellular Zn2+ levels. Our findings clarify the regulatory functions of Zur in Streptomyces, which involve linking environmental Zn2+ status with control of antibiotic biosynthetic pathways and morphological differentiation.
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Liu B, Wei Q, Yang M, Shi L, Zhang K, Ge B. Effect of toyF on wuyiencin and toyocamycin production by Streptomyces albulus CK-15. World J Microbiol Biotechnol 2022; 38:65. [PMID: 35229201 DOI: 10.1007/s11274-022-03234-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
Abstract
Streptomyces albulus CK-15 produces various secondary metabolites, including the antibiotics wuyiencin and toyocamycin, which can reportedly control a broad range of plant fungal diseases. The production of these nucleoside antibiotics in CK-15 is regulated by two biosynthesis gene clusters. To investigate the potential effect of toyocamycin biosynthesis on wuyiencin production, we herein generated S. albulus strains in which a key gene in the toyocamycin biosynthesis gene cluster, namely toyF, was either deleted or overexpressed. The toyF deletion mutant ∆toyF did not produce toyocamycin, while the production of wuyiencin increased by 23.06% in comparison with that in the wild-type (WT) strain. In addition, ΔtoyF reached the highest production level of wuyiencin 4 h faster than the WT strain (60 h vs. and 64 h). Further, toyocamycin production by the toyF overexpression strain was two-fold higher than by the WT strain, while wuyiencin production was reduced by 29.10%. qRT-PCR showed that most genes in the toyocamycin biosynthesis gene cluster were expressed at lower levels in ∆toyF as compared with those in the WT strain, while the expression levels of genes in the wuyiencin biosynthesis gene cluster were upregulated. Finally, the growth rate of ∆toyF was much faster than that of the WT strain when cultured on solid or liquid medium. Based on our findings, we report that in industrial fermentation processes, ∆toyF has the potential to increase the production of wuyiencin and reduce the timeframe of fermentation.
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Affiliation(s)
- Binghua Liu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Qiuhe Wei
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaoling Yang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liming Shi
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kecheng Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Beibei Ge
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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11
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Lewis RA, Devi J, Green K, Li J, Hopkins A, Hayles J, Nurse P, Errington J, Allenby NEE. Screening and Purification of Natural Products from Actinomycetes that Induce a "Rounded" Morphological Phenotype in Fission Yeast. NATURAL PRODUCTS AND BIOPROSPECTING 2021; 11:431-445. [PMID: 33881756 PMCID: PMC8275771 DOI: 10.1007/s13659-021-00304-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
This study was designed to identify and investigate bioactive natural product compounds that alter the cellular shape of the fission yeast Schizosaccharomyces pombe and induce a "rounded" or "small" cellular morphological phenotype. Bioassays using a range of antifungal agents against a multidrug-sensitive fission yeast strain, SAK950 showed that many induced a "rounded" phenotype. We then investigated whether 46 of the actinomycete strains identified in our previous study as inducing a similar phenotype produced antifungal agents of similar classes. We show that five of the strains produced streptothricin and that 26 strains produced polyenes, including fungichromin, filipin and candicidin, the last of which was produced by 24 strains. A taxonomic study of the strains indicated that the majority of the candicidin only producers were Streptomyces hydrogenans and S. albidoflavus whilst those that additionally produced streptothricin were related to S. enissocaesilis. A follow-up study to investigate the natural products made by related strains indicated that they followed a similar pattern. The identification of several compounds from the actinomycete strains similar to the antifungal agents initially tested confirm the validity of an approach using the S. pombe morphological phenotype and actinomycete taxonomy as a predictive tool for natural product identification.
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Affiliation(s)
- Richard Alexander Lewis
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK.
| | - Jenileima Devi
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Katherine Green
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Juanjuan Li
- University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Adam Hopkins
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jeff Errington
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
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Lara AC, Corretto E, Kotrbová L, Lorenc F, Petříčková K, Grabic R, Chroňáková A. The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues. Microorganisms 2021; 9:microorganisms9081547. [PMID: 34442631 PMCID: PMC8401907 DOI: 10.3390/microorganisms9081547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 07/17/2021] [Indexed: 12/16/2022] Open
Abstract
Streptomyces sp. TR1341 was isolated from the sputum of a man with a history of lung and kidney tuberculosis, recurrent respiratory infections, and COPD. It produces secondary metabolites associated with cytotoxicity and immune response modulation. In this study, we complement our previous results by identifying the genetic features associated with the production of these secondary metabolites and other characteristics that could benefit the strain during its colonization of human tissues (virulence factors, modification of the host immune response, or the production of siderophores). We performed a comparative phylogenetic analysis to identify the genetic features that are shared by environmental isolates and human respiratory pathogens. The results showed a high genomic similarity of Streptomyces sp. TR1341 to the plant-associated Streptomyces sp. endophyte_N2, inferring a soil origin of the strain. Putative virulence genes, such as mammalian cell entry (mce) genes were not detected in the TR1341’s genome. The presence of a type VII secretion system, distinct from the ones found in Mycobacterium species, suggests a different colonization strategy than the one used by other actinomycete lung pathogens. We identified a higher diversity of genes related to iron acquisition and demonstrated that the strain produces ferrioxamine B in vitro. These results indicate that TR1341 may have an advantage in colonizing environments that are low in iron, such as human tissue.
