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Tjallinks G, Mattevi A, Fraaije MW. Biosynthetic Strategies of Berberine Bridge Enzyme-like Flavoprotein Oxidases toward Structural Diversification in Natural Product Biosynthesis. Biochemistry 2024; 63:2089-2110. [PMID: 39133819 DOI: 10.1021/acs.biochem.4c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Berberine bridge enzyme-like oxidases are often involved in natural product biosynthesis and are seen as essential enzymes for the generation of intricate pharmacophores. These oxidases have the ability to transfer a hydride atom to the FAD cofactor, which enables complex substrate modifications and rearrangements including (intramolecular) cyclizations, carbon-carbon bond formations, and nucleophilic additions. Despite the diverse range of activities, the mechanistic details of these reactions often remain incompletely understood. In this Review, we delve into the complexity that BBE-like oxidases from bacteria, fungal, and plant origins exhibit by providing an overview of the shared catalytic features and emphasizing the different reactivities. We propose four generalized modes of action by which BBE-like oxidases enable the synthesis of natural products, ranging from the classic alcohol oxidation reactions to less common amine and amide oxidation reactions. Exploring the mechanisms utilized by nature to produce its vast array of natural products is a subject of considerable interest and can lead to the discovery of unique biochemical activities.
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Affiliation(s)
- Gwen Tjallinks
- Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Marco W Fraaije
- Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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2
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Xu Z, Tian P. Rethinking Biosynthesis of Aclacinomycin A. Molecules 2023; 28:molecules28062761. [PMID: 36985733 PMCID: PMC10054333 DOI: 10.3390/molecules28062761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
Aclacinomycin A (ACM-A) is an anthracycline antitumor agent widely used in clinical practice. The current industrial production of ACM-A relies primarily on chemical synthesis and microbial fermentation. However, chemical synthesis involves multiple reactions which give rise to high production costs and environmental pollution. Microbial fermentation is a sustainable strategy, yet the current fermentation yield is too low to satisfy market demand. Hence, strain improvement is highly desirable, and tremendous endeavors have been made to decipher biosynthesis pathways and modify key enzymes. In this review, we comprehensively describe the reported biosynthesis pathways, key enzymes, and, especially, catalytic mechanisms. In addition, we come up with strategies to uncover unknown enzymes and improve the activities of rate-limiting enzymes. Overall, this review aims to provide valuable insights for complete biosynthesis of ACM-A.
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3
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WANG M, ZHANG W, WANG N. Covalent flavoproteins: types, occurrence, biogenesis and catalytic mechanisms. Chin J Nat Med 2022; 20:749-760. [DOI: 10.1016/s1875-5364(22)60194-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Indexed: 11/03/2022]
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4
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Yan B, Gao W, Tian L, Wang S, Dong H. Production enhancement of the glycopeptide antibiotic A40926 by an engineered Nonomuraea gerenzanensis strain. Biotechnol Lett 2021; 44:259-269. [PMID: 34826003 DOI: 10.1007/s10529-021-03210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/16/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To improve the production of A40926, a combined strategy of constructing the engineered strain and optimizing the medium was implemented. RESULTS The engineered strain lcu1 with the genetic features of dbv23 deletion and dbv3-dbv20 coexpression increased by 30.6% in the production of A40926, compared to the original strain. In addition, a combined medium called M9 was designed to be further optimized by the central composite design method. The optimized M9 medium was verified to significantly improve the A40926 yield from 257 to 332 mg l-1. CONCLUSIONS The engineered strain lcu1 could significantly promote A40926 production in the optimized M9 medium, which indicated that the polygenic genetic manipulation and the media optimization played an equally important role in increasing the A40926 yield.
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Affiliation(s)
- Bingyu Yan
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Wen Gao
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Li Tian
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Shuai Wang
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China
| | - Huijun Dong
- School of Pharmacy, Liaocheng University, No. 1, Hunan road, Dongchangfu District, Liaocheng, 252000, Shandong, China.
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5
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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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6
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Dong H, Yue X, Yan B, Gao W, Wang S, Li Y. Improved A40926 production from Nonomuraea gerenzanensis using the promoter engineering and the co-expression of crucial genes. J Biotechnol 2020; 324:28-33. [PMID: 32971181 DOI: 10.1016/j.jbiotec.2020.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
The semi-synthetic antibiotic dalbavancin is clinically used in the treatment of severe infections caused by multidrug resistant Gram-positive pathogens. So far, fermentation has still been the only approach for the production of A40926 in the industrial scale, which is used as the precursor of dalbavancin and biosynthesized by the rare actinomycete Nonomuraea gerenzanensis (N. gerenzanensis). Therefore, it is particularly essential and necessary to enhance the yield of A40926 continually. In this paper, we firstly assessed the activity of 6 heterologous promoters using the enhanced green fluorescence protein (EGFP) reporter system in N. gerenzanensis. Furthermore, the strongest constitutive promoter gapdh confirmed in this study was applied to separately overexpress the total of ten dbv genes involved in the A40926 biosynthesis. PCR and RT-qPCR were successively carried out to verify the mutant and the overexpression of dbv genes. As a consequence, the overexpression of dbv3 and dbv20 genes both increased the A40926 production remarkably. Based on the above consequences, a mutant strain named N320 laboring the co-expression of dbv3 and dbv20 was constructed. The results of fermentation showed that the N320 strain enhanced the yield of A40926 from 163 mg/L to 272 mg/L.
