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Yushchuk O, Zhukrovska K, Berini F, Fedorenko V, Marinelli F. Genetics Behind the Glycosylation Patterns in the Biosynthesis of Dalbaheptides. Front Chem 2022; 10:858708. [PMID: 35402387 PMCID: PMC8987122 DOI: 10.3389/fchem.2022.858708] [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: 01/20/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Glycopeptide antibiotics are valuable natural metabolites endowed with different pharmacological properties, among them are dalbaheptides used to treat different infections caused by multidrug-resistant Gram-positive pathogens. Dalbaheptides are produced by soil-dwelling high G-C Gram-positive actinobacteria. Their biosynthetic pathways are encoded within large biosynthetic gene clusters. A non-ribosomally synthesized heptapeptide aglycone is the common scaffold for all dalbaheptides. Different enzymatic tailoring steps, including glycosylation, are further involved in decorating it. Glycosylation of dalbaheptides is a crucial step, conferring them specific biological activities. It is achieved by a plethora of glycosyltransferases, encoded within the corresponding biosynthetic gene clusters, able to install different sugar residues. These sugars might originate from the primary metabolism, or, alternatively, their biosynthesis might be encoded within the biosynthetic gene clusters. Already installed monosaccharides might be further enzymatically modified or work as substrates for additional glycosylation. In the current minireview, we cover recent updates concerning the genetics and enzymology behind the glycosylation of dalbaheptides, building a detailed and consecutive picture of this process and of its biological evolution. A thorough understanding of how glycosyltransferases function in dalbaheptide biosynthesis might open new ways to use them in chemo-enzymatic synthesis and/or in combinatorial biosynthesis for building novel glycosylated antibiotics.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Kseniia Zhukrovska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- *Correspondence: Flavia Marinelli,
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Xia TY, Chen XA, Liu YQ, Scharf DH, Zhao QW, Li YQ. Redirection of acyl donor metabolic flux for lipopeptide A40926B0 biosynthesis. Microb Biotechnol 2022; 15:1852-1866. [PMID: 35213090 PMCID: PMC9151331 DOI: 10.1111/1751-7915.14021] [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: 09/28/2021] [Revised: 02/13/2022] [Accepted: 02/13/2022] [Indexed: 11/30/2022] Open
Abstract
The metabolic flux of fatty acyl‐CoAs determines lipopeptide biosynthesis efficiency, because acyl donor competition often occurs from polyketide biosynthesis and homologous pathways. We used A40926B0 as a model to investigate this mechanism. The lipopeptide A40926B0 with a fatty acyl group is the active precursor of dalbavancin, which is considered as a new lipoglycopeptide antibiotic. The biosynthetic pathway of fatty acyl‐CoAs in the A40926B0 producer Nonomuraea gerenzanensis L70 was efficiently engineered using endogenous replicon CRISPR (erCRISPR). A polyketide pathway and straight‐chain fatty acid biosynthesis were identified as major competitors in the malonyl‐CoA pool. Therefore, we modified both pathways to concentrate acyl donors for the production of the desired compound. Combined with multiple engineering approaches, including blockage of an acetylation side reaction, overexpression of acetyl‐CoA carboxylase, duplication of the dbv gene cluster and optimization of the fermentation parameters, the final strain produced 702.4 mg l‐1 of A40926B0, a 2.66‐fold increase, and the ratio was increased from 36.2% to 81.5%. Additionally, an efficient erCRISPR‐Cas9 editing system based on an endogenous replicon was specifically developed for L70, which increased conjugation efficiency by 660% and gene‐editing efficiency was up to 90%. Our strategy of redirecting acyl donor metabolic flux can be widely adopted for the metabolic engineering of lipopeptide biosynthesis.
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Affiliation(s)
- Tian-Yu Xia
- 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
| | - Yan-Qiu Liu
- 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
| | - Daniel H Scharf
- 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
| | - 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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Yan B, Gao W, Tian L, Wang S, Dong H. Production enhancement of the glycopeptide antibiotic A40926 by an engineered Nonomuraea gerenzanensis strain. Biotechnol Lett 2021; 44:259-269. [PMID: 34826003 DOI: 10.1007/s10529-021-03210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/16/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To improve the production of A40926, a combined strategy of constructing the engineered strain and optimizing the medium was implemented. RESULTS The engineered strain lcu1 with the genetic features of dbv23 deletion and dbv3-dbv20 coexpression increased by 30.6% in the production of A40926, compared to the original strain. In addition, a combined medium called M9 was designed to be further optimized by the central composite design method. The optimized M9 medium was verified to significantly improve the A40926 yield from 257 to 332 mg l-1. CONCLUSIONS The engineered strain lcu1 could significantly promote A40926 production in the optimized M9 medium, which indicated that the polygenic genetic manipulation and the media optimization played an equally important role in increasing the A40926 yield.