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Affiliation(s)
- Ana Catalina Lara
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Erika Corretto
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Lucie Kotrbová
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - František Lorenc
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Kateřina Petříčková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 12800 Prague 2, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 37005 České Budějovice, Czech Republic
| | - Roman Grabic
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, Zátiší 728/II, 38925 Vodňany, Czech Republic;
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
- Correspondence:
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13
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Production, Detection, Extraction, and Quantification of Polyene Antibiotics. Methods Mol Biol 2021. [PMID: 33977457 DOI: 10.1007/978-1-0716-1358-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Polyene antibiotics are macrolide antifungal compounds obtained by fermentation of producer Streptomyces strains. Here we describe commonly used methods for polyene production, detection, and their subsequent extraction and purification. While bioassays are used to detect these compounds based on their biological activity, quantification by spectrophotometry or high-performance liquid chromatography (HPLC ) relies on their physiochemical properties and is more reliable.
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14
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Ma Z, Hu Y, Liao Z, Xu J, Xu X, Bechthold A, Yu X. Cloning and Overexpression of the Toy Cluster for Titer Improvement of Toyocamycin in Streptomyces diastatochromogenes. Front Microbiol 2020; 11:2074. [PMID: 32983052 PMCID: PMC7492574 DOI: 10.3389/fmicb.2020.02074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023] Open
Abstract
The nucleoside antibiotic toyocamycin (TM) is a potential fungicide that can control plant diseases, and it has become an attractive target for research. Streptomyces diastatochromogenes 1628, a TM-producing strain, was isolated by our laboratory and was considered to be a potent industrial producer of TM. Recently, the putative TM biosynthetic gene cluster (toy cluster) in S. diastatochromogenes 1628 was found by genome sequencing. In this study, the role of toy cluster for TM biosynthesis in S. diastatochromogenes 1628 was investigated by heterologous expression, deletion, and complementation. The extract of the recombinant strain S. albusJ1074-TC harboring a copy of toy cluster produced TM as shown by HPLC analysis. The Δcluster mutant completely lost its ability to produce TM. TM production in the complemented strain was restored to a level comparable to that of the wild-type strain. These results confirmed that the toy cluster is responsible for TM biosynthesis. Moreover, the introduction of an extra copy of the toy cluster into S. diastatochromogenes 1628 led to onefold increase in TM production (312.9 mg/l vs. 152.1 mg/l) as well as the transcription of all toy genes. The toy gene cluster was engineered in which the native promoter of toyA gene, toyM gene, toyBD operon, and toyEI operon was, respectively, replaced by permE∗ or SPL57. To further improve TM production, the engineered toy gene cluster was, respectively, introduced and overexpressed in S. diastatochromogenes 1628 to generate recombinant strains S. diastatochromogenes 1628-EC and 1628-SC. After 84 h, S. diastatochromogenes 1628-EC and 1628-SC produced 456.5 mg/l and 638.9 mg/l TM, respectively, which is an increase of 2- and 3.2-fold compared with the wild-type strain.
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Affiliation(s)
- Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Yefeng Hu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Zhijun Liao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Jie Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xianhao Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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The Streptomyces filipinensis Gamma-Butyrolactone System Reveals Novel Clues for Understanding the Control of Secondary Metabolism. Appl Environ Microbiol 2020; 86:AEM.00443-20. [PMID: 32631864 PMCID: PMC7480387 DOI: 10.1128/aem.00443-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/26/2020] [Indexed: 11/20/2022] Open
Abstract
Streptomyces GBLs are important signaling molecules that trigger antibiotic production in a quorum sensing-dependent manner. We have characterized the GBL system from S. filipinensis, finding that two key players of this system, the GBL receptor and the pseudo-receptor, each counteracts the transcription of the other for the modulation of filipin production and that such control over antifungal production involves an indirect effect on the transcription of filipin biosynthetic genes. Additionally, the two regulators bind the same sites, are self-regulated, and repress the transcription of three other genes of the GBL cluster, including that encoding the GBL synthase. In contrast to all the GBL receptors known, SfbR activates its own synthesis. Moreover, the pseudo-receptor was identified as the receptor of antimycin A, thus extending the range of examples supporting the idea of signaling effects of antibiotics in Streptomyces. The intricate regulatory network depicted here should provide important clues for understanding the regulatory mechanism governing secondary metabolism. Streptomyces γ-butyrolactones (GBLs) are quorum sensing communication signals triggering antibiotic production. The GBL system of Streptomyces filipinensis, the producer of the antifungal agent filipin, has been investigated. Inactivation of sfbR (for S. filipinensis γ-butyrolactone receptor), a GBL receptor, resulted in a strong decrease in production of filipin, and deletion of sfbR2, a pseudo-receptor, boosted it, in agreement with lower and higher levels of transcription of filipin biosynthetic genes, respectively. It is noteworthy that none of the mutations affected growth or morphological development. While no ARE (autoregulatory element)-like sequences were found in the promoters of filipin genes, suggesting indirect control of production, five ARE sequences were found in five genes of the GBL cluster, whose transcription has been shown to be controlled by both S. filipinensis SfbR and SfbR2. In vitro binding of recombinant SfbR and SfbR2 to such sequences indicated that such control is direct. Transcription start points were identified by 5′ rapid amplification of cDNA ends, and precise binding regions were investigated by the use of DNase I protection studies. Binding of both regulators took place in the promoter of target genes and at the same sites. Information content analysis of protected sequences in target promoters yielded an 18-nucleotide consensus ARE sequence. Quantitative transcriptional analyses revealed that both regulators are self-regulated and that each represses the transcription of the other as well as that of the remaining target genes. Unlike other GBL receptor homologues, SfbR activates its own transcription whereas SfbR2 has a canonical autorepression profile. Additionally, SfbR2 was found here to bind the antifungal antimycin A as a way to modulate its DNA-binding activity. IMPORTANCEStreptomyces GBLs are important signaling molecules that trigger antibiotic production in a quorum sensing-dependent manner. We have characterized the GBL system from S. filipinensis, finding that two key players of this system, the GBL receptor and the pseudo-receptor, each counteracts the transcription of the other for the modulation of filipin production and that such control over antifungal production involves an indirect effect on the transcription of filipin biosynthetic genes. Additionally, the two regulators bind the same sites, are self-regulated, and repress the transcription of three other genes of the GBL cluster, including that encoding the GBL synthase. In contrast to all the GBL receptors known, SfbR activates its own synthesis. Moreover, the pseudo-receptor was identified as the receptor of antimycin A, thus extending the range of examples supporting the idea of signaling effects of antibiotics in Streptomyces. The intricate regulatory network depicted here should provide important clues for understanding the regulatory mechanism governing secondary metabolism.