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Affiliation(s)
- Huijun Dong
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China.
| | - Xue Yue
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Bingyu Yan
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Wen Gao
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Shuai Wang
- School of Pharmacy, Liaocheng University, 1 Hunan Road, Liaocheng, Shandong 252000, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
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Marschall E, Cryle MJ, Tailhades J. Biological, chemical, and biochemical strategies for modifying glycopeptide antibiotics. J Biol Chem 2019; 294:18769-18783. [PMID: 31672921 DOI: 10.1074/jbc.rev119.006349] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the discovery of vancomycin in the 1950s, the glycopeptide antibiotics (GPAs) have been of great interest to the scientific community. These nonribosomally biosynthesized peptides are highly cross-linked, often glycosylated, and inhibit bacterial cell wall assembly by interfering with peptidoglycan synthesis. Interest in glycopeptide antibiotics covers many scientific disciplines, due to their challenging total syntheses, complex biosynthesis pathways, mechanism of action, and high potency. After intense efforts, early enthusiasm has given way to a recognition of the challenges in chemically synthesizing GPAs and of the effort needed to study and modify GPA-producing strains to prepare new GPAs to address the increasing threat of microbial antibiotic resistance. Although the preparation of GPAs, either by modifying the pendant groups such as saccharides or by functionalizing the N- or C-terminal moieties, is readily achievable, the peptide core of these molecules-the GPA aglycone-remains highly challenging to modify. This review aims to present a summary of the results of GPA modification obtained with the three major approaches developed to date: in vivo strain manipulation, total chemical synthesis, and chemoenzymatic synthesis methods.
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Affiliation(s)
- Edward Marschall
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.
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8
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Alt S, Bernasconi A, Sosio M, Brunati C, Donadio S, Maffioli SI. Toward Single-Peak Dalbavancin Analogs through Biology and Chemistry. ACS Chem Biol 2019; 14:356-360. [PMID: 30830742 DOI: 10.1021/acschembio.9b00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycopeptide antibiotics are used to treat severe multidrug resistant infections caused by Gram-positive bacteria. Dalbavancin is a second generation glycopeptide approved for human use, which is obtained from A40926, a lipoglycopeptide produced by Nonomuraea sp. ATCC39727 as a mixture of biologically active congeners mainly differing in the fatty acid chains present on the glucuronic moiety. In this study, we constructed a double mutant of the A40926 producer strain lacking dbv23, and thus defective in mannose acetylation, a feature that increases A40926 production, and lacking the acyltransferases Dbv8, and thus incapable of installing the fatty acid chains. The double mutant afforded the desired deacyl, deacetyl A40926 intermediates, which could be converted by chemical reacylation yielding A40926 analogs with a greatly reduced number of congeners. The newly acylated analogs could then be transformed into dalbavancin analogs possessing the same in vitro properties as the approved drug.
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Affiliation(s)
- Silke Alt
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Margherita Sosio
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | - Sonia I. Maffioli
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
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9
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Huang CM, Lyu SY, Lin KH, Chen CL, Chen MH, Shih HW, Hsu NS, Lo IW, Wang YL, Li YS, Wu CJ, Li TL. Teicoplanin Reprogrammed with the N-Acyl-Glucosamine Pharmacophore at the Penultimate Residue of Aglycone Acquires Broad-Spectrum Antimicrobial Activities Effectively Killing Gram-Positive and -Negative Pathogens. ACS Infect Dis 2019; 5:430-442. [PMID: 30599088 DOI: 10.1021/acsinfecdis.8b00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipoglycopeptide antibiotics, for example, teicoplanin (Tei) and A40926, are more potent than vancomycin against Gram-positive (Gram-(+)) drug-resistant pathogens, for example, methicillin-resistant Staphylococcus aureus (MRSA). To extend their therapeutic effectiveness on vancomycin-resistant S. aureus (VRSA), the biosynthetic pathway of the N-acyl glucosamine (Glc) pharmacophore at residue 4 (r4) of teicoplanin pseudoaglycone redirection to residue 6 (r6) was attempted. On the basis of crystal structures, two regioselective biocatalysts Orf2*T (a triple-mutation mutant S98A/V121A/F193Y) and Orf11*S (a single-mutation mutant W163A) were engineered, allowing them to act on GlcNAc at r6. New analogs thereby made show marked antimicrobial activity against MRSA and VRSA by 2-3 orders of magnitude better than teicoplanin and vancomycin. The lipid side chain of the Tei-analogs armed with a terminal mono- or diguanidino group extends the antimicrobial specificity from Gram-(+) to Gram-negative (Gram-(-)), comparable to that of kanamycin. In addition to low cytotoxicity and high safety, the Tei analogs exhibit new modes of action as a result of resensitization of VRSA and Acinetobacter baumannii. The redirection of the biosynthetic pathway for the N-acyl-Glc pharmacophore from r4 to r6 bodes well for large-scale production of selected r6,Tei congeners in an environmentally friendly synthetic biology approach.
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Affiliation(s)
- Chun-Man Huang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
- Department of Microbiology and Immunology, National Yang-Ming University, 155 Linong Street, Section 2,
Beitou, Taipei 11221, Taiwan
| | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Mei-Hua Chen
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Hao-Wei Shih
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chang-Jer Wu
- National Taiwan Ocean University, 2 Peining Road, Jhongjhong, Keelung 20224, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
- National Chung-Hsing University, 145 Xingda Road, South Taichung 402, Taiwan
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10
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Guo L, Wang H, Wang Y, Feng L. Facile core–shell nanoparticles with controllable antibacterial activity assembled by chemical and biological molecules. Biomater Sci 2019; 7:5528-5534. [DOI: 10.1039/c9bm01367a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A newly switchable antibacterial self-assembly was developed by conjugated polymer nanoparticles, DNA, Hoechst 33258 and deoxyribonuclease I.
