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Lin J, Xiao Y, Liu H, Gao D, Duan Y, Zhu X. Combined transcriptomic and pangenomic analyses guide metabolic amelioration to enhance tiancimycins production. Appl Microbiol Biotechnol 2024; 108:18. [PMID: 38170317 DOI: 10.1007/s00253-023-12937-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 01/05/2024]
Abstract
Exploration of high-yield mechanism is important for further titer improvement of valuable antibiotics, but how to achieve this goal is challenging. Tiancimycins (TNMs) are anthraquinone-fused enediynes with promising drug development potentials, but their prospective applications are limited by low titers. This work aimed to explore the intrinsic high-yield mechanism in previously obtained TNMs high-producing strain Streptomyces sp. CB03234-S for the further titer amelioration of TNMs. First, the typical ribosomal RpsL(K43N) mutation in CB03234-S was validated to be merely responsible for the streptomycin resistance but not the titer improvement of TNMs. Subsequently, the combined transcriptomic, pan-genomic and KEGG analyses revealed that the significant changes in the carbon and amino acid metabolisms could reinforce the metabolic fluxes of key CoA precursors, and thus prompted the overproduction of TNMs in CB03234-S. Moreover, fatty acid metabolism was considered to exert adverse effects on the biosynthesis of TNMs by shunting and reducing the accumulation of CoA precursors. Therefore, different combinations of relevant genes were respectively overexpressed in CB03234-S to strengthen fatty acid degradation. The resulting mutants all showed the enhanced production of TNMs. Among them, the overexpression of fadD, a key gene responsible for the first step of fatty acid degradation, achieved the highest 21.7 ± 1.1 mg/L TNMs with a 63.2% titer improvement. Our studies suggested that comprehensive bioinformatic analyses are effective to explore metabolic changes and guide rational metabolic reconstitution for further titer improvement of target products. KEY POINTS: • Comprehensive bioinformatic analyses effectively reveal primary metabolic changes. • Primary metabolic changes cause precursor enrichment to enhance TNMs production. • Strengthening of fatty acid degradation further improves the titer of TNMs.
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Affiliation(s)
- Jing Lin
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yu Xiao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Huiming Liu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Die Gao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
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Zhu CY, Zhao XY, Lyu ZY, Gao WL, Zhao QW, Chen XA, Li YQ. Daptomycin production enhancement by ARTP mutagenesis and fermentation optimization in Streptomyces roseosporus. J Appl Microbiol 2023; 134:lxad230. [PMID: 37873659 DOI: 10.1093/jambio/lxad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/23/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
AIMS We evaluated whether the randomness of mutation breeding can be regulated through a double-reporter system. We hope that by establishing a new precursor feeding strategy, the production capacity of industrial microorganisms after pilot scale-up can be further improved. METHODS AND RESULTS In this study, the industrial strain Streptomyces roseosporus L2796 was used as the starter strain for daptomycin production, and a double-reporter system with the kanamycin resistance gene Neo and the chromogenic gene gusA was constructed to screen for high-yield strain L2201 through atmospheric and room temperature plasma (ARTP). Furthermore, the composition of the culture medium and the parameters of precursor replenishment were optimized, resulting in a significant enhancement of the daptomycin yield of the mutant strain L2201(752.67 mg/l). CONCLUSIONS This study successfully screened a high-yield strain of daptomycin through a double-reporter system combined with ARTP mutation. The expression level of two reporter genes can evaluate the strength of dptEp promoter, which can stimulate the expression level of dptE in the biosynthesis of daptomycin, thus producing more daptomycin. The developed multi-stage feeding rate strategy provides a novel way to increase daptomycin in industrial fermentation.