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Affiliation(s)
- Bingyu Yan
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Wen Gao
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Li Tian
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Shuai Wang
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Huijun Dong
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China.
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4
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Heterogeneous A40926 Self-Resistance Profile in Nonomuraea gerenzanensis Population Informs Strain Improvement. FERMENTATION 2021. [DOI: 10.3390/fermentation7030140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nonomuraea gerenzanensis ATCC 39727 produces the glycopeptide antibiotic A40926, which is the natural precursor of the semi-synthetic, last-resort drug dalbavancin. To reduce the cost of dalbavancin production, it is mandatory to improve the productivity of the producing strain. Here, we report that the exposure of N. gerenzanensis wild-type population to sub-inhibitory concentrations of A40926 led to the isolation of differently resistant phenotypes to which a diverse A40926 productivity was associated. The most resistant population (G, grand colonies) represented at least the 20% of the colonies growing on 2 µg/mL of A40926. It showed a stable phenotype after sub-culturing and a homogeneous profile of self-resistance to A40926 in population analysis profile (PAP) experiments. The less resistant population (P, petit) was represented by slow-growing colonies to which a lower A40926 productivity was associated. At bioreactor scale, the G variant produced twice more than the wild-type (ca. 400 mg/L A40926 versus less than 200 mg/L, respectively), paving the way for a rational strain improvement based on the selection of increasingly self-resistant colonies.
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Yushchuk O, Vior NM, Andreo-Vidal A, Berini F, Rückert C, Busche T, Binda E, Kalinowski J, Truman AW, Marinelli F. Genomic-Led Discovery of a Novel Glycopeptide Antibiotic by Nonomuraea coxensis DSM 45129. ACS Chem Biol 2021; 16:915-928. [PMID: 33913701 PMCID: PMC8291499 DOI: 10.1021/acschembio.1c00170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Glycopeptide antibiotics
(GPAs) are last defense line drugs against
multidrug-resistant Gram-positive pathogens. Natural GPAs teicoplanin
and vancomycin, as well as semisynthetic oritavancin, telavancin,
and dalbavancin, are currently approved for clinical use. Although
these antibiotics remain efficient, emergence of novel GPA-resistant
pathogens is a question of time. Therefore, it is important to investigate
the natural variety of GPAs coming from so-called “rare”
actinobacteria. Herein we describe a novel GPA producer—Nonomuraea coxensis DSM 45129. Its de novo sequenced and completely assembled genome harbors a biosynthetic
gene cluster (BGC) similar to the dbv BGC of A40926,
the natural precursor to dalbavancin. The strain produces a novel
GPA, which we propose is an A40926 analogue lacking the carboxyl group
on the N-acylglucosamine moiety. This structural
difference correlates with the absence of dbv29—coding
for an enzyme responsible for the oxidation of the N-acylglucosamine moiety. Introduction of dbv29 into N. coxensis led to A40926 production in this strain.
Finally, we successfully applied dbv3 and dbv4 heterologous transcriptional regulators to trigger
and improve A50926 production in N. coxensis, making them prospective tools for screening other Nonomuraea spp. for GPA production. Our work highlights
genus Nonomuraea as a still untapped
source of novel GPAs.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Andres Andreo-Vidal
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
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Dong H, Yue X, Yan B, Gao W, Wang S, Li Y. Improved A40926 production from Nonomuraea gerenzanensis using the promoter engineering and the co-expression of crucial genes. J Biotechnol 2020; 324:28-33. [PMID: 32971181 DOI: 10.1016/j.jbiotec.2020.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
The semi-synthetic antibiotic dalbavancin is clinically used in the treatment of severe infections caused by multidrug resistant Gram-positive pathogens. So far, fermentation has still been the only approach for the production of A40926 in the industrial scale, which is used as the precursor of dalbavancin and biosynthesized by the rare actinomycete Nonomuraea gerenzanensis (N. gerenzanensis). Therefore, it is particularly essential and necessary to enhance the yield of A40926 continually. In this paper, we firstly assessed the activity of 6 heterologous promoters using the enhanced green fluorescence protein (EGFP) reporter system in N. gerenzanensis. Furthermore, the strongest constitutive promoter gapdh confirmed in this study was applied to separately overexpress the total of ten dbv genes involved in the A40926 biosynthesis. PCR and RT-qPCR were successively carried out to verify the mutant and the overexpression of dbv genes. As a consequence, the overexpression of dbv3 and dbv20 genes both increased the A40926 production remarkably. Based on the above consequences, a mutant strain named N320 laboring the co-expression of dbv3 and dbv20 was constructed. The results of fermentation showed that the N320 strain enhanced the yield of A40926 from 163 mg/L to 272 mg/L.