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Affiliation(s)
- Lixia Guo
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| | - Haoping Wang
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| | - Yunxia Wang
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| | - Liheng Feng
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
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11
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Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era. Biotechnol Adv 2018; 36:534-554. [PMID: 29454983 DOI: 10.1016/j.biotechadv.2018.02.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
Abstract
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.
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12
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Ewing TA, Fraaije MW, Mattevi A, van Berkel WJ. The VAO/PCMH flavoprotein family. Arch Biochem Biophys 2017; 632:104-117. [DOI: 10.1016/j.abb.2017.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/26/2017] [Accepted: 06/29/2017] [Indexed: 01/15/2023]
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13
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Song LQ, Zhang YY, Pu JY, Tang MC, Peng C, Tang GL. Catalysis of Extracellular Deamination by a FAD-Linked Oxidoreductase after Prodrug Maturation in the Biosynthesis of Saframycin A. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Li-Qiang Song
- Key Laboratory of Bio-organic and Natural Products Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences (CAS); Shanghai 200032 China
| | - Ying-Ying Zhang
- Key Laboratory of Bio-organic and Natural Products Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences (CAS); Shanghai 200032 China
| | - Jin-Yue Pu
- Key Laboratory of Bio-organic and Natural Products Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences (CAS); Shanghai 200032 China
| | - Man-Cheng Tang
- Key Laboratory of Bio-organic and Natural Products Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences (CAS); Shanghai 200032 China
| | - Chao Peng
- National Center for Protein Science (Shanghai); Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences, CAS; Shanghai 200031 China
| | - Gong-Li Tang
- Key Laboratory of Bio-organic and Natural Products Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences (CAS); Shanghai 200032 China
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14
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Ewing TA, Nguyen QT, Allan RC, Gygli G, Romero E, Binda C, Fraaije MW, Mattevi A, van Berkel WJH. Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase. J Biol Chem 2017; 292:14668-14679. [PMID: 28717004 DOI: 10.1074/jbc.m117.778449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
A number of oxidoreductases from the VAO/para-cresol methylhydroxylase flavoprotein family catalyze the oxidation of para-substituted phenols. One of the best-studied is vanillyl-alcohol oxidase (VAO) from the fungus Penicillium simplicissimum For oxidation of phenols by VAO to occur, they must first be bound in the active site of the enzyme in their phenolate anion form. The crystal structure of VAO reveals that two tyrosine residues, Tyr-108 and Tyr-503, are positioned to facilitate this deprotonation. To investigate their role in catalysis, we created three VAO variants, Y108F, Y503F, and Y108F/Y503F, and studied their biochemical properties. Steady-state kinetics indicated that the presence of at least one of the tyrosine residues is essential for efficient catalysis by VAO. Stopped-flow kinetics revealed that the reduction of VAO by chavicol or vanillyl alcohol occurs at two different rates: kobs1, which corresponds to its reaction with the deprotonated form of the substrate, and kobs2, which corresponds to its reaction with the protonated form of the substrate. In Y108F, Y503F, and Y108F/Y503F, the relative contribution of kobs2 to the reduction is larger than in wild-type VAO, suggesting deprotonation is impaired in these variants. Binding studies disclosed that the competitive inhibitor isoeugenol is predominantly in its deprotonated form when bound to wild-type VAO, but predominantly in its protonated form when bound to the variants. These results indicate that Tyr-108 and Tyr-503 are responsible for the activation of substrates in VAO, providing new insights into the catalytic mechanism of VAO and related enzymes that oxidize para-substituted phenols.
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Affiliation(s)
- Tom A Ewing
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Quoc-Thai Nguyen
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.,the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and.,the Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang Street, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Robert C Allan
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Gudrun Gygli
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Elvira Romero
- the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and
| | - Claudia Binda
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Marco W Fraaije
- the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and
| | - Andrea Mattevi
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Willem J H van Berkel
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands,
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15
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Peng R. Promoting active learning of graduate student by deep reading in biochemistry and microbiology pharmacy curriculum. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 45:305-312. [PMID: 28059472 DOI: 10.1002/bmb.21038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/08/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
To promote graduate students' active learning, deep reading of high quality papers was done by graduate students enrolled in biochemistry and microbiology pharmacy curriculum offered by college of life science, Jiangxi Normal University from 2013 to 2015. The number of graduate students, who participated in the course in 2013, 2014, and 2015 were eleven, thirteen and fifteen, respectively. Through deep reading of papers, presentation, and group discussion in the lecture, these graduate students have improved their academic performances effectively, such as literature search, PPT document production, presentation management, specialty document reading, academic inquiry, and analytical and comprehensive ability. The graduate students also have increased their understanding level of frontier research, scientific research methods, and experimental methods. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):305-312, 2017.
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Affiliation(s)
- Ren Peng
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
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16
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Song LQ, Zhang YY, Pu JY, Tang MC, Peng C, Tang GL. Catalysis of Extracellular Deamination by a FAD-Linked Oxidoreductase after Prodrug Maturation in the Biosynthesis of Saframycin A. Angew Chem Int Ed Engl 2017; 56:9116-9120. [PMID: 28561936 DOI: 10.1002/anie.201704726] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/28/2022]
Abstract
The biosynthesis of antibiotics in bacteria is usually believed to be an intracellular process, at the end of which the matured compounds are exported outside the cells. The biosynthesis of saframycin A (SFM-A), an antitumor antibiotic, requires a cryptic fatty acyl chain to guide the construction of a pentacyclic tetrahydroisoquinoline scaffold; however, the follow-up deacylation and deamination steps remain unknown. Herein we demonstrate that SfmE, a membrane-bound peptidase, hydrolyzes the fatty acyl chain to release the amino group; and SfmCy2, a secreted oxidoreductase covalently associated with FAD, subsequently performs an oxidative deamination extracellularly. These results not only fill in the missing steps of SFM-A biosynthesis, but also reveal that a FAD-binding oxidoreductase catalyzes an unexpected deamination reaction through an unconventional extracellular pathway in Streptmyces bacteria.
