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Oliveira GSD, Dos S Bury P, Huang F, Li Y, Araújo NCD, Zhou J, Sun Y, Leeper FJ, Leadlay PF, Dias MVB. Structural and Functional Basis of GenB2 Isomerase Activity from Gentamicin Biosynthesis. ACS Chem Biol 2024. [PMID: 39207862 DOI: 10.1021/acschembio.4c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Aminoglycosides are essential antibiotics used to treat severe infections caused mainly by Gram-negative bacteria. Gentamicin is an aminoglycoside and, despite its toxicity, is clinically used to treat several pulmonary and urinary infections. The commercial form of gentamicin is a mixture of five compounds with minor differences in the methylation of one of their aminosugars. In the case of two compounds, gentamicin C2 and C2a, the only difference is the stereochemistry of the methyl group attached to C-6'. GenB2 is the enzyme responsible for this epimerization and is one of the four PLP-dependent enzymes encoded by the gentamicin biosynthetic gene cluster. Herein, we have determined the structure of GenB2 in its holo form in complex with PMP and also in the ternary complex with gentamicin X2 and G418, two substrate analogues. Based on the structural analysis, we were able to identify the structural basis for the catalytic mechanism of this enzyme, which was also studied by site-directed mutagenesis. Unprecedently, GenB2 is a PLP-dependent enzyme from fold I, which is able to catalyze an epimerization but with a mechanism distinct from that of fold III PLP-dependent epimerases using a cysteine residue near the N-terminus. The substitution of this cysteine residue for serine or alanine completely abolished the epimerase function of the enzyme, confirming its involvement. This study not only contributes to the understanding of the enzymology of gentamicin biosynthesis but also provides valuable details for exploring the enzymatic production of new aminoglycoside derivatives.
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Affiliation(s)
- Gabriel S de Oliveira
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Priscila Dos S Bury
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Natália C de Araújo
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Jiahai Zhou
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS, Shenzhen 518055, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Finian J Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
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2
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Stojanovski G, Hailes HC, Ward JM. Facile and selective N-alkylation of gentamicin antibiotics via chemoenzymatic synthesis. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2022; 24:9542-9551. [PMID: 36544494 PMCID: PMC9744104 DOI: 10.1039/d2gc03600b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The rise and spread of antimicrobial resistance has necessitated the development of novel antimicrobials which are effective against drug resistant pathogens. Aminoglycoside antibiotics (AGAs) remain one of our most effective classes of bactericidal drugs. However, they are challenging molecules to selectively modify by chemical synthesis, requiring the use of extensive protection and deprotection steps leading to long, atom- and step-inefficient synthetic routes. Biocatalytic and chemoenzymatic approaches for the generation of AGA derivatives are of interest as they allow access to more concise and sustainable synthetic routes to novel compounds. This work presents a two-step chemoenzymatic route to regioselectively modify the C-6' position of AGAs. The approach uses a transaminase enzyme to generate an aldehyde on the C-6' position in the absence of protecting groups, followed by reductive amination to introduce substituents selectively on this position. Seven candidate transaminases were tested for their ability to deaminate a panel of commercially available AGAs. The C-6' transaminases could deaminate both pseudo di- and trisaccharide AGAs and tolerate the presence or absence of hydroxyl groups on the C-3'- and C-4'-positions. Additionally, sugar substituents on the C-6 hydroxyl were accepted but not on the C-5 hydroxyl. The most promising enzyme, GenB4, was then coupled with a reductive amination step to synthesise eleven novel 6'-gentamicin C1a analogues with conversions of 13-90%. Five of these compounds were active antimicrobials and four of these retained activity against an aminoglycoside-resistant Escherichia coli. This approach allows facile and step-efficient access to novel aminoglycoside compounds under mild reaction conditions and could potentially enable the development of greener, sustainable, and more cost-effective syntheses of novel AGAs.
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Affiliation(s)
- Gorjan Stojanovski
- Department of Biochemical Engineering, University College London London WC1E 6BT UK
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Helen C Hailes
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - John M Ward
- Department of Biochemical Engineering, University College London London WC1E 6BT UK
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3
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Xu F, Zhang X, Liu L, Ke X, Wu J, Guo Y, Tian X, Chu J. Engineering the methyltransferase through inactivation of the genK and genL leads to a significant increase of gentamicin C1a production in an industrial strain of Micromonospora echinospora 49-92S. Bioprocess Biosyst Eng 2022; 45:1693-1703. [PMID: 36029348 DOI: 10.1007/s00449-022-02774-0] [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: 06/01/2022] [Accepted: 08/06/2022] [Indexed: 05/31/2023]
Abstract
In this study, a single-component high-yielding Micromonospora echinospora strain 49-92S-KL01 was constructed by deleting methyltransferase-encoding genes genK and genL. In 5-L fermentation trials, gentamicin C1a titers in the mutant strain were 3.22-fold higher than that in the parental strain (211 U/mL vs. 50 U/mL). The glycolysis pathway and tricarboxylic acid cycle fluxes were reduced by 26.8% and 26.6%, respectively, compared to the parental strain according to the metabolic flux analysis during the stationary phase, resulting in lower levels of energy supplements required for the cellular maintenance. Meanwhile, a significant enhancement in precursor (paromamine) accumulation and availability was observed in 49-92S-KL01 compared to parental strain. These results indicate that genK and genL significantly affect the synthesis of gentamicin C1a. In addition, this study provides a more rational strategy for gentamicin C1a production.