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Lu X, Liu X, Chen Z, Li J, van Wezel GP, Chen W, Wen Y. The ROK-family regulator Rok7B7 directly controls carbon catabolite repression, antibiotic biosynthesis, and morphological development in Streptomyces avermitilis. Environ Microbiol 2020; 22:5090-5108. [PMID: 32452104 DOI: 10.1111/1462-2920.15094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/10/2020] [Accepted: 05/19/2020] [Indexed: 11/30/2022]
Abstract
Carbon catabolite repression (CCR) is a common phenomenon in bacteria that modulates expression of genes involved in uptake of alternative carbon sources. In the filamentous streptomycetes, which produce half of all known antibiotics, the precise mechanism of CCR is yet unknown. We report here that the ROK-family regulator Rok7B7 pleiotropically controls xylose and glucose uptake, CCR, development, as well as production of the macrolide antibiotics avermectin and oligomycin A in Streptomyces avermitilis. Rok7B7 directly repressed structural genes for avermectin biosynthesis, whereas it activated olmRI, the cluster-situated activator gene for oligomycin A biosynthesis. Rok7B7 also directly repressed the xylose uptake operon xylFGH, whose expression was induced by xylose and repressed by glucose. Both xylose and glucose served as Rok7B7 ligands. rok7B7 deletion led to enhancement and reduction of avermectin and oligomycin A production, respectively, relieved CCR of xylFGH, and increased co-uptake efficiency of xylose and glucose. A consensus Rok7B7-binding site, 5'-TTKAMKHSTTSAV-3', was identified within aveA1p, olmRIp, and xylFp, which allowed prediction of the Rok7B7 regulon and confirmation of 11 additional targets involved in development, secondary metabolism, glucose uptake, and primary metabolic processes. Our findings will facilitate methods for strain improvement, antibiotic overproduction, and co-uptake of xylose and glucose in Streptomyces species.
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Affiliation(s)
- Xiaorui Lu
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xingchao Liu
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
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Yang J, Xu D, Yu W, Hao R, Wei J. Regulation of aureofuscin production by the PAS-LuxR family regulator AurJ3M. Enzyme Microb Technol 2020; 137:109532. [DOI: 10.1016/j.enzmictec.2020.109532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/09/2020] [Accepted: 02/05/2020] [Indexed: 01/17/2023]
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18
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Herbrík A, Corretto E, Chroňáková A, Langhansová H, Petrásková P, Hrdý J, Čihák M, Krištůfek V, Bobek J, Petříček M, Petříčková K. A Human Lung-Associated Streptomyces sp. TR1341 Produces Various Secondary Metabolites Responsible for Virulence, Cytotoxicity and Modulation of Immune Response. Front Microbiol 2020; 10:3028. [PMID: 32010093 PMCID: PMC6978741 DOI: 10.3389/fmicb.2019.03028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Streptomycetes, typical soil dwellers, can be detected as common colonizers of human bodies, especially the skin, the respiratory tract, the guts and the genital tract using molecular techniques. However, their clinical manifestations and isolations are rare. Recently they were discussed as possible "coaches" of the human immune system in connection with certain immune disorders and cancer. This work aimed for the characterization and evaluation of genetic adaptations of a human-associated strain Streptomyces sp. TR1341. The strain was isolated from sputum of a senior male patient with a history of lung and kidney TB, recurrent respiratory infections and COPD. It manifested remarkably broad biological activities (antibacterial, antifungal, beta-hemolytic, etc.). We found that, by producing specific secondary metabolites, it is able to modulate host immune responses and the niche itself, which increase its chances for long-term survival in the human tissue. The work shows possible adaptations or predispositions of formerly soil microorganism to survive in human tissue successfully. The strain produces two structural groups of cytotoxic compounds: 28-carbon cytolytic polyenes of the filipin type and actinomycin X2. Additionally, we summarize and present data about streptomycete-related human infections known so far.
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Affiliation(s)
- Andrej Herbrík
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Erika Corretto
- Institute of Soil Biology, Biology Centre Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Helena Langhansová
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Petra Petrásková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Jiří Hrdý
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Matouš Čihák
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Václav Krištůfek
- Institute of Soil Biology, Biology Centre Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Jan Bobek
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia.,Department of Chemistry, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Ústí nad Labem, Czechia
| | - Miroslav Petříček
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Kateřina Petříčková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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Characterization and overproduction of cell-associated cholesterol oxidase ChoD from Streptomyces lavendulae YAKB-15. Sci Rep 2019; 9:11850. [PMID: 31413341 PMCID: PMC6694107 DOI: 10.1038/s41598-019-48132-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/25/2019] [Indexed: 11/30/2022] Open
Abstract
Cholesterol oxidases are important enzymes with a wide range of applications from basic research to industry. In this study, we have discovered and described the first cell-associated cholesterol oxidase, ChoD, from Streptomyces lavendulae YAKB-15. This strain is a naturally high producer of ChoD, but only produces ChoD in a complex medium containing whole yeast cells. For characterization of ChoD, we acquired a draft genome sequence of S. lavendulae YAKB-15 and identified a gene product containing a flavin adenine dinucleotide binding motif, which could be responsible for the ChoD activity. The enzymatic activity was confirmed in vitro with histidine tagged ChoD produced in Escherichia coli TOP10, which lead to the determination of basic kinetic parameters with Km 15.9 µM and kcat 10.4/s. The optimum temperature and pH was 65 °C and 5, respectively. In order to increase the efficiency of production, we then expressed the cholesterol oxidase, choD, gene heterologously in Streptomyces lividans TK24 and Streptomyces albus J1074 using two different expression systems. In S. albus J1074, the ChoD activity was comparable to the wild type S. lavendulae YAKB-15, but importantly allowed production of ChoD without the presence of yeast cells.