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Affiliation(s)
- Huijun Dong
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China.
| | - Xue Yue
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Bingyu Yan
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Wen Gao
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Shuai Wang
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
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7
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Yue X, Xia T, Wang S, Dong H, Li Y. Highly efficient genome editing in N. gerenzanensis using an inducible CRISPR/Cas9-RecA system. Biotechnol Lett 2020; 42:1699-1706. [PMID: 32314149 DOI: 10.1007/s10529-020-02893-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVE To develop an inducible CRISPR/Cas9-Recombinase A (RecA) system to manipulate genes in Nonomuraea gerenzanensis effectively. RESULTS Compared with traditional homologous recombination, the inducible CRISPR/Cas9 system achieved 68.8% editing efficiency, whereas, with both the inducible Cas9 and the overexpressed RecA, the efficiency of the combined genome editing system reached 100%. The dbv23-deleted mutant obtained by the inducible CRISPR/Cas9-RecA system was confirmed to produce more A40926 with an approximate yield of 200 mg L-1 than that of around 150 mg L-1 produced by the wild-type strain. CONCLUSIONS This inducible CRISPR/Cas9-RecA system was successfully constructed and can be utilized as an efficient genome editing tool for Actinomyces able to shorten editing time simultaneously.
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Affiliation(s)
- Xue Yue
- School of Pharmacy, Liaocheng University, 1 Hunan Rd, Liaocheng, 252000, Shandong, People's Republic of China
| | - Tianyu Xia
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Shuai Wang
- School of Pharmacy, Liaocheng University, 1 Hunan Rd, Liaocheng, 252000, Shandong, People's Republic of China
| | - Huijun Dong
- School of Pharmacy, Liaocheng University, 1 Hunan Rd, Liaocheng, 252000, Shandong, People's Republic of China.
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, Zhejiang, People's Republic of China.
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8
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A Two-Component regulatory system with opposite effects on glycopeptide antibiotic biosynthesis and resistance. Sci Rep 2020; 10:6200. [PMID: 32277112 PMCID: PMC7148328 DOI: 10.1038/s41598-020-63257-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/03/2020] [Indexed: 02/07/2023] Open
Abstract
The glycopeptide A40926, produced by the actinomycete Nonomuraea gerenzanensis, is the precursor of dalbavancin, a second-generation glycopeptide antibiotic approved for clinical use in the USA and Europe in 2014 and 2015, respectively. The final product of the biosynthetic pathway is an O-acetylated form of A40926 (acA40926). Glycopeptide biosynthesis in N. gerenzanensis is dependent upon the dbv gene cluster that encodes, in addition to the two essential positive regulators Dbv3 and Dbv4, the putative members of a two-component signal transduction system, specifically the response regulator Dbv6 and the sensor kinase Dbv22. The aim of this work was to assign a role to these two genes. Our results demonstrate that deletion of dbv22 leads to an increased antibiotic production with a concomitant reduction in glycopeptide resistance. Deletion of dbv6 results in a similar phenotype, although the effects are not as strong as in the Δdbv22 mutant. Consistently, quantitative RT-PCR analysis showed that Dbv6 and Dbv22 negatively regulate the regulatory genes (dbv3 and dbv4), as well as some dbv biosynthetic genes (dbv23 and dbv24), whereas Dbv6 and Dbv22 positively regulate transcription of the single, cluster-associated resistance gene. Finally, we demonstrate that exogenously added acA40926 and its precursor A40926 can modulate transcription of dbv genes but with an opposite extent: A40926 strongly stimulates transcription of the Dbv6/Dbv22 target genes while acA40926 has a neutral or negative effect on transcription of those genes. We propose a model in which glycopeptide biosynthesis in N. gerenzanensis is modulated through a positive feedback by the biosynthetic precursor A40926 and a negative feedback by the final product acA40926. In addition to previously reported control systems, this sophisticated control loop might help the producing strain cope with the toxicity of its own product. This work, besides leading to improved glycopeptide producing strains, enlarges our knowledge on the regulation of glycopeptide biosynthesis in actinomycetes, setting N. gerenzanensis and its two-component system Dbv6-Dbv22 apart from other glycopeptide producers.