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Affiliation(s)
- Chen-Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Xin-Yi Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Zhong-Yuan Lyu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wen-Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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3
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Jiang Y, Zhang J, Huang X, Ma Z, Zhang Y, Bechthold A, Yu X. Improvement of rimocidin production in Streptomyces rimosus M527 by reporter-guided mutation selection. J Ind Microbiol Biotechnol 2022; 49:6961051. [PMID: 36572395 PMCID: PMC9923380 DOI: 10.1093/jimb/kuac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
In this study, we employed a reporter-guided mutation selection (RGMS) strategy to improve the rimocidin production of Streptomyces rimosus M527, which is based on a single-reporter plasmid pAN and atmospheric and room temperature plasma (ARTP). In plasmid pAN, PrimA, a native promoter of the loading module of rimocidin biosynthesis (RimA) was chosen as a target, and the kanamycin resistance gene (neo) under the control of PrimA was chosen as the reporter gene. The integrative plasmid pAN was introduced into the chromosome of S. rimosus M527 by conjugation to yield the initial strain S. rimosus M527-pAN. Subsequently, mutants of M527-pAN were generated by ARTP. 79 mutants were obtained in total, of which 67 mutants showed a higher level of kanamycin resistance (Kanr) than that of the initial strain M527-pAN. The majority of mutants exhibited a slight increase in rimocidin production compared with M527-pAN. Notably, 3 mutants, M527-pAN-S34, S38, and S52, which exhibited highest kanamycin resistance among all Kanr mutants, showed 34%, 52%, and 45% increase in rimocidin production compared with M527-pAN, respectively. Quantitative RT-PCR analysis revealed that the transcriptional levels of neo and rim genes were increased in mutants M527-pAN-S34, S38, and S52 compared with M527-pAN. These results confirmed that the RGMS approach was successful in improving the rimocidin production in S. rimosus M527.
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Affiliation(s)
| | | | - Xinyi Huang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province 310018, China
| | - Zheng Ma
- Correspondence should be addressed to: Zheng Ma, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, Zhejiang Province 310018, P.R. China. Phone: +86-571-868-36062. Fax: +86-571-869-14449. E-mail:
| | - Yongyong Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province 310018, China
| | - Andreas Bechthold
- University of Freiburg, Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, 79104 Freiburg, Germany
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4
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Liu X, Li J, Li Y, Li J, Sun H, Zheng J, Zhang J, Tan H. A visualization reporter system for characterizing antibiotic biosynthetic gene clusters expression with high-sensitivity. Commun Biol 2022; 5:901. [PMID: 36056143 PMCID: PMC9440138 DOI: 10.1038/s42003-022-03832-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/11/2022] [Indexed: 11/09/2022] Open
Abstract
The crisis of antibiotic resistance has become an impending global problem. Genome sequencing reveals that streptomycetes have the potential to produce many more bioactive compounds that may combat the emerging pathogens. The existing challenge is to devise sensitive reporter systems for mining valuable antibiotics. Here, we report a visualization reporter system based on Gram-negative bacterial acyl-homoserine lactone quorum-sensing (VRS-bAHL). AHL synthase gene (cviI) of Chromobacterium violaceum as reporter gene is expressed in Gram-positive Streptomyces to synthesize AHL, which is detected with CV026, an AHL deficient mutant of C. violaceum, via its violacein production upon AHL induction. Validation assays prove that VRS-bAHL can be widely used for characterizing gene expression in Streptomyces. With the guidance of VRS-bAHL, a novel oxazolomycin derivative is discovered to the best of our knowledge. The results demonstrate that VRS-bAHL is a powerful tool for advancing genetic regulation studies and discovering valuable active metabolites in microorganisms. A quorum sensing based visualization reporter system is presented for the characterization of promoters in Gram-positive bacteria, utilizing violacein production, especially for use in the identification of secondary metabolites.
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Affiliation(s)
- Xiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jine Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junyue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huiying Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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5
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A novel strategy of gene screen based on multi-omics in Streptomyces roseosporus. Appl Microbiol Biotechnol 2022; 106:3103-3112. [PMID: 35389068 DOI: 10.1007/s00253-022-11904-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/02/2022]
Abstract
Daptomycin is a new lipopeptide antibiotic for treatment of severe infection caused by multi-drug-resistant bacteria, but its production cost remains high currently. Thus, it is very important to improve the fermentation ability of the daptomycin producer Streptomyces roseosporus. Here, we found that the deletion of proteasome in S. roseosporus would result in the loss of ability to produce daptomycin. Therefore, transcriptome and 4D label-free proteome analyses of the proteasome mutant (Δprc) and wild type were carried out, showing 457 differential genes. Further, five genes were screened by integrated crotonylation omics analysis. Among them, two genes (orf04750/orf05959) could significantly promote the daptomycin synthesis by overexpression, and the fermentation yield in shake flask increased by 54% and 76.7%, respectively. By enhancing the crotonylation modification via lysine site mutation (K-Q), the daptomycin production in shake flask was finally increased by 98.8% and 206.3%, respectively. This result proved that the crotonylation modification of appropriate proteins could effectively modulate daptomycin biosynthesis. In summary, we established a novel strategy of gene screen for antibiotic biosynthesis process, which is more convenient than the previous screening method based on pathway-specific regulators. KEY POINTS: • Δprc strain has lost the ability of daptomycin production • Five genes were screened by multi-omics analysis • Two genes (orf04750/orf05959) could promote the daptomycin synthesis by overexpression.