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20
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Xu J, Song Z, Xu X, Ma Z, Bechthold A, Yu X. ToyA, a positive pathway-specific regulator for toyocamycin biosynthesis in Streptomyces diastatochromogenes 1628. Appl Microbiol Biotechnol 2019; 103:7071-7084. [DOI: 10.1007/s00253-019-09959-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022]
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21
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Zhou S, Song L, Masschelein J, Sumang FAM, Papa IA, Zulaybar TO, Custodio AB, Zabala D, Alcantara EP, de los Santos ELC, Challis GL. Pentamycin Biosynthesis in Philippine Streptomyces sp. S816: Cytochrome P450-Catalyzed Installation of the C-14 Hydroxyl Group. ACS Chem Biol 2019; 14:1305-1309. [PMID: 31095370 DOI: 10.1021/acschembio.9b00270] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pentamycin is a polyene antibiotic, registered in Switzerland for the treatment of vaginal candidiasis, trichomoniasis, and mixed infections. Chemical instability has hindered its widespread application and development as a drug. Here, we report the identification of Streptomyces sp. S816, isolated from Philippine mangrove soil, as a pentamycin producer. Genome sequence analysis identified the putative pentamycin biosynthetic gene cluster, which shows a high degree of similarity to the gene cluster responsible for filipin III biosynthesis. The ptnJ gene, which is absent from the filipin III biosynthetic gene cluster, was shown to encode a cytochrome P450 capable of converting filipin III to pentamycin. This confirms that the cluster directs pentamycin biosynthesis, paving the way for biosynthetic engineering approaches to the production of pentamycin analogues. Several other Streptomyces genomes were found to contain ptnJ orthologues clustered with genes encoding polyketide synthases that appear to have similar architectures to those responsible for the assembly of filipin III and pentamycin, suggesting pentamycin production may be common in Streptomyces species.
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Affiliation(s)
- Shanshan Zhou
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Joleen Masschelein
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Felaine A. M. Sumang
- National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Irene A. Papa
- National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Teofila O. Zulaybar
- National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Aileen B. Custodio
- National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Daniel Zabala
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Edwin P. Alcantara
- National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Emmanuel L. C. de los Santos
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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22
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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23
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Martínez-Burgo Y, Santos-Aberturas J, Rodríguez-García A, Barreales EG, Tormo JR, Truman AW, Reyes F, Aparicio JF, Liras P. Activation of Secondary Metabolite Gene Clusters in Streptomyces clavuligerus by the PimM Regulator of Streptomyces natalensis. Front Microbiol 2019; 10:580. [PMID: 30984130 PMCID: PMC6448028 DOI: 10.3389/fmicb.2019.00580] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/06/2019] [Indexed: 11/13/2022] Open
Abstract
Expression of non-native transcriptional activators may be a powerful general method to activate secondary metabolites biosynthetic pathways. PAS-LuxR regulators, whose archetype is PimM, activate the biosynthesis of polyene macrolide antifungals and other antibiotics, and have been shown to be functionally preserved across multiple Streptomyces strains. In this work we show that constitutive expression of pimM in Streptomyces clavuligerus ATCC 27064 significantly affected its transcriptome and modifies secondary metabolism. Almost all genes in three secondary metabolite clusters were overexpressed, including the clusters responsible for the biosynthesis of the clinically important clavulanic acid and cephamycin C. In comparison to a control strain, this resulted in 10- and 7-fold higher production levels of these metabolites, respectively. Metabolomic and bioactivity studies of S. clavuligerus::pimM also revealed deep metabolic changes. Antifungal activity absent in the control strain was detected in S. clavuligerus::pimM, and determined to be the result of a fivefold increase in the production of the tunicamycin complex.
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Affiliation(s)
| | | | - Antonio Rodríguez-García
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain.,Institute of Biotechnology of León, INBIOTEC, León, Spain
| | - Eva G Barreales
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
| | - José Rubén Tormo
- Centre of Excellence for Research into Innovative Medicine, Health Sciences Technology, MEDINA, Granada, Spain
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Fernando Reyes
- Centre of Excellence for Research into Innovative Medicine, Health Sciences Technology, MEDINA, Granada, Spain
| | - Jesús F Aparicio
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
| | - Paloma Liras
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
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24
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Ward AL, Reddyvari P, Borisova R, Shilabin AG, Lampson BC. An inhibitory compound produced by a soil isolate of Rhodococcus has strong activity against the veterinary pathogen R. equi. PLoS One 2018; 13:e0209275. [PMID: 30592730 PMCID: PMC6310278 DOI: 10.1371/journal.pone.0209275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/03/2018] [Indexed: 01/22/2023] Open
Abstract
Complete genome sequencing of dozens of strains of the soil bacterium Rhodococcus has revealed the presence of many cryptic biosynthetic gene clusters, presumably dedicated to the production of small molecules. This has sparked a renewed interest in this underexplored member of the Actinobacteria as a potential source of new bioactive compounds. Reported here is the discovery of a potent inhibitory molecule produced by a newly isolated strain of Rhodococcus, strain MTM3W5.2. This small inhibitory molecule shows strong activity against all Rhodococcus species tested, including the veterinary pathogen R. equi, and some closely related genera. It is not active against other Gram positive or Gram negative bacteria. A screen of random transposon mutants identified a gene required to produce this inhibitory compound. This gene is a large multi-domain, type I polyketide synthase that is part of a very large multi-gene biosynthetic gene cluster in the chromosome of strain MTM3W5.2. The high resolution mass spectrum of a major chromatogram peak from a broth culture extract of MTM3W5.2 shows the presence of a compound at m/z 911.5490 atomic mass units. This compound is not detected in the culture extracts from a non-producing mutant strain of MTM3W5.2. A large gene cluster containing at least 14 different type I polyketide synthase genes is proposed to be required to synthesize this antibiotic-like compound.