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Affiliation(s)
- Feng Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xinyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Ling Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jie Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yuanxin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Kudo F, Eguchi T. Biosynthesis of cyclitols. Nat Prod Rep 2022; 39:1622-1642. [PMID: 35726901 DOI: 10.1039/d2np00024e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Review covering up to 2021Cyclitols derived from carbohydrates are naturally stable hydrophilic substances under ordinary physiological conditions, increasing the water solubility of whole molecules in cells. The stability of cyclitols is derived from their carbocyclic structures bearing no acetal groups, in contrast to sugar molecules. Therefore, carbocycle-forming reactions are critical for the biosynthesis of cyclitols. Herein, we review naturally occurring cyclitols that have been identified to date and categorize them according to the type of carbocycle-forming enzymatic reaction. Furthermore, the cyclitol-forming enzymatic reaction mechanisms and modification pathways of the initially generated cyclitols are reviewed.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
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5
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Zhang Z, Li P, Wang M, Zhang Y, Wu B, Tao Y, Pan G, Chen Y. ( S)-3-aminopiperidine-2,6-dione is a biosynthetic intermediate of microbial blue pigment indigoidine. MLIFE 2022; 1:146-155. [PMID: 38817675 PMCID: PMC10989907 DOI: 10.1002/mlf2.12023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/10/2022] [Accepted: 04/18/2022] [Indexed: 06/01/2024]
Abstract
The biosynthetic investigations of microbial natural products continuously provide powerful biocatalysts for the preparation of valuable chemicals. Practical methods for preparing (S)-3-aminopiperidine-2,6-dione (2), the pharmacophore of thalidomide (1) and its analog drugs, are highly desired. To develop a biocatalyst for producing (S)-2, we dissected the domain functions of IdgS, which is responsible for the biosynthesis of indigoidine (3), a microbial blue pigment that consists of two 2-like moieties. Our data supported that the L-glutamine tethered to the indigoidine assembly line is first offloaded and cyclized by the thioesterase domain to form (S)-2, which is then dehydrogenated by the oxidation (Ox) domain and finally dimerized to yield 3. Based on this, we developed an IdgS-derived enzyme biocatalyst, IdgS-Ox* R539A, for preparing enantiomerically pure (S)-2. As a proof of concept, one-pot chemoenzymatic synthesis of 1 was achieved by combining the biocatalytic and chemical approaches.
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Affiliation(s)
- Zhilong Zhang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Min Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High‐Efficiency, School of Pharmaceutical Science and TechnologyTianjin UniversityTianjinChina
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong Tao
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Li S, Santos Bury PD, Huang F, Guo J, Sun G, Reva A, Huang C, Jian X, Li Y, Zhou J, Deng Z, Leeper FJ, Leadlay PF, Dias MVB, Sun Y. Mechanistic Insights into Dideoxygenation in Gentamicin Biosynthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sicong Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Priscila Dos Santos Bury
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Junhong Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Anna Reva
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Chuan Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinyun Jian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Finian J. Leeper
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Marcio V. B. Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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7
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Engineering of Streptoalloteichus tenebrarius 2444 for Sustainable Production of Tobramycin. Molecules 2021; 26:molecules26144343. [PMID: 34299618 PMCID: PMC8304502 DOI: 10.3390/molecules26144343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Tobramycin is a broad-spectrum aminoglycoside antibiotic agent. The compound is obtained from the base-catalyzed hydrolysis of carbamoyltobramycin (CTB), which is naturally produced by the actinomycete Streptoalloteichus tenebrarius. However, the strain uses the same precursors to synthesize several structurally related aminoglycosides. Consequently, the production yields of tobramycin are low, and the compound’s purification is very challenging, costly, and time-consuming. In this study, the production of the main undesired product, apramycin, in the industrial isolate Streptoalloteichus tenebrarius 2444 was decreased by applying the fermentation media M10 and M11, which contained high concentrations of starch and dextrin. Furthermore, the strain was genetically engineered by the inactivation of the aprK gene (∆aprK), resulting in the abolishment of apramycin biosynthesis. In the next step of strain development, an additional copy of the tobramycin biosynthetic gene cluster (BGC) was introduced into the ∆aprK mutant. Fermentation by the engineered strain (∆aprK_1-17L) in M11 medium resulted in a 3- to 4-fold higher production than fermentation by the precursor strain (∆aprK). The phenotypic stability of the mutant without selection pressure was validated. The use of the engineered S. tenebrarius 2444 facilitates a step-saving, efficient, and, thus, more sustainable production of the valuable compound tobramycin on an industrial scale.
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Wang J, Ma S, Ding W, Chen T, Zhang Q. Mechanistic Study of Oxidoreductase
AprQ
Involved in Biosynthesis of Aminoglycoside Antibiotic Apramycin. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jinxiu Wang
- State Key Laboratory of Cryospheric Science, Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco‐Environment and Resources, Chinese Academy of Sciences Lanzhou Gansu 730000 China
- Department of Chemistry, Fudan University Shanghai 200433 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Suze Ma
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco‐Environment and Resources, Chinese Academy of Sciences Lanzhou Gansu 730000 China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
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9
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Guo Z, Tang Y, Tang W, Chen Y. Heptose-containing bacterial natural products: structures, bioactivities, and biosyntheses. Nat Prod Rep 2021; 38:1887-1909. [PMID: 33704304 DOI: 10.1039/d0np00075b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2020Glycosylated natural products hold great potential as drugs for the treatment of human and animal diseases. Heptoses, known as seven-carbon-chain-containing sugars, are a group of saccharides that are rarely observed in natural products. Based on the structures of the heptoses, the heptose-containing natural products can be divided into four groups, characterized by heptofuranose, highly-reduced heptopyranose, d-heptopyranose, and l-heptopyranose. Many of them possess remarkable biological properties, including antibacterial, antifungal, antitumor, and pain relief activities, thereby attracting great interest in biosynthesis and chemical synthesis studies to understand their construction mechanisms and structure-activity relationships. In this review, we summarize the structural properties, biological activities, and recent progress in the biosynthesis of bacterial natural products featuring seven-carbon-chain-containing sugars. The biosynthetic origins of the heptose moieties are emphasized.
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Affiliation(s)
- Zhengyan Guo
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
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10
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Zhou S, Chen X, Ni X, Liu Y, Zhang H, Dong M, Xia H. Pyridoxal-5'-phosphate-dependent enzyme GenB3 Catalyzes C-3',4'-dideoxygenation in gentamicin biosynthesis. Microb Cell Fact 2021; 20:65. [PMID: 33750386 PMCID: PMC7941887 DOI: 10.1186/s12934-021-01558-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background The C-3′,4′-dideoxygenation structure in gentamicin can prevent deactivation by aminoglycoside 3′-phosphotransferase (APH(3′)) in drug-resistant pathogens. However, the enzyme catalyzing the dideoxygenation step in the gentamicin biosynthesis pathway remains unknown. Results Here, we report that GenP catalyzes 3′ phosphorylation of the gentamicin biosynthesis intermediates JI-20A, JI-20Ba, and JI-20B. We further demonstrate that the pyridoxal-5′-phosphate (PLP)-dependent enzyme GenB3 uses these phosphorylated substrates to form 3′,4′-dideoxy-4′,5′-ene-6′-oxo products. The following C-6′-transamination and the GenB4-catalyzed reduction of 4′,5′-olefin lead to the formation of gentamicin C. To the best of our knowledge, GenB3 is the first PLP-dependent enzyme catalyzing dideoxygenation in aminoglycoside biosynthesis. Conclusions This discovery solves a long-standing puzzle in gentamicin biosynthesis and enriches our knowledge of the chemistry of PLP-dependent enzymes. Interestingly, these results demonstrate that to evade APH(3′) deactivation by pathogens, the gentamicin producers evolved a smart strategy, which utilized their own APH(3′) to activate hydroxyls as leaving groups for the 3′,4′-dideoxygenation in gentamicin biosynthesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01558-7.