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6
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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7
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Rubio S, Martínez-Cámara S, de la Fuente JL, Rodríguez-Sáiz M, Barredo JL. Strain Improvement Program of Streptomyces roseosporus for Daptomycin Production. Methods Mol Biol 2021; 2296:351-363. [PMID: 33977458 DOI: 10.1007/978-1-0716-1358-0_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Daptomycin is a cyclic lipopeptide antibiotic with potent activity against gram-positive bacteria. It has a calcium-dependent mechanism of action that disrupts multiple features of the bacterial membrane function. This antibiotic is highly demanded due to its effectiveness against to microorganisms resistant to other antibiotics, including vancomycin-resistant Staphylococcus aureus (VRSA) and methicillin-resistant S. aureus (MRSA). Daptomycin is produced by fermentation of Streptomyces roseosporus, currently identified as Streptomyces filamentosus. However, low fermentation yields and high production costs are reported. This chapter describes a method of strain improvement involving random mutagenesis, rational screening by bioassay, and flask fermentation. The ultimate objective is to select mutants of S. roseosporus overproducing daptomycin in order to design a more cost-effective daptomycin production.
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Affiliation(s)
- Sara Rubio
- Department of Biotechnology, Crystal Pharma, A Subsidiary of Albany Molecular Research Inc. (AMRI), Parque Tecnológico de León, León, Spain
| | - Sonia Martínez-Cámara
- Department of Biotechnology, Crystal Pharma, A Subsidiary of Albany Molecular Research Inc. (AMRI), Parque Tecnológico de León, León, Spain
| | - Juan Luis de la Fuente
- Department of Biotechnology, Crystal Pharma, A Subsidiary of Albany Molecular Research Inc. (AMRI), Parque Tecnológico de León, León, Spain
| | - Marta Rodríguez-Sáiz
- Department of Biotechnology, Crystal Pharma, A Subsidiary of Albany Molecular Research Inc. (AMRI), Parque Tecnológico de León, León, Spain
| | - José-Luis Barredo
- Department of Biotechnology, Crystal Pharma, A Subsidiary of Albany Molecular Research Inc. (AMRI), Parque Tecnológico de León, León, Spain.
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8
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Novel Fredericamycin Variant Overproduced by a Streptomycin-resistant Streptomyces albus subsp. chlorinus Strain. Mar Drugs 2020; 18:md18060284. [PMID: 32481766 PMCID: PMC7345809 DOI: 10.3390/md18060284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 11/16/2022] Open
Abstract
Streptomycetes are an important source of natural products potentially applicable in the pharmaceutical industry. Many of these drugs are secondary metabolites whose biosynthetic genes are very often poorly expressed under laboratory cultivation conditions. In many cases, antibiotic-resistant mutants exhibit increased production of natural drugs, which facilitates the identification and isolation of new substances. In this study, we report the induction of a type II polyketide synthase gene cluster in the marine strain Streptomycesalbus subsp. chlorinus through the selection of streptomycin-resistant mutants, resulting in overproduction of the novel compound fredericamycin C2 (1). Fredericamycin C2 (1) is structurally related to the potent antitumor drug lead fredericamycin A.
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9
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Bhattarai K, Bastola R, Baral B. Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance. ADVANCES IN GENETICS 2020; 105:229-292. [PMID: 32560788 DOI: 10.1016/bs.adgen.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.
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Affiliation(s)
- Keshab Bhattarai
- University of Tübingen, Tübingen, Germany; Center for Natural and Applied Sciences (CENAS), Kathmandu, Nepal
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal.