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Affiliation(s)
- Amber L. Ward
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, United States of America
| | - Pushpavathi Reddyvari
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States of America
| | - Ralitsa Borisova
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, United States of America
| | - Abbas G. Shilabin
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States of America
| | - Bert C. Lampson
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, United States of America
- * E-mail:
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Barreales EG, Payero TD, de Pedro A, Aparicio JF. Phosphate effect on filipin production and morphological differentiation in Streptomyces filipinensis and the role of the PhoP transcription factor. PLoS One 2018; 13:e0208278. [PMID: 30521601 PMCID: PMC6283541 DOI: 10.1371/journal.pone.0208278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
The biosynthesis of the antifungal filipin in Streptomyces filipinensis is very sensitive to phosphate regulation. Concentrations as low as 2.5 mM block filipin production. This effect is, at least in part, produced by repression of the transcription of most filipin biosynthetic genes. The role of the two-component PhoRP system in this process was investigated. The phoRP system of S. filipinensis was cloned and transcriptionally characterised. PhoP binds to two PHO boxes present in one of its two promoters. Filipin production was greatly increased in ΔphoP and ΔphoRP mutants, in agreement with a higher transcription of the fil genes, and the effect of phosphate repression on the antibiotic production of these strains was significantly reduced. No PhoP binding was observed by electrophoretic mobility gel shift assays (EMSAs) with the promoter regions of the fil gene cluster thus suggesting an indirect effect of mutations. Binding assays with cell-free extracts from the wild-type and mutant strains on fil genes promoters revealed retardation bands in the parental strain that were absent in the mutants, thus suggesting that binding of the putative transcriptional regulator or regulators controlled by PhoP was PhoP dependent. Noteworthy, PhoP or PhoRP deletion also produced a dramatic decrease in sporulation ability, thus indicating a clear relationship between the phosphate starvation response mediated by PhoP and the sporulation process in S. filipinensis. This effect was overcome upon gene complementation, but also by phosphate addition, thus suggesting that alternative pathways take control in the absence of PhoRP.
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Affiliation(s)
- Eva G. Barreales
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Tamara D. Payero
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Antonio de Pedro
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Jesús F. Aparicio
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
- * E-mail:
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26
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Liu B, Ge B, Ma J, Wei Q, Khan AA, Shi L, Zhang K. Identification of wysPII as an Activator of Morphological Development in Streptomyces albulus CK-15. Front Microbiol 2018; 9:2550. [PMID: 30405594 PMCID: PMC6207912 DOI: 10.3389/fmicb.2018.02550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/05/2018] [Indexed: 11/13/2022] Open
Abstract
Wuyiencin is produced by Streptomyces albulus var. wuyiensis and used widely in agriculture to control a variety of fungal diseases, such as cucumber downy mildew, strawberry powdery mildew, and tomato gray mold. As an industrially-produced biopesticide, reducing production costs is very important for popularization of this approach. To obtain a rapidly growing strain that effectively shortens the fermentation time, we investigated the effects of knockout and overexpression of the wysPII gene, a member of the LuxR regulatory gene family, in S. albulus strain CK-15. The ΔwysPII mutant exhibited a reduced rate of growth and sporulation. The time taken to reach the greatest mycelial biomass was approximately 18 h shorter in the ooPII (wysPII overexpressing) strain compared with that of the wild-type (WT) strain. In addition, the time to reach the greatest wuyiencin production was 56 h in the ooPII strain compared with 62 h in the WT strain. Furthermore, wysPII was shown to act as an activator of morphological development without affecting wuyiencin production. Thus, the ooPII strain can be used to reduce costs and increase efficiency in industrial fermentation processes for wuyiencin production.
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Affiliation(s)
- Binghua Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Beibei Ge
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinjin Ma
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuhe Wei
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Abid Ali Khan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Liming Shi
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kecheng Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Wei J, He L, Niu G. Regulation of antibiotic biosynthesis in actinomycetes: Perspectives and challenges. Synth Syst Biotechnol 2018; 3:229-235. [PMID: 30417136 PMCID: PMC6215055 DOI: 10.1016/j.synbio.2018.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/27/2018] [Accepted: 10/17/2018] [Indexed: 02/08/2023] Open
Abstract
Actinomycetes are the main sources of antibiotics. The onset and level of production of each antibiotic is subject to complex control by multi-level regulators. These regulators exert their functions at hierarchical levels. At the lower level, cluster-situated regulators (CSRs) directly control the transcription of neighboring genes within the gene cluster. Higher-level pleiotropic and global regulators exert their functions mainly through modulating the transcription of CSRs. Advances in understanding of the regulation of antibiotic biosynthesis in actinomycetes have inspired us to engineer these regulators for strain improvement and antibiotic discovery.