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Affiliation(s)
- Shaotong Zhou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xiaotang Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
| | - Yu Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Hui Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
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11
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Kudo F, Kitayama Y, Miyanaga A, Numakura M, Eguchi T. Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis. Chembiochem 2021; 22:1668-1675. [PMID: 33403742 DOI: 10.1002/cbic.202000839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/05/2021] [Indexed: 11/07/2022]
Abstract
Kanamycin A is the major 2-deoxystreptamine (2DOS)-containing aminoglycoside antibiotic produced by Streptomyces kanamyceticus. The 2DOS moiety is linked with 6-amino-6-deoxy-d-glucose (6ADG) at O-4 and 3-amino-3-deoxy-d-glucose at O-6. Because the 6ADG moiety is derived from d-glucosamine (GlcN), deamination at C-2 and introduction of C-6-NH2 are required in the biosynthesis. A dehydrogenase, KanQ, and an aminotransferase, KanB, are presumed to be responsible for the introduction of C-6-NH2 , although the substrates have not been identified. Here, we examined the substrate specificity of KanQ to better understand the biosynthetic pathway. It was found that KanQ oxidized kanamycin C more efficiently than the 3''-deamino derivative. Furthermore, the substrate specificity of an oxygenase, KanJ, that is responsible for deamination at C-2 of the GlcN moiety was examined, and the crystal structure of KanJ was determined. It was found that C-6-NH2 is important for substrate recognition by KanJ. Thus, the modification of the GlcN moiety occurs after pseudo-trisaccharide formation, followed by the introduction of C-6-NH2 by KanQ/KanB and deamination at C-2 by KanJ.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Yukinobu Kitayama
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Mario Numakura
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
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12
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Dissociating antibacterial from ototoxic effects of gentamicin C-subtypes. Proc Natl Acad Sci U S A 2020; 117:32423-32432. [PMID: 33288712 DOI: 10.1073/pnas.2013065117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gentamicin is a potent broad-spectrum aminoglycoside antibiotic whose use is hampered by ototoxic side-effects. Hospital gentamicin is a mixture of five gentamicin C-subtypes and several impurities of various ranges of nonexact concentrations. We developed a purification strategy enabling assaying of individual C-subtypes and impurities for ototoxicity and antimicrobial activity. We found that C-subtypes displayed broad and potent in vitro antimicrobial activities comparable to the hospital gentamicin mixture. In contrast, they showed different degrees of ototoxicity in cochlear explants, with gentamicin C2b being the least and gentamicin C2 the most ototoxic. Structure-activity relationships identified sites in the C4'-C6' region on ring I that reduced ototoxicity while preserving antimicrobial activity, thus identifying targets for future drug design and mechanisms for hair cell toxicity. Structure-activity relationship data suggested and electrophysiological data showed that the C-subtypes both bind and permeate the hair cell mechanotransducer channel, with the stronger the binding the less ototoxic the compound. Finally, both individual and reformulated mixtures of C-subtypes demonstrated decreased ototoxicity while maintaining antimicrobial activity, thereby serving as a proof-of-concept of drug reformulation to minimizing ototoxicity of gentamicin in patients.
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13
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Li S, Liu Q, Zhong Z, Deng Z, Sun Y. Exploration of Hygromycin B Biosynthesis Utilizing CRISPR-Cas9-Associated Base Editing. ACS Chem Biol 2020; 15:1417-1423. [PMID: 32275383 DOI: 10.1021/acschembio.0c00071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hygromycin B is an aminoglycoside antibiotic widely used in industry and biological research. However, most of its biosynthetic pathway has not been completely identified due to the immense difficulty in genetic manipulation of the producing strain. To address this problem, we developed an efficient system that combines clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-associated base editing and site-specific recombination instead of conventional double-crossover-based homologous recombination. This strategy was successfully applied to the in vivo inactivation of five candidate genes involved in the biosynthesis of hygromycin B by generating stop codons or mutating conserved residues within the encoding region. The results revealed that HygJ, HygL, and HygD are responsible for successive dehydrogenation, transamination, and transglycosylation of nucleoside diphosphate (NDP)-heptose. Notably, HygY acts as an unusual radical S-adenosylmethionine (SAM)-dependent epimerase for hydroxyl carbons, and HygM serves as a versatile methyltransferase in multiple parallel metabolic networks. Based on in vivo and in vitro evidence, the biosynthetic pathway for hygromycin B is proposed.
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Affiliation(s)
- Sicong Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
| | - Qian Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
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Xie X, Zhu JW, Liu Y, Jiang H. Application of Genetic Engineering Approaches to Improve Bacterial Metabolite Production. Curr Protein Pept Sci 2020; 21:488-496. [DOI: 10.2174/1389203721666191223145827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/28/2019] [Accepted: 10/27/2019] [Indexed: 02/06/2023]
Abstract
Genetic engineering is a powerful method to improve the fermentation yield of bacterial
metabolites. Since many biosynthetic mechanisms of bacterial metabolites have been unveiled, genetic
engineering approaches have been applied to various issues of biosynthetic pathways, such as transcription,
translation, post-translational modification, enzymes, transporters, etc. In this article, natamycin,
avermectins, gentamicins, piperidamycins, and β-valienamine have been chosen as examples
to review recent progress in improving their production by genetic engineering approaches. In these
cases, not only yields of target products have been increased, but also yields of by-products have been
decreased, and new products have been created.