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Musiol-Kroll EM, Tocchetti A, Sosio M, Stegmann E. Challenges and advances in genetic manipulation of filamentous actinomycetes - the remarkable producers of specialized metabolites. Nat Prod Rep 2019; 36:1351-1369. [PMID: 31517370 DOI: 10.1039/c9np00029a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to February 2019Actinomycetes are Gram positive bacteria of the phylum Actinobacteria. These organisms are one of the most important sources of structurally diverse, clinically used antibiotics and other valuable bioactive products, as well as biotechnologically relevant enzymes. Most strains were discovered by their ability to produce a given molecule and were often poorly characterized, physiologically and genetically. The development of genetic methods for Streptomyces and related filamentous actinomycetes has led to the successful manipulation of antibiotic biosynthesis to attain structural modification of microbial metabolites that would have been inaccessible by chemical means and improved production yields. Moreover, genome mining reveals that actinomycete genomes contain multiple biosynthetic gene clusters (BGCs), however only a few of them are expressed under standard laboratory conditions, leading to the production of the respective compound(s). Thus, to access and activate the so-called "silent" BGCs, to improve their biosynthetic potential and to discover novel natural products methodologies for genetic manipulation are required. Although different methods have been applied for many actinomycete strains, genetic engineering is still remaining very challenging for some "underexplored" and poorly characterized actinomycetes. This review summarizes the strategies developed to overcome the obstacles to genetic manipulation of actinomycetes and allowing thereby rational genetic engineering of this industrially relevant group of microorganisms. At the end of this review we give some tips to researchers with limited or no previous experience in genetic manipulation of actinomycetes. The article covers the most relevant literature published until February 2019.
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Affiliation(s)
- Ewa M Musiol-Kroll
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
| | | | | | - Evi Stegmann
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
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Alt S, Bernasconi A, Sosio M, Brunati C, Donadio S, Maffioli SI. Toward Single-Peak Dalbavancin Analogs through Biology and Chemistry. ACS Chem Biol 2019; 14:356-360. [PMID: 30830742 DOI: 10.1021/acschembio.9b00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycopeptide antibiotics are used to treat severe multidrug resistant infections caused by Gram-positive bacteria. Dalbavancin is a second generation glycopeptide approved for human use, which is obtained from A40926, a lipoglycopeptide produced by Nonomuraea sp. ATCC39727 as a mixture of biologically active congeners mainly differing in the fatty acid chains present on the glucuronic moiety. In this study, we constructed a double mutant of the A40926 producer strain lacking dbv23, and thus defective in mannose acetylation, a feature that increases A40926 production, and lacking the acyltransferases Dbv8, and thus incapable of installing the fatty acid chains. The double mutant afforded the desired deacyl, deacetyl A40926 intermediates, which could be converted by chemical reacylation yielding A40926 analogs with a greatly reduced number of congeners. The newly acylated analogs could then be transformed into dalbavancin analogs possessing the same in vitro properties as the approved drug.
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Affiliation(s)
- Silke Alt
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Margherita Sosio
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | - Sonia I. Maffioli
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
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11
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Complex Regulatory Networks Governing Production of the Glycopeptide A40926. Antibiotics (Basel) 2018; 7:antibiotics7020030. [PMID: 29621136 PMCID: PMC6022936 DOI: 10.3390/antibiotics7020030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 01/11/2023] Open
Abstract
Glycopeptides (GPAs) are an important class of antibiotics, with vancomycin and teicoplanin being used in the last 40 years as drugs of last resort to treat infections caused by Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus. A few new GPAs have since reached the market. One of them is dalbavancin, a derivative of A40926 produced by the actinomycete Nonomuraea sp. ATCC 39727, recently classified as N. gerenzanensis. This review summarizes what we currently know on the multilevel regulatory processes governing production of the glycopeptide A40926 and the different approaches used to increase antibiotic yields. Some nutrients, e.g., valine, l-glutamine and maltodextrin, and some endogenous proteins, e.g., Dbv3, Dbv4 and RpoBR, have a positive role on A40926 biosynthesis, while other factors, e.g., phosphate, ammonium and Dbv23, have a negative effect. Overall, the results available so far point to a complex regulatory network controlling A40926 in the native producing strain.