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Affiliation(s)
- Li-Qiang Song
- Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Ying-Ying Zhang
- Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Jin-Yue Pu
- Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Man-Cheng Tang
- Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Chao Peng
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China
| | - Gong-Li Tang
- Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences (CAS), Shanghai, 200032, China
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17
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The family of berberine bridge enzyme-like enzymes: A treasure-trove of oxidative reactions. Arch Biochem Biophys 2017; 632:88-103. [PMID: 28676375 DOI: 10.1016/j.abb.2017.06.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/18/2022]
Abstract
Biological oxidations form the basis of life on earth by utilizing organic compounds as electron donors to drive the generation of metabolic energy carriers, such as ATP. Oxidative reactions are also important for the biosynthesis of complex compounds, i.e. natural products such as alkaloids that provide vital benefits for organisms in all kingdoms of life. The vitamin B2-derived cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) enable an astonishingly diverse array of oxidative reactions that is based on the versatility of the redox-active isoalloxazine ring. The family of FAD-linked oxidases can be divided into subgroups depending on specific sequence features in an otherwise very similar structural context. The sub-family of berberine bridge enzyme (BBE)-like enzymes has recently attracted a lot of attention due to the challenging chemistry catalyzed by its members and the unique and unusual bi-covalent attachment of the FAD cofactor. This family is the focus of the present review highlighting recent advancements into the structural and functional aspects of members from bacteria, fungi and plants. In view of the unprecedented reaction catalyzed by the family's namesake, BBE from the California poppy, recent studies have provided further insights into nature's treasure chest of oxidative reactions.
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18
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Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics. Biochem Pharmacol 2017; 134:56-73. [DOI: 10.1016/j.bcp.2016.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
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19
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Flieger J, Feder-Kubis J, Tatarczak-Michalewska M, Płazińska A, Madejska A, Swatko-Ossor M. Natural terpene derivatives as new structural task-specific ionic liquids to enhance the enantiorecognition of acidic enantiomers on teicoplanin-based stationary phase by high-performance liquid chromatography. J Sep Sci 2017; 40:2374-2381. [PMID: 28426156 DOI: 10.1002/jssc.201700197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/31/2017] [Accepted: 04/01/2017] [Indexed: 11/06/2022]
Abstract
We present the specific cooperative effect of a semisynthetic glycopeptide antibiotic teicoplanin and chiral ionic liquids containing the (1R,2S,5R)-(-)-menthol moiety on the chiral recognition of enantiomers of mandelic acid, vanilmandelic acid, and phenyllactic acid. Experiments were performed chromatographically on an Astec Chirobiotic T chiral stationary phase applying the mobile phase with the addition of the chiral ionic liquids. The stereoselective binding of enantiomers to teicoplanin in presence of new chiral ionic liquids were evaluated applying thermodynamic measurements and the docking simulations. Both the experimental and theoretical methods revealed that the chiral recognition of enantiomers in the presence of new chiral ionic liquids was enthalpy driven. The changes of the teicoplanin conformation occurring upon binding of the chiral ionic liquids are responsible for the differences in the standard changes in Gibbs energy (ΔG0 ) values obtained for complexes formed by the R and S enantiomers and teicoplanin. Docking simulations revealed the steric adjustment between the chiral ionic liquids cyclohexane ring (chair conformation) and the β-d-glucosamine ring of teicoplanin and additionally hydrophobic interactions between the decanoic aliphatic chain of teicoplanin and the alkyl group of the tested salts. The obtained terpene derivatives can be considered as "structural task-specific ionic liquids" responsible for enhancing the chiral resolution in synergistic systems with two chiral selectors.
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Affiliation(s)
- Jolanta Flieger
- Department of Analytical Chemistry, Medical University of Lublin, Lublin, Poland
| | - Joanna Feder-Kubis
- Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Anita Płazińska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Anna Madejska
- Department of Analytical Chemistry, Medical University of Lublin, Lublin, Poland
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology, Medical University of Lublin, Lublin, Poland
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20
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Bai J, Yan D, Zhang T, Guo Y, Liu Y, Zou Y, Tang M, Liu B, Wu Q, Yu S, Tang Y, Hu Y. A Cascade of Redox Reactions Generates Complexity in the Biosynthesis of the Protein Phosphatase-2 Inhibitor Rubratoxin A. Angew Chem Int Ed Engl 2017; 56:4782-4786. [DOI: 10.1002/anie.201701547] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Daojiang Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Tao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yongzhi Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yunbao Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Zou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Mancheng Tang
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Qiong Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Shishan Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
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21
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Bai J, Yan D, Zhang T, Guo Y, Liu Y, Zou Y, Tang M, Liu B, Wu Q, Yu S, Tang Y, Hu Y. A Cascade of Redox Reactions Generates Complexity in the Biosynthesis of the Protein Phosphatase-2 Inhibitor Rubratoxin A. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Daojiang Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Tao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yongzhi Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yunbao Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Zou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Mancheng Tang
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Qiong Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Shishan Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
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22
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Agirre J. Strategies for carbohydrate model building, refinement and validation. Acta Crystallogr D Struct Biol 2017; 73:171-186. [PMID: 28177313 PMCID: PMC5297920 DOI: 10.1107/s2059798316016910] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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23
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Feder-Kubis J, Flieger J, Tatarczak-Michalewska M, Płazińska A, Madejska A, Swatko-Ossor M. Renewable sources from plants as the starting material for designing new terpene chiral ionic liquids used for the chromatographic separation of acidic enantiomers. RSC Adv 2017. [DOI: 10.1039/c7ra03310a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesis of cheap and natural resources is an important topic in green chemistry.