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10
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Xia H, Li X, Li Z, Zhan X, Mao X, Li Y. The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining. Front Microbiol 2020; 11:406. [PMID: 32265866 PMCID: PMC7105598 DOI: 10.3389/fmicb.2020.00406] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xuming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongquan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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11
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The Application of Ribosome Engineering to Natural Product Discovery and Yield Improvement in Streptomyces. Antibiotics (Basel) 2019; 8:antibiotics8030133. [PMID: 31480298 PMCID: PMC6784132 DOI: 10.3390/antibiotics8030133] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/10/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022] Open
Abstract
Microbial natural product drug discovery and development has entered a new era, driven by microbial genomics and synthetic biology. Genome sequencing has revealed the vast potential to produce valuable secondary metabolites in bacteria and fungi. However, many of the biosynthetic gene clusters are silent under standard fermentation conditions. By rational screening for mutations in bacterial ribosomal proteins or RNA polymerases, ribosome engineering is a versatile approach to obtain mutants with improved titers for microbial product formation or new natural products through activating silent biosynthetic gene clusters. In this review, we discuss the mechanism of ribosome engineering and its application to natural product discovery and yield improvement in Streptomyces. Our analysis suggests that ribosome engineering is a rapid and cost-effective approach and could be adapted to speed up the discovery and development of natural product drug leads in the post-genomic era.
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12
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Yu G, Hui M, Li R, Chen L, Tian H, Wang L. Enhancement of Daptomycin Production by the Method of Combining Ribosome Engineering and Genome Shuffling in Streptomyces roseosporus. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818060169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Baral B, Akhgari A, Metsä-Ketelä M. Activation of microbial secondary metabolic pathways: Avenues and challenges. Synth Syst Biotechnol 2018; 3:163-178. [PMID: 30345402 PMCID: PMC6190515 DOI: 10.1016/j.synbio.2018.09.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial natural products are a tremendous source of new bioactive chemical entities for drug discovery. Next generation sequencing has revealed an unprecedented genomic potential for production of secondary metabolites by diverse micro-organisms found in the environment and in the microbiota. Genome mining has further led to the discovery of numerous uncharacterized 'cryptic' metabolic pathways in the classical producers of natural products such as Actinobacteria and fungi. These biosynthetic gene clusters may code for improved biologically active metabolites, but harnessing the full genetic potential has been hindered by the observation that many of the pathways are 'silent' under laboratory conditions. Here we provide an overview of the various biotechnological methodologies, which can be divided to pleiotropic, biosynthetic gene cluster specific, and targeted genome-wide approaches that have been developed for the awakening of microbial secondary metabolic pathways.
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Affiliation(s)
| | | | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014, Turku, Finland
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14
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Transposon-based identification of a negative regulator for the antibiotic hyper-production in Streptomyces. Appl Microbiol Biotechnol 2018; 102:6581-6592. [DOI: 10.1007/s00253-018-9103-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 05/14/2018] [Accepted: 05/16/2018] [Indexed: 11/29/2022]
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15
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Lee SK, Kim HR, Jin YY, Yang SH, Suh JW. Improvement of daptomycin production via increased resistance to decanoic acid in Streptomyces roseosporus. J Biosci Bioeng 2016; 122:427-33. [DOI: 10.1016/j.jbiosc.2016.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 02/02/2016] [Accepted: 03/18/2016] [Indexed: 11/26/2022]
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16
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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Insights into microbial cryptic gene activation and strain improvement: principle, application and technical aspects. J Antibiot (Tokyo) 2016; 70:25-40. [PMID: 27381522 DOI: 10.1038/ja.2016.82] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/22/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022]
Abstract
As bacteria and fungi have been found to contain genes encoding enzymes that synthesize a plethora of potential secondary metabolites, interest has grown in the activation of these cryptic pathways. Homologous and heterologous expression of these cryptic secondary metabolite-biosynthetic genes, often silent under ordinary laboratory fermentation conditions, may lead to the discovery of novel secondary metabolites. This review addresses current progress in the activation of these pathways, describing methods for activating silent genes. It especially focuses on genetic manipulation of transcription and translation (ribosome engineering), the utilization of elicitors, metabolism remodeling and co-cultivation. In particular, the principles and technical points of ribosome engineering and the significance of S-adenosylmethionine in bacterial physiology, especially secondary metabolism, are described in detail.