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Affiliation(s)
- Junhong Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Lang He
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
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Promoter Engineering Reveals the Importance of Heptameric Direct Repeats for DNA Binding by Streptomyces Antibiotic Regulatory Protein-Large ATP-Binding Regulator of the LuxR Family (SARP-LAL) Regulators in Streptomyces natalensis. Appl Environ Microbiol 2018; 84:AEM.00246-18. [PMID: 29500267 PMCID: PMC5930380 DOI: 10.1128/aem.00246-18] [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: 01/30/2018] [Accepted: 02/24/2018] [Indexed: 02/04/2023] Open
Abstract
The biosynthesis of small-size polyene macrolides is ultimately controlled by a couple of transcriptional regulators that act in a hierarchical way. A Streptomyces antibiotic regulatory protein–large ATP-binding regulator of the LuxR family (SARP-LAL) regulator binds the promoter of a PAS-LuxR regulator-encoding gene and activates its transcription, and in turn, the gene product of the latter activates transcription from various promoters of the polyene gene cluster directly. The primary operator of PimR, the archetype of SARP-LAL regulators, contains three heptameric direct repeats separated by four-nucleotide spacers, but the regulator can also bind a secondary operator with only two direct repeats separated by a 3-nucleotide spacer, both located in the promoter region of its unique target gene, pimM. A similar arrangement of operators has been identified for PimR counterparts encoded by gene clusters for different antifungal secondary metabolites, including not only polyene macrolides but peptidyl nucleosides, phoslactomycins, or cycloheximide. Here, we used promoter engineering and quantitative transcriptional analyses to determine the contributions of the different heptameric repeats to transcriptional activation and final polyene production. Optimized promoters have thus been developed. Deletion studies and electrophoretic mobility assays were used for the definition of DNA-binding boxes formed by 22-nucleotide sequences comprising two conserved heptameric direct repeats separated by four-nucleotide less conserved spacers. The cooperative binding of PimRSARP appears to be the mechanism involved in the binding of regulator monomers to operators, and at least two protein monomers are required for efficient binding. IMPORTANCE Here, we have shown that a modulation of the production of the antifungal pimaricin in Streptomyces natalensis can be accomplished via promoter engineering of the PAS-LuxR transcriptional activator pimM. The expression of this gene is controlled by the Streptomyces antibiotic regulatory protein–large ATP-binding regulator of the LuxR family (SARP-LAL) regulator PimR, which binds a series of heptameric direct repeats in its promoter region. The structure and importance of such repeats in protein binding, transcriptional activation, and polyene production have been investigated. These findings should provide important clues to understand the regulatory machinery that modulates antibiotic biosynthesis in Streptomyces and open new possibilities for the manipulation of metabolite production. The presence of PimR orthologues encoded by gene clusters for different secondary metabolites and the conservation of their operators suggest that the improvements observed in the activation of pimaricin biosynthesis by Streptomyces natalensis could be extrapolated to the production of different compounds by other species.
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Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment. Sci Rep 2018; 8:1594. [PMID: 29371699 PMCID: PMC5785472 DOI: 10.1038/s41598-018-20018-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/11/2018] [Indexed: 11/25/2022] Open
Abstract
Streptomyces are a genus of Actinobacteria capable of producing structurally diverse natural products. Here we report the isolation and characterization of a biosynthetically talented Streptomyces (Streptomyces sp. SD85) from tropical mangrove sediments. Whole-genome sequencing revealed that Streptomyces sp. SD85 harbors at least 52 biosynthetic gene clusters (BGCs), which constitute 21.2% of the 8.6-Mb genome. When cultivated under lab conditions, Streptomyces sp. SD85 produces sceliphrolactam, a 26-membered polyene macrolactam with unknown biosynthetic origin. Genome mining yielded a putative sceliphrolactam BGC (sce) that encodes a type I modular polyketide synthase (PKS) system, several β-amino acid starter biosynthetic enzymes, transporters, and transcriptional regulators. Using the CRISPR/Cas9–based gene knockout method, we demonstrated that the sce BGC is essential for sceliphrolactam biosynthesis. Unexpectedly, the PKS system encoded by sce is short of one module required for assembling the 26-membered macrolactam skeleton according to the collinearity rule. With experimental data disfavoring the involvement of a trans-PKS module, the biosynthesis of sceliphrolactam seems to be best rationalized by invoking a mechanism whereby the PKS system employs an iterative module to catalyze two successive chain extensions with different outcomes. The potential violation of the collinearity rule makes the mechanism distinct from those of other polyene macrolactams.
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Coordinate Regulation of Antimycin and Candicidin Biosynthesis. mSphere 2016; 1:mSphere00305-16. [PMID: 27981234 PMCID: PMC5143413 DOI: 10.1128/msphere.00305-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/11/2016] [Indexed: 12/14/2022] Open
Abstract
Natural products produced by members of the phylum Actinobacteria underpin many industrially and medically important compounds; however, the majority of the ~30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. Understanding the diversity of regulatory strategies controlling the expression of these pathways is therefore critical if their biosynthetic potential is to be explored for new drug leads. Our findings reveal that the candicidin cluster-situated regulator FscRI coordinately controls the biosynthesis of both candicidin and antimycin, which is the first observation of cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products. We anticipate that this will emerge as a major strategy by which members of the phylum Actinobacteria coordinately produce natural products, which will advance our understanding of how the expression of secondary metabolism is controlled and will aid the pursuit of “silent” biosynthetic pathway activation. Streptomyces species produce an incredible array of high-value specialty chemicals and medicinal therapeutics. A single species typically harbors ~30 biosynthetic pathways, but only a few them are expressed in the laboratory; thus, poor understanding of how natural-product biosynthesis is regulated is a major bottleneck in drug discovery. Antimycins are a large family of anticancer compounds widely produced by Streptomyces species, and their regulation is atypical compared to that of most other natural products. Here we demonstrate that antimycin production by Streptomyces albus S4 is regulated by FscRI, a PAS-LuxR family cluster-situated regulator of the polyene antifungal agent candicidin. We report that heterologous production of antimycins by Streptomyces coelicolor is dependent on FscRI and show that FscRI activates the transcription of key biosynthetic genes. We also demonstrate through chromatin immunoprecipitation sequencing that FscRI regulation is direct, and we provide evidence that this regulation strategy is conserved and unique to short-form antimycin gene clusters. Our study provides direct in vivo evidence of the cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products and expands the paradigmatic understanding of the regulation of secondary metabolism. IMPORTANCE Natural products produced by members of the phylum Actinobacteria underpin many industrially and medically important compounds; however, the majority of the ~30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. Understanding the diversity of regulatory strategies controlling the expression of these pathways is therefore critical if their biosynthetic potential is to be explored for new drug leads. Our findings reveal that the candicidin cluster-situated regulator FscRI coordinately controls the biosynthesis of both candicidin and antimycin, which is the first observation of cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products. We anticipate that this will emerge as a major strategy by which members of the phylum Actinobacteria coordinately produce natural products, which will advance our understanding of how the expression of secondary metabolism is controlled and will aid the pursuit of “silent” biosynthetic pathway activation.