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Affiliation(s)
- Joanna Feder-Kubis
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Jolanta Flieger
- Department of Analytical Chemistry
- Medical University of Lublin
- 20-093 Lublin
- Poland
| | | | - Anita Płazińska
- Department of Biopharmacy
- Medical University of Lublin
- 093 Lublin
- Poland
| | - Anna Madejska
- Department of Analytical Chemistry
- Medical University of Lublin
- 20-093 Lublin
- Poland
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology
- Medical University of Lublin
- 20-093 Lublin
- Poland
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24
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Yim G, Wang W, Thaker MN, Tan S, Wright GD. How To Make a Glycopeptide: A Synthetic Biology Approach To Expand Antibiotic Chemical Diversity. ACS Infect Dis 2016; 2:642-650. [PMID: 27759388 DOI: 10.1021/acsinfecdis.6b00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Modification of natural product backbones is a proven strategy for the development of clinically useful antibiotics. Such modifications have traditionally been achieved through medicinal chemistry strategies or via in vitro enzymatic activities. In an orthogonal approach, engineering of biosynthetic pathways using synthetic biology techniques can generate chemical diversity. Here we report the use of a minimal teicoplanin class glycopeptide antibiotic (GPA) scaffold expressed in a production-optimized Streptomyces coelicolor strain to expand GPA chemical diversity. Thirteen scaffold-modifying enzymes from 7 GPA biosynthetic gene clusters in different combinations were introduced into S. coelicolor, enabling us to explore the criteria for in-cell GPA modification. These include identifying specific isozymes that tolerate the unnatural GPA scaffold and modifications that prevent or allow further elaboration by other enzymes. Overall, 15 molecules were detected, 9 of which have not been reported previously. Some of these compounds showed activity against GPA-resistant bacteria. This system allows us to observe the complex interplay between substrates and both non-native and native tailoring enzymes in a cell-based system and establishes rules for GPA synthetic biology and subsequent expansion of GPA chemical diversity.
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Affiliation(s)
- Grace Yim
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Wenliang Wang
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Maulik N. Thaker
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Stephanie Tan
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Gerard D. Wright
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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25
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Yushchuk O, Ostash B, Pham TH, Luzhetskyy A, Fedorenko V, Truman AW, Horbal L. Characterization of the Post-Assembly Line Tailoring Processes in Teicoplanin Biosynthesis. ACS Chem Biol 2016; 11:2254-64. [PMID: 27285718 DOI: 10.1021/acschembio.6b00018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Actinoplanes teichomyceticus produces teicoplanin (Tcp), a "last resort" lipoglycopeptide antibiotic used to treat severe multidrug resistant infections such as methicillin-resistant Staphylococcus aureus (MRSA). A number of studies have addressed various steps of Tcp biosynthesis using in vitro assays, although the exact sequence of Tcp peptide core tailoring reactions remained speculative. Here, we describe the generation and analysis of a set of A. teichomyceticus mutant strains that have been used to elucidate the sequence of reactions from the Tcp aglycone to mature Tcp. By combining these results with previously published data, we propose an updated order of post-assembly line tailoring processes in Tcp biosynthesis. We also demonstrate that the acyl-CoA-synthetase Tei13* and the type II thioesterase Tei30* are dispensable for Tcp production. Five Tcp derivatives featuring hitherto undescribed combinations of glycosylation and acylation patterns are described. The generation of strains that produce novel Tcp analogues now provides a platform for the production of additional Tcp-like molecules via combinatorial biosynthesis or chemical derivatization.
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Affiliation(s)
- Oleksandr Yushchuk
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Bohdan Ostash
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Thu H. Pham
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infectious Research (HZI), Saarbrucken, Germany
| | - Victor Fedorenko
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Liliya Horbal
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
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26
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Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae. PLoS One 2016; 11:e0156892. [PMID: 27276217 PMCID: PMC4898691 DOI: 10.1371/journal.pone.0156892] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/21/2016] [Indexed: 01/15/2023] Open
Abstract
Berberine bridge enzyme-like (BBE-like) proteins form a multigene family (pfam 08031), which is present in plants, fungi and bacteria. They adopt the vanillyl alcohol-oxidase fold and predominantly show bi-covalent tethering of the FAD cofactor to a cysteine and histidine residue, respectively. The Arabidopsis thaliana genome was recently shown to contain genes coding for 28 BBE-like proteins, while featuring four distinct active site compositions. We determined the structure of a member of the AtBBE-like protein family (termed AtBBE-like 28), which has an active site composition that has not been structurally and biochemically characterized thus far. The most salient and distinguishing features of the active site found in AtBBE-like 28 are a mono-covalent linkage of a histidine to the 8α-position of the flavin-isoalloxazine ring and the lack of a second covalent linkage to the 6-position, owing to the replacement of a cysteine with a histidine. In addition, the structure reveals the interaction of a glutamic acid (Glu426) with an aspartic acid (Asp369) at the active site, which appear to share a proton. This arrangement leads to the delocalization of a negative charge at the active site that may be exploited for catalysis. The structure also indicates a shift of the position of the isoalloxazine ring in comparison to other members of the BBE-like family. The dioxygen surrogate chloride was found near the C(4a) position of the isoalloxazine ring in the oxygen pocket, pointing to a rapid reoxidation of reduced enzyme by dioxygen. A T-DNA insertional mutant line for AtBBE-like 28 results in a phenotype, that is characterized by reduced biomass and lower salt stress tolerance. Multiple sequence analysis showed that the active site composition found in AtBBE-like 28 is only present in the Brassicaceae, suggesting that it plays a specific role in the metabolism of this plant family.