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Affiliation(s)
- Xin Xie
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jia-Wei Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yi Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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15
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Chen X, Zhang H, Zhou S, Bi M, Qi S, Gao H, Ni X, Xia H. The bifunctional enzyme, GenB4, catalyzes the last step of gentamicin 3',4'-di-deoxygenation via reduction and transamination activities. Microb Cell Fact 2020; 19:62. [PMID: 32156271 PMCID: PMC7063804 DOI: 10.1186/s12934-020-01317-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/25/2020] [Indexed: 12/02/2022] Open
Abstract
Background New semi-synthetic aminoglycoside antibiotics generally use chemical modifications to avoid inactivity from pathogens. One of the most used modifications is 3′,4′-di-deoxygenation, which imitates the structure of gentamicin. However, the mechanism of di-deoxygenation has not been clearly elucidated. Results Here, we report that the bifunctional enzyme, GenB4, catalyzes the last step of gentamicin 3′,4′-di-deoxygenation via reduction and transamination activities. Following disruption of genB4 in wild-type M. echinospora, its products accumulated in 6′-deamino-6′-oxoverdamicin (1), verdamicin C2a (2), and its epimer, verdamicin C2 (3). Following disruption of genB4 in M. echinospora ΔgenK, its products accumulated in sisomicin (4) and 6′-N-methylsisomicin (5, G-52). Following in vitro catalytic reactions, GenB4 transformed sisomicin (4) to gentamicin C1a (9) and transformed verdamicin C2a (2) and its epimer, verdamicin C2 (3), to gentamicin C2a (11) and gentamicin C2 (12), respectively. Conclusion This finding indicated that in addition to its transamination activity, GenB4 exhibits specific 4′,5′ double-bond reducing activity and is responsible for the last step of gentamicin 3′,4′-di-deoxygenation. Taken together, we propose three new intermediates that may refine and supplement the specific biosynthetic pathway of gentamicin C components and lay the foundation for the complete elucidation of di-deoxygenation mechanisms.
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Affiliation(s)
- Xiaotang Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Hui Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Shaotong Zhou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Mingjun Bi
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Shizhou Qi
- School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Huiyuan Gao
- School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
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16
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Ban YH, Song MC, Park JW, Yoon YJ. Minor components of aminoglycosides: recent advances in their biosynthesis and therapeutic potential. Nat Prod Rep 2020; 37:301-311. [DOI: 10.1039/c9np00041k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This Highlight covers the recent advances in the biosynthetic pathways of aminoglycosides including their minor components, together with the therapeutic potential for minor aminoglycoside components and semi-synthetic aminoglycosides.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Je Won Park
- School of Biosystems and Biomedical Sciences
- Korea University
- Seoul 02841
- Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
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17
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Exclusive Production of Gentamicin C1a from Micromonospora purpurea by Metabolic Engineering. Antibiotics (Basel) 2019; 8:antibiotics8040267. [PMID: 31847403 PMCID: PMC6963548 DOI: 10.3390/antibiotics8040267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Gentamicin C1a is an important precursor to the synthesis of etimicin, a potent antibiotic. Wild type Micromonospora purpurea Gb1008 produces gentamicin C1a, besides four other gentamicin C components: C1, C2, C2a, and C2b. While the previously reported engineered strain M. purpurea GK1101 can produce relatively high titers of C1a by blocking the genK pathway, a small amount of undesirable C2b is still being synthesized in cells. Gene genL (orf6255) is reported to be responsible for converting C1a to C2b and C2 to C1 in Micromonospora echinospora ATCC15835. In this work, we identify the genL that is also responsible for the same methylation in Micromonospora purpurea. Based on M. purpurea GK1101, we construct a new strain with genL inactivated and show that no C2b is produced in this strain. Therefore, we successfully engineer a strain of M. purpurea that solely produces gentamicin C1a. This strain can potentially be used in the industrial production of C1a for the synthesis of etimicin.
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18
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Chang Y, Chai B, Ding Y, He M, Zheng L, Teng Y, Deng Z, Yu Y, Liu T. Overproduction of gentamicin B in industrial strain Micromonospora echinospora CCTCC M 2018898 by cloning of the missing genes genR and genS. Metab Eng Commun 2019; 9:e00096. [PMID: 31720212 PMCID: PMC6838515 DOI: 10.1016/j.mec.2019.e00096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/01/2019] [Accepted: 07/18/2019] [Indexed: 01/28/2023] Open
Abstract
In pharmaceutical industry, isepamicin is mainly manufactured from gentamicin B, which is produced by Micromonospora echinospora as a minor component of the gentamicin complex. Improvement of gentamicin B production through metabolic engineering is therefore important to satisfy the increasing demand for isepamicin. We hypothesized that gentamicin B was generated from gentamicin JI-20A via deamination of the C2’ amino group. Using kanJ and kanK as the gene probes, we identified the putative deamination-related genes, genR and genS, through genome mining of the gentamicin B producing strain M. echinospora CCTCC M 2018898. Interestingly, genR and genS constitute a gene cassette located approximately 28.7 kb away from the gentamicin gene cluster. Gene knockout of genR and genS almost abolished the production of gentamicin B in the mutant strain, suggesting that these two genes, which are responsible for the last steps in gentamicin B biosynthesis, constitute the missing part of the known gentamicin biosynthetic pathway. Based on these finding, we successfully constructed a gentamicin B high-yielding strain (798 mg/L), in which an overexpression cassette of genR and genS was introduced. Our work fills the missing piece to solve the puzzle of gentamicin B biosynthesis and may inspire future metabolic engineering efforts to generate gentamycin B high-yielding strains that could eventually satisfy the need for industrial manufacturing of isepamicin. Two missing genes in the biosynthetic pathway of gentamicin B were found. CRISPR/Cas9 was applied successfully to delete genes in Micromonospora echinospora. Overexpression of genR/S cassette improved gentamicin B titer by 64% in current industrial strain.
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Affiliation(s)
- Yingying Chang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, China
| | - Baozhong Chai
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co, Ltd, Taizhou, 318000, China
| | - Yunkun Ding
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, China
| | - Min He
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co, Ltd, Taizhou, 318000, China
| | - Linghui Zheng
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co, Ltd, Taizhou, 318000, China
| | - Yun Teng
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co, Ltd, Taizhou, 318000, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, China
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, China
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19
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de Araújo NC, Bury PDS, Tavares MT, Huang F, Parise-Filho R, Leadlay P, Dias MVB. Crystal Structure of GenD2, an NAD-Dependent Oxidoreductase Involved in the Biosynthesis of Gentamicin. ACS Chem Biol 2019; 14:925-933. [PMID: 30995396 DOI: 10.1021/acschembio.9b00115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Gentamicins are clinically relevant aminoglycoside antibiotics produced by several Micromonospora species. Gentamicins are highly methylated and functionalized molecules, and their biosynthesis include glycosyltransferases, dehydratase/oxidoreductases, aminotransferases, and methyltransferases. The biosynthesis of gentamicin A from gentamicin A2 involves three enzymatic steps that modify the hydroxyl group at position 3″ of the unusual garosamine sugar to provide its substitution for an amino group, followed by an N-methylation. The first of these reactions is catalyzed by GenD2, an oxidoreductase from the Gfo/Idh/MocA protein family, which reduces the hydroxyl at the C3″ of gentamicin A to produce 3''-dehydro-3''-oxo-gentamicin A2 (DOA2). In this work, we solved the structure of GenD2 in complex with NAD+. Although the structure of GenD2 has a similar fold to other members of the Gfo/Idh/MocA family, this enzyme has several new features, including a 3D-domain swapping of two β-strands that are involved in a novel oligomerization interface for this protein family. In addition, the active site of this enzyme also has several specialties which are possibly involved in the substrate specificity, including a number of aromatic residues and a negatively charged region, which is complementary to the polycationic aminoglycoside-substrate. Therefore, docking simulations provided insights into the recognition of gentamicin A2 and into the catalytic mechanism of GenD2. This is the first report describing the structure of an oxidoreductase involved in aminoglycoside biosynthesis and could open perspectives into producing new aminoglycoside derivatives by protein engineering.