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Sun D, Zhu J, Chen Z, Li J, Wen Y. SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development. Sci Rep 2016; 6:36915. [PMID: 27841302 PMCID: PMC5107987 DOI: 10.1038/srep36915] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/20/2016] [Indexed: 11/09/2022] Open
Abstract
Avermectins are useful anthelmintic antibiotics produced by Streptomyces avermitilis. We demonstrated that a novel AraC-family transcriptional regulator in this species, SAV742, is a global regulator that negatively controls avermectin biosynthesis and cell growth, but positively controls morphological differentiation. Deletion of its gene, sav_742, increased avermectin production and dry cell weight, but caused delayed formation of aerial hyphae and spores. SAV742 directly inhibited avermectin production by repressing transcription of ave structural genes, and also directly regulated its own gene (sav_742) and adjacent gene sig8 (sav_741). The precise SAV742-binding site on its own promoter region was determined by DNase I footprinting assay coupled with site-directed DNA mutagenesis, and 5-nt inverted repeats (GCCGA-n10/n12-TCGGC) were found to be essential for SAV742 binding. Similar 5-nt inverted repeats separated by 3, 10 or 15 nt were found in the promoter regions of target ave genes and sig8. The SAV742 regulon was predicted based on bioinformatic analysis. Twenty-six new SAV742 targets were identified and experimentally confirmed, including genes involved in primary metabolism, secondary metabolism and development. Our findings indicate that SAV742 plays crucial roles in not only avermectin biosynthesis but also coordination of complex physiological processes in S. avermitilis.
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Affiliation(s)
- Di Sun
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianya Zhu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Aparicio JF, Barreales EG, Payero TD, Vicente CM, de Pedro A, Santos-Aberturas J. Biotechnological production and application of the antibiotic pimaricin: biosynthesis and its regulation. Appl Microbiol Biotechnol 2015; 100:61-78. [PMID: 26512010 PMCID: PMC4700089 DOI: 10.1007/s00253-015-7077-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/06/2015] [Accepted: 10/11/2015] [Indexed: 12/27/2022]
Abstract
Pimaricin (natamycin) is a small polyene macrolide antibiotic used worldwide. This efficient antimycotic and antiprotozoal agent, produced by several soil bacterial species of the genus Streptomyces, has found application in human therapy, in the food and beverage industries and as pesticide. It displays a broad spectrum of activity, targeting ergosterol but bearing a particular mode of action different to other polyene macrolides. The biosynthesis of this only antifungal agent with a GRAS status has been thoroughly studied, which has permitted the manipulation of producers to engineer the biosynthetic gene clusters in order to generate several analogues. Regulation of its production has been largely unveiled, constituting a model for other polyenes and setting the leads for optimizing the production of these valuable compounds. This review describes and discusses the molecular genetics, uses, mode of action, analogue generation, regulation and strategies for increasing pimaricin production yields.
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Affiliation(s)
- Jesús F Aparicio
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Eva G Barreales
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain
| | - Tamara D Payero
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain
| | - Cláudia M Vicente
- Dynamique des Génomes et Adaptation Microbienne, UMR 1128, INRA, Université de Lorraine, 54506, Vandoeuvre-lès-Nancy, France
| | - Antonio de Pedro
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain
| | - Javier Santos-Aberturas
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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33
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Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J Ind Microbiol Biotechnol 2015; 43:343-70. [PMID: 26364200 DOI: 10.1007/s10295-015-1682-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/28/2015] [Indexed: 12/18/2022]
Abstract
Actinomycetes continue to be important sources for the discovery of secondary metabolites for applications in human medicine, animal health, and crop protection. With the maturation of actinomycete genome mining as a robust approach to identify new and novel cryptic secondary metabolite gene clusters, it is critical to continue developing methods to activate and enhance secondary metabolite biosynthesis for discovery, development, and large-scale manufacturing. This review covers recent reports on promising new approaches and further validations or technical improvements of existing approaches to strain improvement applicable to a wide range of Streptomyces species and other actinomycetes.