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27
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Zhu Y, Picard MÈ, Zhang Q, Barma J, Després XM, Mei X, Zhang L, Duvignaud JB, Couture M, Zhu W, Shi R, Zhang C. Flavoenzyme CrmK-mediated substrate recycling in caerulomycin biosynthesis. Chem Sci 2016; 7:4867-4874. [PMID: 30155134 PMCID: PMC6016722 DOI: 10.1039/c6sc00771f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/11/2016] [Indexed: 11/29/2022] Open
Abstract
Biochemical and structural investigations into the flavoenzyme CrmK reveal a substrate recycling/salvaging mechanism in caerulomycin biosynthesis.
Substrate salvage or recycling is common and important for primary metabolism in cells but is rare in secondary metabolism. Herein we report flavoenzyme CrmK-mediated shunt product recycling in the biosynthesis of caerulomycin A (CRM A 1), a 2,2′-bipyridine-containing natural product that is under development as a potent novel immunosuppressive agent. We demonstrated that the alcohol oxidase CrmK, belonging to the family of bicovalent FAD-binding flavoproteins, catalyzed the conversion of an alcohol into a carboxylate via an aldehyde. The CrmK-mediated reactions were not en route to 1 biosynthesis but played an unexpectedly important role by recycling shunt products back to the main pathway of 1. Crystal structures and site-directed mutagenesis studies uncovered key residues for FAD-binding, substrate binding and catalytic activities, enabling the proposal for the CrmK catalytic mechanism. This study provides the first biochemical and structural evidence for flavoenzyme-mediated substrate recycling in secondary metabolism.
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Affiliation(s)
- Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China .
| | - Marie-Ève Picard
- Département de biochimie , de microbiologie et de bio-informatique , PROTEO , Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval , Québec G1V 0A6 , Canada .
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China .
| | - Julie Barma
- Département de biochimie , de microbiologie et de bio-informatique , PROTEO , Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval , Québec G1V 0A6 , Canada .
| | - Xavier Murphy Després
- Département de biochimie , de microbiologie et de bio-informatique , PROTEO , Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval , Québec G1V 0A6 , Canada .
| | - Xiangui Mei
- Key Laboratory of Marine Drugs , Chinese Ministry of Education , School of Medicine and Pharmacy , Ocean University of China , 5 Yushan Road , Qingdao 266003 , China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China .
| | - Jean-Baptiste Duvignaud
- Département de biochimie , de microbiologie et de bio-informatique , PROTEO , Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval , Québec G1V 0A6 , Canada .
| | - Manon Couture
- Département de biochimie , de microbiologie et de bio-informatique , PROTEO , Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval , Québec G1V 0A6 , Canada .
| | - Weiming Zhu
- Key Laboratory of Marine Drugs , Chinese Ministry of Education , School of Medicine and Pharmacy , Ocean University of China , 5 Yushan Road , Qingdao 266003 , China
| | - Rong Shi
- Département de biochimie , de microbiologie et de bio-informatique , PROTEO , Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval , Québec G1V 0A6 , Canada .
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China .
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28
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Gill EE, Franco OL, Hancock REW. Antibiotic adjuvants: diverse strategies for controlling drug-resistant pathogens. Chem Biol Drug Des 2015; 85:56-78. [PMID: 25393203 PMCID: PMC4279029 DOI: 10.1111/cbdd.12478] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/08/2023]
Abstract
The growing number of bacterial pathogens that are resistant to numerous antibiotics is a cause for concern around the globe. There have been no new broad-spectrum antibiotics developed in the last 40 years, and the drugs we have currently are quickly becoming ineffective. In this article, we explore a range of therapeutic strategies that could be employed in conjunction with antibiotics and may help to prolong the life span of these life-saving drugs. Discussed topics include antiresistance drugs, which are administered to potentiate the effects of current antimicrobials in bacteria where they are no longer (or never were) effective; antivirulence drugs, which are directed against bacterial virulence factors; host-directed therapies, which modulate the host's immune system to facilitate infection clearance; and alternative treatments, which include such therapies as oral rehydration for diarrhea, phage therapy, and probiotics. All of these avenues show promise for the treatment of bacterial infections and should be further investigated to explore their full potential in the face of a postantibiotic era.
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Affiliation(s)
- Erin E Gill
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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29
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Bai H, Yuan H, Nie C, Wang B, Lv F, Liu L, Wang S. A Supramolecular Antibiotic Switch for Antibacterial Regulation. Angew Chem Int Ed Engl 2015; 54:13208-13. [PMID: 26307170 DOI: 10.1002/anie.201504566] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/15/2015] [Indexed: 12/14/2022]
Abstract
A supramolecular antibiotic switch is described that can reversibly "turn-on" and "turn-off" its antibacterial activity on demand, providing a proof-of-concept for a way to regulate antibacterial activity of biotics. The switch relies on supramolecular assembly and disassembly of cationic poly(phenylene vinylene) derivative (PPV) with cucurbit[7]uril (CB[7]) to regulate their different interactions with bacteria. This simple but efficient strategy does not require any chemical modification on the active sites of the antibacterial agent, and could also regulate the antibacterial activity of classical antibiotics or photosensitizers in photodynamic therapy. This supramolecular antibiotic switch may be a successful strategy to fight bacterial infections and decrease the emergence of bacterial resistance to antibiotics from a long-term point of view.
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Affiliation(s)
- Haotian Bai
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Huanxiang Yuan
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Chenyao Nie
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Bing Wang
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China).
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China).