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Affiliation(s)
- Natalia Cerrone de Araújo
- Department of Microbiology, Institute of Biomedical Science , University of São Paulo , Avenida Prof. Lineu Prestes 1374 , 05508-900 São Paulo , Brazil
| | - Priscila Dos Santos Bury
- Department of Microbiology, Institute of Biomedical Science , University of São Paulo , Avenida Prof. Lineu Prestes 1374 , 05508-900 São Paulo , Brazil
| | - Maurício Temotheo Tavares
- Department of Pharmacy, Faculty of Pharmaceutical Sciences , University of São Paulo , Prof. Lineu Prestes Avenue 580 , 05508-900 São Paulo , Brazil
| | - Fanglu Huang
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , U.K
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences , University of São Paulo , Prof. Lineu Prestes Avenue 580 , 05508-900 São Paulo , Brazil
| | - Peter Leadlay
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , U.K
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science , University of São Paulo , Avenida Prof. Lineu Prestes 1374 , 05508-900 São Paulo , Brazil.,Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
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20
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Chen W, Yao J, Meng J, Han W, Tao Y, Chen Y, Guo Y, Shi G, He Y, Jin JM, Tang SY. Promiscuous enzymatic activity-aided multiple-pathway network design for metabolic flux rearrangement in hydroxytyrosol biosynthesis. Nat Commun 2019; 10:960. [PMID: 30814511 PMCID: PMC6393456 DOI: 10.1038/s41467-019-08781-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/11/2019] [Indexed: 12/04/2022] Open
Abstract
Genetic diversity is a result of evolution, enabling multiple ways for one particular physiological activity. Here, we introduce this strategy into bioengineering. We design two hydroxytyrosol biosynthetic pathways using tyrosine as substrate. We show that the synthetic capacity is significantly improved when two pathways work simultaneously comparing to each individual pathway. Next, we engineer flavin-dependent monooxygenase HpaBC for tyrosol hydroxylase, tyramine hydroxylase, and promiscuous hydroxylase active on both tyrosol and tyramine using directed divergent evolution strategy. Then, the mutant HpaBCs are employed to catalyze two missing steps in the hydroxytyrosol biosynthetic pathways designed above. Our results demonstrate that the promiscuous tyrosol/tyramine hydroxylase can minimize the cell metabolic burden induced by protein overexpression and allow the biosynthetic carbon flow to be divided between two pathways. Thus, the efficiency of the hydroxytyrosol biosynthesis is significantly improved by rearranging the metabolic flux among multiple pathways.
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Affiliation(s)
- Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Meng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenjing Han
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yihua Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yixin Guo
- Center for Drug Discovery & Technology Development of Yunnan Traditional Medicine, Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Guizhi Shi
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang He
- Life Science Institute, Zhejiang University, Hangzhou, China.
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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21
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Complete reconstitution of the diverse pathways of gentamicin B biosynthesis. Nat Chem Biol 2019; 15:295-303. [PMID: 30643280 PMCID: PMC6488028 DOI: 10.1038/s41589-018-0203-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/13/2018] [Indexed: 11/13/2022]
Abstract
Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. While the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6′-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2′-deamination enzymes, limit GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6′-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.
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22
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Peracchi A. The Limits of Enzyme Specificity and the Evolution of Metabolism. Trends Biochem Sci 2018; 43:984-996. [DOI: 10.1016/j.tibs.2018.09.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022]
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23
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Li S, Zhang J, Liu Y, Sun G, Deng Z, Sun Y. Direct Genetic and Enzymatic Evidence for Oxidative Cyclization in Hygromycin B Biosynthesis. ACS Chem Biol 2018; 13:2203-2210. [PMID: 29878752 DOI: 10.1021/acschembio.8b00375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hygromycin B is an aminoglycoside antibiotic with a structurally distinctive orthoester linkage. Despite its long history of use in industry and in the laboratory, its biosynthesis remains poorly understood. We show here, by in-frame gene deletion in vivo and detailed enzyme characterization in vitro, that formation of the unique orthoester moiety is catalyzed by the α-ketoglutarate- and non-heme iron-dependent oxygenase HygX. In addition, we identify HygF as a glycosyltransferase adding UDP-hexose to 2-deoxystreptamine, HygM as a methyltransferase responsible for N-3 methylation, and HygK as an epimerase. These experimental results and bioinformatic analyses allow a detailed pathway for hygromycin B biosynthesis to be proposed, including the key oxidative cyclization reactions.
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Affiliation(s)
- Sicong Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Jun Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Yuanzhen Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
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24
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Dow GT, Thoden JB, Holden HM. The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin. Protein Sci 2018. [PMID: 29516565 DOI: 10.1002/pro.3400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The aminoglycoside antibiotics, discovered as natural products in the 1940s, demonstrate a broad antimicrobial spectrum. Due to their nephrotoxic and ototoxic side effects, however, their widespread clinical usage has typically been limited to the treatment of serious infections. Neomycin B, first isolated from strains of Streptomyces in 1948, is one such drug that was approved for human use by the U.S. Food and Drug Administration in 1964. Only within the last 11 years has the biochemical pathway for its production been elaborated, however. Here we present the three-dimensional architecture of NeoB from Streptomyces fradiae, which is a pyridoxal 5'-phosphate or PLP-dependent aminotransferase that functions on two different substrates in neomycin B biosynthesis. For this investigation, four high resolution X-ray structures of NeoB were determined in various complexed states. The overall fold of NeoB is that typically observed for members of the "aspartate aminotransferase" family with the exception of an additional three-stranded antiparallel β-sheet that forms part of the subunit-subunit interface of the dimer. The manner in which the active site of NeoB accommodates quite different substrates has been defined by this investigation. In addition, during the course of this study, we also determined the structure of the aminotransferase GenB1 to high resolution. GenB1 functions as an aminotransferase in gentamicin biosynthesis. Taken together, the structures of NeoB and GenB1, presented here, provide the first detailed descriptions of aminotransferases that specifically function on aldehyde moieties in aminoglycoside biosynthesis.