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Payero TD, Vicente CM, Rumbero Á, Barreales EG, Santos-Aberturas J, de Pedro A, Aparicio JF. Functional analysis of filipin tailoring genes from Streptomyces filipinensis reveals alternative routes in filipin III biosynthesis and yields bioactive derivatives. Microb Cell Fact 2015; 14:114. [PMID: 26246267 PMCID: PMC4527110 DOI: 10.1186/s12934-015-0307-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022] Open
Abstract
Background Streptomyces filipinensis is the industrial producer of filipin, a pentaene macrolide, archetype of non-glycosylated polyenes, and widely used for the detection and the quantitation of cholesterol in biological membranes and as a tool for the diagnosis of Niemann–Pick type C disease. Genetic manipulations of polyene biosynthetic pathways have proven useful for the discovery of products with improved properties. Here, we describe the late biosynthetic steps for filipin III biosynthesis and strategies for the generation of bioactive filipin III derivatives at high yield. Results A region of 13,778 base pairs of DNA from the S. filipinensis genome was isolated, sequenced, and characterized. Nine complete genes and two truncated ORFs were located. Disruption of genes proved that this genomic region is part of the biosynthetic cluster for the 28-membered ring of the polyene macrolide filipin. This set of genes includes two cytochrome P450 monooxygenase encoding genes, filC and filD, which are proposed to catalyse specific hydroxylations of the macrolide ring at C26 and C1′ respectively. Gene deletion and complementation experiments provided evidence for their role during filipin III biosynthesis. Filipin III derivatives were accumulated by the recombinant mutants at high yield. These have been characterized by mass spectrometry and nuclear magnetic resonance following high-performance liquid chromatography purification thus revealing the post-polyketide steps during polyene biosynthesis. Two alternative routes lead to the formation of filipin III from the initial product of polyketide synthase chain assembly and cyclization filipin I, one trough filipin II, and the other one trough 1′-hydroxyfilipin I, all filipin III intermediates being biologically active. Moreover, minimal inhibitory concentration values against Candida utilis and Saccharomyces cerevisiae were obtained for all filipin derivatives, finding that 1′-hydroxyfilipin and especially filipin II show remarkably enhanced antifungal bioactivity. Complete nuclear magnetic resonance assignments have been obtained for the first time for 1′-hydroxyfilipin I. Conclusions This report reveals the existence of two alternative routes for filipin III formation and opens new possibilities for the generation of biologically active filipin derivatives at high yield and with improved properties. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0307-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamara D Payero
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain. .,Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain.
| | - Cláudia M Vicente
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain. .,Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain.
| | - Ángel Rumbero
- Department of Organic Chemistry, Faculty of Sciences, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Eva G Barreales
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Javier Santos-Aberturas
- Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain. .,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Antonio de Pedro
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Jesús F Aparicio
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
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Regulation of coronafacoyl phytotoxin production by the PAS-LuxR family regulator CfaR in the common scab pathogen Streptomyces scabies. PLoS One 2015; 10:e0122450. [PMID: 25826255 PMCID: PMC4380410 DOI: 10.1371/journal.pone.0122450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
Potato common scab is an economically important crop disease that is characterized by the formation of superficial, raised or pitted lesions on the potato tuber surface. The most widely distributed causative agent of the disease is Streptomyces scabies, which produces the phytotoxic secondary metabolite thaxtomin A that serves as a key virulence factor for the organism. Recently, it was demonstrated that S. scabies can also produce the phytotoxic secondary metabolite coronafacoyl-L-isoleucine (CFA-L-Ile) as well as other related metabolites in minor amounts. The expression of the biosynthetic genes for CFA-L-Ile production is dependent on a PAS-LuxR family transcriptional regulator, CfaR, which is encoded within the phytotoxin biosynthetic gene cluster in S. scabies. In this study, we show that CfaR activates coronafacoyl phytotoxin production by binding to a single site located immediately upstream of the putative -35 hexanucleotide box within the promoter region for the biosynthetic genes. The binding activity of CfaR was shown to require both the LuxR and PAS domains, the latter of which is involved in protein homodimer formation. We also show that CFA-L-Ile production is greatly enhanced in S. scabies by overexpression of both cfaR and a downstream co-transcribed gene, orf1. Our results provide important insight into the regulation of coronafacoyl phytotoxin production, which is thought to contribute to the virulence phenotype of S. scabies. Furthermore, we provide evidence that CfaR is a novel member of the PAS-LuxR family of regulators, members of which are widely distributed among actinomycete bacteria.
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36
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Vicente CM, Payero TD, Santos-Aberturas J, Barreales EG, de Pedro A, Aparicio JF. Pathway-specific regulation revisited: cross-regulation of multiple disparate gene clusters by PAS-LuxR transcriptional regulators. Appl Microbiol Biotechnol 2015; 99:5123-35. [PMID: 25715784 DOI: 10.1007/s00253-015-6472-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 12/12/2022]
Abstract
PAS-LuxR regulators are highly conserved proteins devoted to the control of antifungal production by binding to operators located in given promoters of polyene biosynthetic genes. The canonical operator of PimM, archetype of this class of regulators, has been used here to search for putative targets of orthologous protein PteF in the genome of Streptomyces avermitilis, finding 97 putative operators outside the pentaene filipin gene cluster (pte). The processes putatively affected included genetic information processing; energy, carbohydrate, and lipid metabolism; DNA replication and repair; morphological differentiation; secondary metabolite biosynthesis; and transcriptional regulation, among others. Seventeen of these operators were selected, and their binding to PimM DNA-binding domain was assessed by electrophoretic mobility shift assays. Strikingly, the protein bound all predicted operators suggesting a direct control over targeted processes. As a proof of concept, we studied the biosynthesis of the ATP-synthase inhibitor oligomycin whose gene cluster included two operators. Regulator mutants showed a severe loss of oligomycin production, whereas gene complementation of the mutant restored phenotype, and gene duplication in the wild-type strain boosted oligomycin production. Comparative gene expression analyses in parental and mutant strains by reverse transcription-quantitative polymerase chain reaction of selected olm genes corroborated production results. These results demonstrate that PteF is able to cross-regulate the biosynthesis of two related secondary metabolites, filipin and oligomycin, but might be extended to all the processes indicated above. This study highlights the complexity of the network of interactions in which PAS-LuxR regulators are involved and opens new possibilities for the manipulation of metabolite production in Streptomycetes.
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Affiliation(s)
- Cláudia M Vicente
- Area of Microbiology, Faculty of Biology, University of León, León, 24071, Spain
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