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30
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Bai H, Yuan H, Nie C, Wang B, Lv F, Liu L, Wang S. A Supramolecular Antibiotic Switch for Antibacterial Regulation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504566] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Haotian Bai
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Huanxiang Yuan
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Chenyao Nie
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Bing Wang
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences,, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
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31
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Pickl M, Fuchs M, Glueck SM, Faber K. The substrate tolerance of alcohol oxidases. Appl Microbiol Biotechnol 2015; 99:6617-42. [PMID: 26153139 PMCID: PMC4513209 DOI: 10.1007/s00253-015-6699-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/10/2015] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Abstract
Alcohols are a rich source of compounds from renewable sources, but they have to be activated in order to allow the modification of their carbon backbone. The latter can be achieved via oxidation to the corresponding aldehydes or ketones. As an alternative to (thermodynamically disfavoured) nicotinamide-dependent alcohol dehydrogenases, alcohol oxidases make use of molecular oxygen but their application is under-represented in synthetic biotransformations. In this review, the mechanism of copper-containing and flavoprotein alcohol oxidases is discussed in view of their ability to accept electronically activated or non-activated alcohols and their propensity towards over-oxidation of aldehydes yielding carboxylic acids. In order to facilitate the selection of the optimal enzyme for a given biocatalytic application, the substrate tolerance of alcohol oxidases is compiled and discussed: Substrates are classified into groups (non-activated prim- and sec-alcohols; activated allylic, cinnamic and benzylic alcohols; hydroxy acids; sugar alcohols; nucleotide alcohols; sterols) together with suitable alcohol oxidases, their microbial source, relative activities and (stereo)selectivities.
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Affiliation(s)
- Mathias Pickl
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010, Graz, Austria
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32
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Daniel B, Pavkov-Keller T, Steiner B, Dordic A, Gutmann A, Nidetzky B, Sensen CW, van der Graaff E, Wallner S, Gruber K, Macheroux P. Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Plant Cell Wall Metabolism. J Biol Chem 2015; 290:18770-81. [PMID: 26037923 PMCID: PMC4513132 DOI: 10.1074/jbc.m115.659631] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 12/27/2022] Open
Abstract
Plant genomes contain a large number of genes encoding for berberine bridge enzyme (BBE)-like enzymes. Despite the widespread occurrence and abundance of this protein family in the plant kingdom, the biochemical function remains largely unexplored. In this study, we have expressed two members of the BBE-like enzyme family from Arabidopsis thaliana in the host organism Komagataella pastoris. The two proteins, termed AtBBE-like 13 and AtBBE-like 15, were purified, and their catalytic properties were determined. In addition, AtBBE-like 15 was crystallized and structurally characterized by x-ray crystallography. Here, we show that the enzymes catalyze the oxidation of aromatic allylic alcohols, such as coumaryl, sinapyl, and coniferyl alcohol, to the corresponding aldehydes and that AtBBE-like 15 adopts the same fold as vanillyl alcohol oxidase as reported previously for berberine bridge enzyme and other FAD-dependent oxidoreductases. Further analysis of the substrate range identified coniferin, the glycosylated storage form of coniferyl alcohol, as a substrate of the enzymes, whereas other glycosylated monolignols were rather poor substrates. A detailed analysis of the motifs present in the active sites of the BBE-like enzymes in A. thaliana suggested that 14 out of 28 members of the family might catalyze similar reactions. Based on these findings, we propose a novel role of BBE-like enzymes in monolignol metabolism that was previously not recognized for this enzyme family.
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Affiliation(s)
| | - Tea Pavkov-Keller
- the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the ACIB GmbH, 8010 Graz, Austria, and
| | | | - Andela Dordic
- the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the ACIB GmbH, 8010 Graz, Austria, and
| | | | | | - Christoph W Sensen
- Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Eric van der Graaff
- the Section for Crop Sciences, Copenhagen University, 2630 Copenhagen, Denmark
| | | | - Karl Gruber
- the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
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33
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Liu YC, Li YS, Lyu SY, Hsu LJ, Chen YH, Huang YT, Chan HC, Huang CJ, Chen GH, Chou CC, Tsai MD, Li TL. Addendum: Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds. Nat Chem Biol 2015; 11:361. [DOI: 10.1038/nchembio0515-361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Thaker MN, Wright GD. Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity. ACS Synth Biol 2015; 4:195-206. [PMID: 23654249 PMCID: PMC4384835 DOI: 10.1021/sb300092n] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Synthetic
biology offers a new path for the exploitation and improvement
of natural products to address the growing crisis in antibiotic resistance.
All antibiotics in clinical use are facing eventual obsolesce as a
result of the evolution and dissemination of resistance mechanisms,
yet there are few new drug leads forthcoming from the pharmaceutical
sector. Natural products of microbial origin have proven over the
past 70 years to be the wellspring of antimicrobial drugs. Harnessing
synthetic biology thinking and strategies can provide new molecules
and expand chemical diversity of known antibiotic scaffolds to provide
much needed new drug leads. The glycopeptide antibiotics offer paradigmatic
scaffolds suitable for such an approach. We review these strategies
here using the glycopeptides as an example and demonstrate how synthetic
biology can expand antibiotic chemical diversity to help address the
growing resistance crisis.