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12
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Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era. Biotechnol Adv 2018; 36:534-554. [PMID: 29454983 DOI: 10.1016/j.biotechadv.2018.02.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
Abstract
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.
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13
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Chen M, Xu T, Zhang G, Zhao J, Gao Z, Zhang C. High-yield production of lipoglycopeptide antibiotic A40926 using a mutant strain Nonomuraea sp. DP-13 in optimized medium. Prep Biochem Biotechnol 2016; 46:171-5. [PMID: 25831044 DOI: 10.1080/10826068.2015.1015561] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The lipoglycopeptide antibiotic A40926 produced by Nonomuraea sp. is a complex of structurally related components differing in the fatty acid moiety. Besides showing an intrinsic antibacterial activity, A40926 is the precursor of the semisynthetic antibiotic Dalvance. In this work, A40926 production by a mutant strain Nonomuraea sp. DP-13 was investigated. It was found that A40926 production was markedly promoted by using poorly assimilated carbon source maltodextrin and nitrogen source soybean meal. Addition of Cu(2+) resulted in a stimulation of A40926 production, but Co(2+) had an inhibitory effect. L-Leucine addition greatly improved total A40926 production and modified the complex composition toward factor B0. An optimized production medium IM-3 was developed and a maximum A40926 production of 1096 mg/L was obtained in the 10-L fermenter. This was the highest A40926 productivity so far reported.
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Affiliation(s)
- Ming Chen
- a School of Biological Engineering , Dalian Polytechnic University , Dalian , China
| | - Tao Xu
- a School of Biological Engineering , Dalian Polytechnic University , Dalian , China
| | - Guanghao Zhang
- a School of Biological Engineering , Dalian Polytechnic University , Dalian , China
| | - Jing Zhao
- b College of Life Science , Dalian Nationalities University , Dalian , China
| | - Ziqing Gao
- a School of Biological Engineering , Dalian Polytechnic University , Dalian , China
| | - Chunzhi Zhang
- a School of Biological Engineering , Dalian Polytechnic University , Dalian , China
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Maffioli SI, Cruz JCS, Monciardini P, Sosio M, Donadio S. Advancing cell wall inhibitors towards clinical applications. J Ind Microbiol Biotechnol 2015; 43:177-84. [PMID: 26515981 DOI: 10.1007/s10295-015-1703-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022]
Abstract
Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity. Consistently, 2014 has seen new, natural product-derived antibiotics approved for human use by the US Food and Drug Administration. One of the recently approved second-generation glycopeptides is dalbavancin, a semi-synthetic derivative of the natural product A40,926. This compound inhibits bacterial growth by binding to lipid intermediate II (Lipid II), a key intermediate in peptidoglycan biosynthesis. Like other recently approved antibiotics, dalbavancin has a complex history of preclinical and clinical development, with several companies contributing to different steps in different years. While our work on dalbavancin development stopped at the previous company, intriguingly our current pipeline includes two more Lipid II-binding natural products or derivatives thereof. In particular, we will focus on the properties of NAI-107 and related lantibiotics, which originated from recent screening and characterization efforts.
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Affiliation(s)
- Sonia I Maffioli
- KtedoGen Srl, Viale Ortles 22/4, 20139, Milan, Italy.,Naicons Srl, Viale Ortles 22/4, 20139, Milan, Italy
| | - João C S Cruz
- KtedoGen Srl, Viale Ortles 22/4, 20139, Milan, Italy
| | - Paolo Monciardini
- KtedoGen Srl, Viale Ortles 22/4, 20139, Milan, Italy.,Naicons Srl, Viale Ortles 22/4, 20139, Milan, Italy
| | - Margherita Sosio
- KtedoGen Srl, Viale Ortles 22/4, 20139, Milan, Italy.,Naicons Srl, Viale Ortles 22/4, 20139, Milan, Italy
| | - Stefano Donadio
- KtedoGen Srl, Viale Ortles 22/4, 20139, Milan, Italy. .,Naicons Srl, Viale Ortles 22/4, 20139, Milan, Italy.