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Affiliation(s)
- Garrett T Dow
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706
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25
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Abstract
Aminoglycosides remain a vital clinical asset. Gentamicin C complex in particular is remarkably potent in treating systemic Gram-negative infections, and semisynthetic gentamicins that combat pathogen resistance or show reduced toxicity remain attractive goals. We report here the roles of clustered genes and enzymes that define a methylation network in gentamicin biosynthesis and also identify a remote gene on the chromosome encoding the essential methyltransferase GenL, which is decisive for the proportions of the five major components present in the gentamicin C complex. This is an important step toward engineered fermentation to produce single components as valuable starting materials for semisynthesis of next-generation aminoglycoside antibiotics. Gentamicin C complex from Micromonospora echinospora remains a globally important antibiotic, and there is revived interest in the semisynthesis of analogs that might show improved therapeutic properties. The complex consists of five components differing in their methylation pattern at one or more sites in the molecule. We show here, using specific gene deletion and chemical complementation, that the gentamicin pathway up to the branch point is defined by the selectivity of the methyltransferases GenN, GenD1, and GenK. Unexpectedly, they comprise a methylation network in which early intermediates are ectopically modified. Using whole-genome sequence, we have also discovered the terminal 6′-N-methyltransfer required to produce gentamicin C2b from C1a or gentamicin C1 from C2, an example of an essential biosynthetic enzyme being located not in the biosynthetic gene cluster but far removed on the chromosome. These findings fully account for the methylation pattern in gentamicins and open the way to production of individual gentamicins by fermentation, as starting materials for semisynthesis.
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26
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Bury PDS, Huang F, Li S, Sun Y, Leadlay PF, Dias MVB. Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis. ACS Chem Biol 2017; 12:2779-2787. [PMID: 28876898 DOI: 10.1021/acschembio.7b00466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gentamicins are heavily methylated, clinically valuable pseudotrisaccharide antibiotics produced by Micromonospora echinospora. GenN has been characterized as an S-adenosyl-l-methionine-dependent methyltransferase with low sequence similarity to other enzymes. It is responsible for the 3″-N-methylation of 3″-dehydro-3″-amino-gentamicin A2, an essential modification of ring III in the biosynthetic pathway to the gentamicin C complex. Purified recombinant GenN also efficiently catalyzes 3″-N-methylation of related aminoglycosides kanamycin B and tobramycin, which both contain an additional hydroxymethyl group at the C5″ position in ring III. We have obtained eight cocrystal structures of GenN, at a resolution of 2.2 Å or better, including the binary complex of GenN and S-adenosyl-l-homocysteine (SAH) and the ternary complexes of GenN, SAH, and several aminoglycosides. The GenN structure reveals several features not observed in any other N-methyltransferase that fit it for its role in gentamicin biosynthesis. These include a novel N-terminal domain that might be involved in protein:protein interaction with upstream enzymes of the gentamicin X2 biosynthesis and two long loops that are involved in aminoglycoside substrate recognition. In addition, the analysis of structures of GenN in complex with different ligands, supported by the results of active site mutagenesis, has allowed us to propose a catalytic mechanism and has revealed the structural basis for the surprising ability of native GenN to act on these alternative substrates.
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Affiliation(s)
- Priscila dos Santos Bury
- Department
of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Fanglu Huang
- Department
of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Sicong Li
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yuhui Sun
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Peter F. Leadlay
- Department
of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
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Wu Z, Gao W, Zhou S, Wen Z, Ni X, Xia H. Improving gentamicin B and gentamicin C1a production by engineering the glycosyltransferases that transfer primary metabolites into secondary metabolites biosynthesis. Microbiol Res 2017; 203:40-46. [PMID: 28754206 DOI: 10.1016/j.micres.2017.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/08/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
Abstract
Gentamicin B and gentamicin C1a are the direct precursor for Isepamicin and Etimicin synthesis, respectively. Although producing strains have been improved for many years, both gentamicin B titer and gentamicin C1a titer in the fermentation are still low. Because all gentamicin components are biosynthesized using UDP-N-acetyl-d-glucosamine (UDP-GlcNAc) and UDP-xylose as precursors, we tried to explore strategies for development of strains capable of directing greater fluxes of these precursors into production of gentamicins. The glycosyltransferases KanM1 and GenM2, which are responsible for UDP-GlcNAc and UDP-xylose transfer, respectively, were overexpressed in gentamicin B producing strain Micromonospora echinospora JK4. It was found that gentamicin B could be improved by up to 54% with improvement of KanM1 and GenM2 expression during appropriately glucose feeding. To prove this strategy is widely usable, the KanM1 and GenM2 were also overexpressed in gentamicin C1a producing strain, titers of gentamicin C1a improved by 45% when compared with titers of the starting strain. These results demonstrated overexpression the glycosyltransferases that transfer primary metabolites into secondary metabolites is workable for improvement of gentamicins production.
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Affiliation(s)
- Zheng Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning, China
| | - Wenli Gao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning, China
| | - Shaotong Zhou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning, China
| | - Zhaolin Wen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning, China.
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Abstract
Despite their inherent toxicity and the global spread of bacterial resistance, aminoglycosides (AGs), an old class of microbial drugs, remain a valuable component of the antibiotic arsenal. Recent studies have continued to reveal the fascinating biochemistry of AG biosynthesis and the rich potential in their pathway engineering. In particular, parallel pathways have been shown to be common and widespread in AG biosynthesis, highlighting nature’s ingenuity in accessing diverse natural products from a limited set of genes. In this review, we discuss the parallel biosynthetic pathways of three representative AG antibiotics—kanamycin, gentamicin, and apramycin—as well as future directions towards the discovery and development of novel AGs.