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Mao XM, Luo S, Zhou RC, Wang F, Yu P, Sun N, Chen XX, Tang Y, Li YQ. Transcriptional regulation of the daptomycin gene cluster in Streptomyces roseosporus by an autoregulator, AtrA. J Biol Chem 2015; 290:7992-8001. [PMID: 25648897 DOI: 10.1074/jbc.m114.608273] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic produced by Streptomyces roseosporus. To reveal the transcriptional regulatory mechanism of daptomycin biosynthesis, we used the biotinylated dptE promoter (dptEp) as a probe to affinity isolate the dptEp-interactive protein AtrA, a TetR family transcriptional regulator, from the proteome of mycelia. AtrA bound directly to dptEp to positively regulate gene cluster expression and daptomycin production. Meanwhile, both ΔatrA and ΔadpA mutants showed bald phenotype and null production of daptomycin. AdpA positively regulated atrA expression by direct interaction with atrA promoter (atrAp), and removal of ArpA in S. roseosporus, a homolog of the A-factor receptor, resulted in accelerated morphological development and increased daptomycin production, suggesting that atrA was the target of AdpA to mediate the A-factor signaling pathway. Furthermore, AtrA was positively autoregulated by binding to its own promoter atrAp. Thus, for the first time at the transcriptional level, we have identified an autoregulator, AtrA, that directly mediates the A-factor signaling pathway to regulate the proper production of daptomycin.
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Affiliation(s)
- Xu-Ming Mao
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, Department of Chemical and Biomolecular Engineering, UCLA, Los, Angeles, California 90095, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Shuai Luo
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Ri-Cheng Zhou
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Feng Wang
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Pin Yu
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Ning Sun
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Xiao-Xia Chen
- the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and the Hangzhou Huadong Medicine Group Biotechnology Institute Company, Ltd., Hangzhou 310011, China
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, UCLA, Los, Angeles, California 90095
| | - Yong-Quan Li
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
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Geys R, Soetaert W, Van Bogaert I. Biotechnological opportunities in biosurfactant production. Curr Opin Biotechnol 2014; 30:66-72. [PMID: 24995572 DOI: 10.1016/j.copbio.2014.06.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/27/2014] [Accepted: 06/05/2014] [Indexed: 11/30/2022]
Abstract
In the recent years, biosurfactants proved to be an interesting alternative to petrochemically derived surfactants. Two classes of biosurfactants, namely glycolipids and lipopeptides, have attracted significant commercial interest. Despite their environmental advantages and equal performance, commercialization of these molecules remains a challenge due to missing acquaintance of the applicants, higher price and lack of structural variation. The latter two issues can partially be tackled by screening for novel and better wild-type producers and optimizing the fermentation process. Yet, these traditional approaches cannot overcome all hurdles. In this review, an overview is given on how biotechnology offers opportunities for increased biosurfactant production and the creation of new types of molecules, in this way enhancing their commercial potential.
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Affiliation(s)
- Robin Geys
- Centre of Expertise for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Wim Soetaert
- Centre of Expertise for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Inge Van Bogaert
- Centre of Expertise for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
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Rebets Y, Brötz E, Tokovenko B, Luzhetskyy A. Actinomycetes biosynthetic potential: how to bridge in silico and in vivo? J Ind Microbiol Biotechnol 2013; 41:387-402. [PMID: 24127068 DOI: 10.1007/s10295-013-1352-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of "cryptic" gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.