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Two Master Switch Regulators Trigger A40926 Biosynthesis in Nonomuraea sp. Strain ATCC 39727. J Bacteriol 2015; 197:2536-44. [PMID: 25986904 DOI: 10.1128/jb.00262-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 05/13/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED The actinomycete Nonomuraea sp. strain ATCC 39727 produces the glycopeptide A40926, the precursor of dalbavancin. Biosynthesis of A40926 is encoded by the dbv gene cluster, which contains 37 protein-coding sequences that participate in antibiotic biosynthesis, regulation, immunity, and export. In addition to the positive regulatory protein Dbv4, the A40926-biosynthetic gene cluster encodes two additional putative regulators, Dbv3 and Dbv6. Independent mutations in these genes, combined with bioassays and liquid chromatography-mass spectrometry (LC-MS) analyses, demonstrated that Dbv3 and Dbv4 are both required for antibiotic production, while inactivation of dbv6 had no effect. In addition, overexpression of dbv3 led to higher levels of A40926 production. Transcriptional and quantitative reverse transcription (RT)-PCR analyses showed that Dbv4 is essential for the transcription of two operons, dbv14-dbv8 and dbv30-dbv35, while Dbv3 positively controls the expression of four monocistronic transcription units (dbv4, dbv29, dbv36, and dbv37) and of six operons (dbv2-dbv1, dbv14-dbv8, dbv17-dbv15, dbv21-dbv20, dbv24-dbv28, and dbv30-dbv35). We propose a complex and coordinated model of regulation in which Dbv3 directly or indirectly activates transcription of dbv4 and controls biosynthesis of 4-hydroxyphenylglycine and the heptapeptide backbone, A40926 export, and some tailoring reactions (mannosylation and hexose oxidation), while Dbv4 directly regulates biosynthesis of 3,5-dihydroxyphenylglycine and other tailoring reactions, including the four cross-links, halogenation, glycosylation, and acylation. IMPORTANCE This report expands knowledge of the regulatory mechanisms used to control the biosynthesis of the glycopeptide antibiotic A40926 in the actinomycete Nonomuraea sp. strain ATCC 39727. A40926 is the precursor of dalbavancin, approved for treatment of skin infections by Gram-positive bacteria. Therefore, understanding the regulation of its biosynthesis is also of industrial importance. So far, the regulatory mechanisms used to control two other similar glycopeptides (balhimycin and teicoplanin) have been elucidated, and beyond a common step, different clusters seem to have devised different strategies to control glycopeptide production. Thus, our work provides one more example of the pitfalls of deducing regulatory roles from bioinformatic analyses only, even when analyzing gene clusters directing the synthesis of structurally related compounds.
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Sungthong R, Nakaew N. The genus Nonomuraea: A review of a rare actinomycete taxon for novel metabolites. J Basic Microbiol 2014; 55:554-65. [PMID: 24633812 DOI: 10.1002/jobm.201300691] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 02/18/2014] [Indexed: 11/11/2022]
Abstract
The genus Nonomuraea is a rare actinomycete taxon with a long taxonomic history, while its generic description was recently emended. The genus is less known among the rare actinomycete genera as its taxonomic position was revised several times. It can be found in diverse ecological niches, while most of its member species were isolated from soil samples. However, new trends to discover the genus in other habitats are increasing. Generic abundance of the genus was found to be dependent on geographical changes. Novel sources together with selective and invented isolation techniques might increase a chance to explore the genus and its novel candidates. Interestingly, some of its members have been revealed as a valuable source of novel metabolites for medical and industrial purposes. Broad-range of potent bioactive compounds including antimicrobial, anticancer, and antipsychotic substances, broad-spectrum antibiotics and biocatalysts can be synthesized by the genus. In order to investigate biosynthetic pathways of the bioactive compounds and self-resistant mechanisms to these compounds, the links from genes to metabolites have yet been needed for further discovery and biotechnological development of the genus Nonomuraea.
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Affiliation(s)
- Rungroch Sungthong
- Departamento de Agroquímica y Conservación de Suelos, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
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18
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Glycopeptide biosynthesis in the context of basic cellular functions. Curr Opin Microbiol 2010; 13:595-602. [DOI: 10.1016/j.mib.2010.08.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 08/30/2010] [Accepted: 08/30/2010] [Indexed: 12/17/2022]
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