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Affiliation(s)
- Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
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Park JW, Ban YH, Nam SJ, Cha SS, Yoon YJ. Biosynthetic pathways of aminoglycosides and their engineering. Curr Opin Biotechnol 2017; 48:33-41. [PMID: 28365471 DOI: 10.1016/j.copbio.2017.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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Hoang NH, Huong NL, Kim B, Sohng JK, Yoon YJ, Park JW. Istamycin aminoglycosides profiling and their characterization in Streptomyces tenjimariensis ATCC 31603 culture using high-performance liquid chromatography with tandem mass spectrometry. J Sep Sci 2016; 39:4712-4722. [PMID: 27778478 DOI: 10.1002/jssc.201600925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 10/12/2016] [Accepted: 10/22/2016] [Indexed: 11/08/2022]
Abstract
A high-performance liquid chromatography with electrospray ionization ion trap tandem mass spectrometry method was developed and validated for the robust profiling and characterization of biosynthetic congeners in the 2-deoxy-aminocyclitol istamycin pathway, from the fermentation broth of Streptomyces tenjimariensis ATCC 31603. Gradient elution on an Acquity CSH C18 column was performed with a gradient of 5 mM aqueous pentafluoropropionic acid and 50% acetonitrile. Sixteen natural istamycin congeners were profiled and quantified in descending order; istamycin A, istamycin B, istamycin A0 , istamycin B0 , istamycin B1 , istamycin A1 , istamycin C, istamycin A2 , istamycin C1 , istamycin C0 , istamycin X0 , istamycin A3 , istamycin Y0 , istamycin B3 , and istamycin FU-10 plus istamycin AP. In addition, a total of five sets of 1- or 3-epimeric pairs were chromatographically separated using a macrocyclic glycopeptide-bonded chiral column. The lower limit of quantification of istamycin-A present in S. tenjimariensis fermentation was estimated to be 2.2 ng/mL. The simultaneous identification of a wide range of 2-deoxy-aminocyclitol-type istamycin profiles from bacterial fermentation was determined for the first time by employing high-performance liquid chromatography with tandem mass spectrometry analysis and the separation of istamycin epimers.
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Affiliation(s)
- Nguyen Huu Hoang
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, Republic of Korea
| | - Nguyen Lan Huong
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, Republic of Korea
| | - Byul Kim
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
| | - Jae Kyung Sohng
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
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Mullins ND, Deadman BJ, Moynihan HA, McCarthy FO, Lawrence SE, Thompson J, Maguire AR. The impact of storage conditions upon gentamicin coated antimicrobial implants. J Pharm Anal 2016; 6:374-381. [PMID: 29404006 PMCID: PMC5762933 DOI: 10.1016/j.jpha.2016.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 11/24/2022] Open
Abstract
A systematic approach was developed to investigate the stability of gentamicin sulfate (GS) and GS/poly (lactic-co-glycolic acid) (PLGA) coatings on hydroxyapatite surfaces. The influence of environmental factors (light, humidity, oxidation and heat) upon degradation of the drug in the coatings was investigated using liquid chromatography with evaporative light scattering detection and mass spectrometry. GS coated rods were found to be stable across the range of environments assessed, with only an oxidizing atmosphere resulting in significant changes to the gentamicin composition. In contrast, rods coated with GS/PLGA were more sensitive to storage conditions with compositional changes being detected after storage at 60 °C, 75% relative humidity or exposure to light. The effect of γ-irradiation on the coated rods was also investigated and found to have no significant effect. Finally, liquid chromatography-mass spectrometry analysis revealed that known gentamines C1, C1a and C2 were the major degradants formed. Forced degradation of gentamicin coatings did not produce any unexpected degradants or impurities.
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Affiliation(s)
- Nicholas D. Mullins
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
| | - Benjamin J. Deadman
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
| | - Humphrey A. Moynihan
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
| | - Florence O. McCarthy
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
| | - Simon E. Lawrence
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
| | | | - Anita R. Maguire
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
- School of Pharmacy, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
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33
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Lv M, Ji X, Zhao J, Li Y, Zhang C, Su L, Ding W, Deng Z, Yu Y, Zhang Q. Characterization of a C3 Deoxygenation Pathway Reveals a Key Branch Point in Aminoglycoside Biosynthesis. J Am Chem Soc 2016; 138:6427-35. [PMID: 27120352 DOI: 10.1021/jacs.6b02221] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Apramycin is a clinically interesting aminoglycoside antibiotic (AGA) containing a highly unique bicyclic octose moiety, and this octose is deoxygenated at the C3 position. Although the biosynthetic pathways for most 2-deoxystreptamine-containing AGAs have been well characterized, the pathway for apramycin biosynthesis, including the C3 deoxygenation process, has long remained unknown. Here we report detailed investigation of apramycin biosynthesis by a series of genetic, biochemical and bioinformatical studies. We show that AprD4 is a novel radical S-adenosyl-l-methionine (SAM) enzyme, which uses a noncanonical CX3CX3C motif for binding of a [4Fe-4S] cluster and catalyzes the dehydration of paromamine, a pseudodisaccharide intermediate in apramycin biosynthesis. We also show that AprD3 is an NADPH-dependent reductase that catalyzes the reduction of the dehydrated product from AprD4-catalyzed reaction to generate lividamine, a C3' deoxygenated product of paromamine. AprD4 and AprD3 do not form a tight catalytic complex, as shown by protein complex immunoprecipitation and other assays. The AprD4/AprD3 enzyme system acts on different pseudodisaccharide substrates but does not catalyze the deoxygenation of oxyapramycin, an apramycin analogue containing a C3 hydroxyl group on the octose moiety, suggesting that oxyapramycin and apramycin are partitioned into two parallel pathways at an early biosynthetic stage. Functional dissection of the C6 dehydrogenase AprQ shows the crosstalk between different AGA biosynthetic gene clusters from the apramycin producer Streptomyces tenebrarius, and reveals the remarkable catalytic versatility of AprQ. Our study highlights the intriguing chemistry in apramycin biosynthesis and nature's ingenuity in combinatorial biosynthesis of natural products.