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Affiliation(s)
- Yuriy Rebets
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, Saarbrücken, 66123, Germany
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Rao M, Feng L, Ruan L, Ge M, Sheng X. UPLC-MS-Based Metabolomic Study ofStreptomycesStrain HCCB10043 Under Different pH Conditions Reveals Important Pathways Affecting the Biosynthesis of A21978C Compounds. ANAL LETT 2013. [DOI: 10.1080/00032719.2013.800538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Li L, Ma T, Liu Q, Huang Y, Hu C, Liao G. Improvement of daptomycin production in Streptomyces roseosporus through the acquisition of pleuromutilin resistance. BIOMED RESEARCH INTERNATIONAL 2013; 2013:479742. [PMID: 24106707 PMCID: PMC3782809 DOI: 10.1155/2013/479742] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 07/08/2013] [Accepted: 07/22/2013] [Indexed: 11/23/2022]
Abstract
Daptomycin, a cyclic lipopeptide antibiotic produced by Streptomyces roseosporus, displays potent activity against a variety of gram-positive pathogens. There is a demand for generating high-producing strains for industrial production of this valuable antibiotic. Ribosome engineering is a powerful strategy to enhance the yield of secondary metabolites. In this study, the effect of a diterpenoid antibiotic pleuromutilin resistance mutation on daptomycin production was assessed. Spontaneous pleuromutilin-resistant derivatives of S. roseosporus were isolated. Sequencing of rplC locus (encoding the ribosomal protein L3) showed a point mutation at nt 455, resulting in the substitution of glycine with valine. G152V mutants showed increased production of daptomycin by approximately 30% in comparison with the wild-type strain. Its effect on daptomycin production was due to enhanced gene transcription of the daptomycin biosynthetic genes. In conclusion, pleuromutilin could be used as a novel ribosome engineering agent to improve the production of desired secondary metabolites.
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Affiliation(s)
- Linli Li
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Tingmei Ma
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Qing Liu
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuqi Huang
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Changhua Hu
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing 400715, China
| | - Guojian Liao
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing 400715, China
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Chaudhary AK, Dhakal D, Sohng JK. An insight into the "-omics" based engineering of streptomycetes for secondary metabolite overproduction. BIOMED RESEARCH INTERNATIONAL 2013; 2013:968518. [PMID: 24078931 PMCID: PMC3775442 DOI: 10.1155/2013/968518] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/26/2013] [Accepted: 07/28/2013] [Indexed: 11/25/2022]
Abstract
Microorganisms produce a range of chemical substances representing a vast diversity of fascinating molecular architectures not available in any other system. Among them, Streptomyces are frequently used to produce useful enzymes and a wide variety of secondary metabolites with potential biological activities. Streptomyces are preferred over other microorganisms for producing more than half of the clinically useful naturally originating pharmaceuticals. However, these compounds are usually produced in very low amounts (or not at all) under typical laboratory conditions. Despite the superiority of Streptomyces, they still lack well documented genetic information and a large number of in-depth molecular biological tools for strain improvement. Previous attempts to produce high yielding strains required selection of the genetic material through classical mutagenesis for commercial production of secondary metabolites, optimizing culture conditions, and random selection. However, a profound effect on the strategy for strain development has occurred with the recent advancement of whole-genome sequencing, systems biology, and genetic engineering. In this review, we demonstrate a few of the major issues related to the potential of "-omics" technology (genomics, transcriptomics, proteomics, and metabolomics) for improving streptomycetes as an intelligent chemical factory for enhancing the production of useful bioactive compounds.
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Affiliation(s)
- Amit Kumar Chaudhary
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, SunMoon University, 100 Kalsan-ri, Tangjeongmyeon, Asan-si, Chungnam 336-708, Republic of Korea
| | - Dipesh Dhakal
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, SunMoon University, 100 Kalsan-ri, Tangjeongmyeon, Asan-si, Chungnam 336-708, Republic of Korea
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, SunMoon University, 100 Kalsan-ri, Tangjeongmyeon, Asan-si, Chungnam 336-708, Republic of Korea
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Ng IS, Ye C, Zhang Z, Lu Y, Jing K. Daptomycin antibiotic production processes in fed-batch fermentation by Streptomyces roseosporus NRRL11379 with precursor effect and medium optimization. Bioprocess Biosyst Eng 2013; 37:415-23. [PMID: 23828246 DOI: 10.1007/s00449-013-1007-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/23/2013] [Indexed: 01/29/2023]
Abstract
Sodium decanoate was first found to be an effective precursor for synthesis of daptomycin from Streptomyces roseosporus NRRL11379 which was increased to 71.55-fold, compared with decanoic acid. The optimal flow rate of precursor was at 600 mg/(L day) after 48 h fermentation. From protein analysis via SDS-PAGE and identification of Tandem MS/MS afterwards, it deciphered that guanosine pentaphosphate synthetase, PNPase, tripeptidylamino peptidase primarily dealing with daptomycin synthesis. By applying Taguchi's L16 in culture optimization, the best yield was obtained from the medium with 60 g/L dextrin, 10 g/L dextrose, 1.0 g/L molasses, and 8 g/L yeast extract, respectively. The fed-batch fermentation, applied with feedback control of dextrin, stimulated the production up to 812 mg/L at 288 h. To our best knowledge, the daptomycin production in this study is significantly higher than that in previous studies and can make it more widely used in pharmaceutical industry.
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Affiliation(s)
- I-Son Ng
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China,
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Liao G, Wang L, Liu Q, Guan F, Huang Y, Hu C. Manipulation of kynurenine pathway for enhanced daptomycin production inStreptomyces roseosporus. Biotechnol Prog 2013; 29:847-52. [DOI: 10.1002/btpr.1740] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/31/2013] [Indexed: 01/30/2023]
Affiliation(s)
- Guojian Liao
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences; Southwest University; Chongqing 400715 China
| | - Lei Wang
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences; Southwest University; Chongqing 400715 China
| | - Qing Liu
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences; Southwest University; Chongqing 400715 China
| | - Feifei Guan
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences; Southwest University; Chongqing 400715 China
| | - Yuqi Huang
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences; Southwest University; Chongqing 400715 China
| | - Changhu Hu
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences; Southwest University; Chongqing 400715 China
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Liao G, Liu Q, Xie J. Transcriptional analysis of the effect of exogenous decanoic acid stress on Streptomyces roseosporus. Microb Cell Fact 2013; 12:19. [PMID: 23432849 PMCID: PMC3724488 DOI: 10.1186/1475-2859-12-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 02/19/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Daptomycin is an important antibiotic against infections caused by drug-resistant pathogens. Its production critically depends on the addition of decanoic acid during fermentation. Unfortunately, decanoic acid (>2.5 mM) is toxic to daptomycin producer, Streptomyces roseosporus. RESULTS To understand the mechanism underlying decanoic tolerance or toxicity, the responses of S. roseosporus was determined by a combination of phospholipid fatty acid analysis, reactive oxygen species (ROS) measurement and RNA sequencing. Assays using fluorescent dyes indicated a sharp increase in reactive oxygen species during decanoic acid stress; fatty acid analysis revealed a marked increase in the composition of branched-chain fatty acids by approximately 10%, with a corresponding decrease in straight-chain fatty acids; functional analysis indicated decanoic acid stress has components common to other stress response, including perturbation of respiratory functions (nuo and cyd operons), oxidative stress, and heat shock. Interestingly, our transcriptomic analysis revealed that genes coding for components of proteasome and related to treholase synthesis were up-regulated in the decanoic acid -treated cells. CONCLUSION These findings represent an important first step in understanding mechanism of decanoic acid toxicity and provide a basis for engineering microbial tolerance.
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Affiliation(s)
- Guojian Liao
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of life sciences, School of Pharmaceutical Sciences Southwest University, Chongqing 400715, China
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Ochi K, Hosaka T. New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Appl Microbiol Biotechnol 2012; 97:87-98. [PMID: 23143535 PMCID: PMC3536979 DOI: 10.1007/s00253-012-4551-9] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 11/29/2022]
Abstract
Genome sequencing of Streptomyces, myxobacteria, and fungi showed that although each strain contains genes that encode the enzymes to synthesize a plethora of potential secondary metabolites, only a fraction are expressed during fermentation. Interest has therefore grown in the activation of these cryptic pathways. We review current progress on this topic, describing concepts for activating silent genes, utilization of “natural” mutant-type RNA polymerases and rare earth elements, and the applicability of ribosome engineering to myxobacteria and fungi, the microbial groups known as excellent searching sources, as well as actinomycetes, for secondary metabolites.
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Affiliation(s)
- Kozo Ochi
- Department of Life Science, Hiroshima Institute of Technology, Miyake 2-1-1, Saeki-ku, Hiroshima, 731-5193, Japan.
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