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Affiliation(s)
- Meinan Lv
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Junfeng Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.,Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Chen Zhang
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Li Su
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Wei Ding
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Qi Zhang
- Department of Chemistry, Fudan University , Shanghai, 200433, China
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Huong NL, Hoang NH, Hong SY, Sohng JK, Yoon YJ, Park JW. Characterization of fortimicin aminoglycoside profiles produced from Micromonospora olivasterospora DSM 43868 by high-performance liquid chromatography-electrospray ionization-ion trap-mass spectrometry. Anal Bioanal Chem 2016; 408:1667-78. [PMID: 26753981 DOI: 10.1007/s00216-015-9281-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/11/2015] [Accepted: 12/16/2015] [Indexed: 10/25/2022]
Abstract
In this study, an efficient high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-ion trap-tandem mass spectrometry (MS/MS) was developed for the identification of the biosynthetic congeners involved in the aminocyclitol aminoglycosidic fortimicin pathway from Micromonospora olivasterospora fermentation. The usage of both acid extraction (pH ∼2.5) followed by an cationic-exchanging SPE cleanup and pentafluoropropionic acid mediated ion-pairing chromatography with ESI-ion trap-MS/MS detection was determined to be sufficiently practical to profile the fortimicin (FOR) congeners produced in a culture broth. The limit of the quantification for the fortimicin A (FOR-A) standard spiked in the culture broth was ∼1.6 ng mL(-1). The average recovery rate was 93.6%, and the intra- and inter-day precisions were <5% with accuracy in the range from 87.1 to 94.2%. Moreover, the epimeric mixtures including FOR-KH, FOR-KR, and FOR-B were separately resolved through a macrocyclic glycopeptide (teicoplanin)-bonded chiral column. As a result, ten natural FOR pseudodisaccharide analogs were identified and semi-quantified in descending order as follows: FOR-A, FOR-B, DCM, FOR-KH plus FOR-KR, FOR-KK1, FOR-AP, FOR-KL1, FOR-AO, and FOR-FU-10. This is the first report on both the simultaneous characterization of diverse structurally closely related FORs derived from bacterial fermentation using HPLC-ESI-ion trap-MS/MS analysis and the chromatographic separation of the three FOR epimers.
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Affiliation(s)
- Nguyen Lan Huong
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, 336-708, Republic of Korea
| | - Nguyen Huu Hoang
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, 336-708, Republic of Korea
| | - Sung-Yong Hong
- School of Biosystem and Biomedical Science, Korea University, Seoul, 136-713, Republic of Korea
| | - Jae Kyung Sohng
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, 336-708, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Sciences, Ewha Womans University, Seoul, 136-750, Republic of Korea
| | - Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul, 136-713, Republic of Korea.
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Ni X, Sun Z, Gu Y, Cui H, Xia H. Assembly of a novel biosynthetic pathway for gentamicin B production in Micromonospora echinospora. Microb Cell Fact 2016; 15:1. [PMID: 26729212 PMCID: PMC4700567 DOI: 10.1186/s12934-015-0402-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/22/2015] [Indexed: 01/09/2023] Open
Abstract
Background Isepamicin is a weakly toxic but highly active aminoglycoside antibiotic derivative of gentamicin B. Gentamicin B is a naturally occurring minor component isolated from Micromonospora echinospora. 2ʹ-NH2-containing gentamicin C complex is a dominant compound produced by wild-type M. echinospora; by contrast, 2ʹ-OH-containing gentamicin B is produced as a minor component. However, the biosynthetic pathway of gentamicin B remains unclear. Considering that gentamicin B shares a unique C2ʹ hydroxyl group with kanamycin A, we aimed to design a new biosynthetic pathway of gentamicin B by combining twelve steps of gentamicin biosynthesis and two steps of kanamycin biosynthesis. Results We blocked the biosynthetic pathway of byproducts and generated a strain overproducing JI-20A, which was used as a precursor of gentamicin B biosynthesis, by disrupting genK and genP. The amount of JI-20A produced in M. echinospora ∆K∆P reached 911 μg/ml, which was 14-fold higher than that of M. echinospora ∆P. The enzymes KanJ and KanK necessary to convert 2ʹ-NH2 into 2ʹ-OH from the kanamycin biosynthetic pathway were heterologously expressed in M. echinospora ΔKΔP to transform JI-20A into gentamicin B. The strain with kanJK under PermE* could produce 80 μg/ml of gentamicin B, which was tenfold higher than that of the wild-type strain. To enhance gentamicin B production, we employed different promoters and gene integration combinations. When a PhrdB promoter was used and kanJ and kanK were integrated in the genome through gene replacement, gentamicin B was generated as the major product with a maximum yield of 880 μg/ml. Conclusion We constructed a new biosynthetic pathway of high-level gentamicin B production; in this pathway, most byproducts were removed. This method also provided novel insights into the biosynthesis of secondary metabolites via the combinatorial biosynthesis. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0402-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
| | - Zhenpeng Sun
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
| | - Yawen Gu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
| | - Hao Cui
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
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Kudo F, Eguchi T. Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs. CHEM REC 2015; 16:4-18. [PMID: 26455715 DOI: 10.1002/tcr.201500210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 11/07/2022]
Abstract
2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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37
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Gu Y, Ni X, Ren J, Gao H, Wang D, Xia H. Biosynthesis of Epimers C2 and C2a in the Gentamicin C Complex. Chembiochem 2015; 16:1933-1942. [DOI: 10.1002/cbic.201500258] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Indexed: 11/09/2022]
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38
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Huang C, Huang F, Moison E, Guo J, Jian X, Duan X, Deng Z, Leadlay PF, Sun Y. Delineating the biosynthesis of gentamicin x2, the common precursor of the gentamicin C antibiotic complex. ACTA ACUST UNITED AC 2015; 22:251-61. [PMID: 25641167 PMCID: PMC4340712 DOI: 10.1016/j.chembiol.2014.12.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/03/2014] [Accepted: 12/06/2014] [Indexed: 11/24/2022]
Abstract
Gentamicin C complex is a mixture of aminoglycoside antibiotics used worldwide to treat severe Gram-negative bacterial infections. Despite its clinical importance, the enzymology of its biosynthetic pathway has remained obscure. We report here insights into the four enzyme-catalyzed steps that lead from the first-formed pseudotrisaccharide gentamicin A2 to gentamicin X2, the last common intermediate for all components of the C complex. We have used both targeted mutations of individual genes and reconstitution of portions of the pathway in vitro to show that the secondary alcohol function at C-3″ of A2 is first converted to an amine, catalyzed by the tandem operation of oxidoreductase GenD2 and transaminase GenS2. The amine is then specifically methylated by the S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase GenN to form gentamicin A. Finally, C-methylation at C-4″ to form gentamicin X2 is catalyzed by the radical SAM-dependent and cobalamin-dependent enzyme GenD1.
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Affiliation(s)
- Chuan Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Eileen Moison
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Junhong Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Xinyun Jian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Xiaobo Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, People's Republic of China
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China.
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