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Affiliation(s)
- Maulik N. Thaker
- M.G. DeGroote
Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON, L8S 4K1 Canada
| | - Gerard D. Wright
- M.G. DeGroote
Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON, L8S 4K1 Canada
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35
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Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P. Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. FEBS J 2015; 282:3060-74. [PMID: 25619330 DOI: 10.1111/febs.13212] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
UNLABELLED The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes. We have identified an alternative gatekeeper residue that similarly controls dioxygen reactivity in the grass pollen allergen Phl p 4, a member of this superfamily that has glucose dehydrogenase activity and the highest redox potential measured in a flavoenzyme. A substitution at the alternative gatekeeper site (I153V) transformed the enzyme into an efficient oxidase by increasing dioxygen reactivity by a factor of 60,000. An inverse exchange (V169I) in the structurally related berberine bridge enzyme (BBE) decreased its dioxygen reactivity by a factor of 500. Structural and biochemical characterization of these and additional variants showed that our model enzymes possess a cavity that binds an anion and resembles the 'oxyanion hole' in the proximity of the flavin ring. We showed also that steric control of access to this site is the most important parameter affecting dioxygen reactivity in BBE-like enzymes. Analysis of flavin-dependent oxidases from other superfamilies revealed similar structural features, suggesting that dioxygen reactivity may be governed by a common mechanistic principle. DATABASE Structural data are available in PDB database under the accession numbers 4PVE, 4PVH, 4PVJ, 4PVK, 4PWB, 4PWC and 4PZF.
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Affiliation(s)
- Domen Zafred
- Institute of Biochemistry, Graz University of Technology, Austria.,Institute of Molecular Biosciences, University of Graz, Austria
| | - Barbara Steiner
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Altijana Hromic
- Institute of Molecular Biosciences, University of Graz, Austria
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | | | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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36
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Yoganathan S, Miller SJ. Structure diversification of vancomycin through peptide-catalyzed, site-selective lipidation: a catalysis-based approach to combat glycopeptide-resistant pathogens. J Med Chem 2015; 58:2367-77. [PMID: 25671771 DOI: 10.1021/jm501872s] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of antibiotic-resistant infections highlights the need for novel antibiotic leads, perhaps with a broader spectrum of activity. Herein, we disclose a semisynthetic, catalytic approach for structure diversification of vancomycin. We have identified three unique peptide catalysts that exhibit site-selectivity for the lipidation of the aliphatic hydroxyls on vancomycin, generating three new derivatives 9a, 9b, and 9c. Incorporation of lipid chains into the vancomycin scaffold provides promising improvement of its bioactivity against vancomycin-resistant enterococci (Van A and Van B phenotypes of VRE). The MICs for 9a, 9b, and 9c against MRSA and VRE (Van B phenotype) range from 0.12 to 0.25 μg/mL. We have also performed a structure-activity relationship (SAR) study to investigate the effect of lipid chain length at the newly accessible G4-OH derivatization site.
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Affiliation(s)
- Sabesan Yoganathan
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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37
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Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
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Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
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38
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Lyu SY, Liu YC, Chang CY, Huang CJ, Chiu YH, Huang CM, Hsu NS, Lin KH, Wu CJ, Tsai MD, Li TL. Multiple complexes of long aliphatic N-acyltransferases lead to synthesis of 2,6-diacylated/2-acyl-substituted glycopeptide antibiotics, effectively killing vancomycin-resistant enterococcus. J Am Chem Soc 2014; 136:10989-95. [PMID: 25095906 DOI: 10.1021/ja504125v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Teicoplanin A2-2 (Tei)/A40926 is the last-line antibiotic to treat multidrug-resistant Gram-positive bacterial infections, e.g., methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococcus (VRE). This class of antibiotics is powered by the N-acyltransferase (NAT) Orf11*/Dbv8 through N-acylation on glucosamine at the central residue of Tei/A40926 pseudoaglycone. The NAT enzyme possesses enormous value in untapped applications; its advanced development is hampered largely due to a lack of structural information. In this report, we present eight high-resolution X-ray crystallographic unary, binary, and ternary complexes in order to decipher the molecular basis for NAT's functionality. The enzyme undergoes a multistage conformational change upon binding of acyl-CoA, thus allowing the uploading of Tei pseudoaglycone to enable the acyl-transfer reaction to take place in the occlusion between the N- and C-halves of the protein. The acyl moiety of acyl-CoA can be bulky or lengthy, allowing a large extent of diversity in new derivatives that can be formed upon its transfer. Vancomycin/synthetic acyl-N-acetyl cysteamine was not expected to be able to serve as a surrogate for an acyl acceptor/donor, respectively. Most strikingly, NAT can catalyze formation of 2-N,6-O-diacylated or C6→C2 acyl-substituted Tei analogues through an unusual 1,4-migration mechanism under stoichiometric/solvational reaction control, wherein selected representatives showed excellent biological activities, effectively counteracting major types (VanABC) of VRE.
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Affiliation(s)
- Syue-Yi Lyu
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
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39
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Zou XW, Liu YC, Hsu NS, Huang CJ, Lyu SY, Chan HC, Chang CY, Yeh HW, Lin KH, Wu CJ, Tsai MD, Li TL. Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. ACTA ACUST UNITED AC 2014; 70:1549-60. [PMID: 24914966 DOI: 10.1107/s1399004714005239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.
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Affiliation(s)
- Xiao-Wei Zou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiu-Chien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-Daw Tsai
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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40
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Yan Y, Chen J, Zhang L, Zheng Q, Han Y, Zhang H, Zhang D, Awakawa T, Abe I, Liu W. Multiplexing of Combinatorial Chemistry in Antimycin Biosynthesis: Expansion of Molecular Diversity and Utility. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305569] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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41
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Yan Y, Chen J, Zhang L, Zheng Q, Han Y, Zhang H, Zhang D, Awakawa T, Abe I, Liu W. Multiplexing of Combinatorial Chemistry in Antimycin Biosynthesis: Expansion of Molecular Diversity and Utility. Angew Chem Int Ed Engl 2013; 52:12308-12. [DOI: 10.1002/anie.201305569] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/21/2013] [Indexed: 12/19/2022]
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42
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Zafred D, Nandy A, Pump L, Kahlert H, Keller W. Crystal structure and immunologic characterization of the major grass pollen allergen Phl p 4. J Allergy Clin Immunol 2013; 132:696-703.e10. [DOI: 10.1016/j.jaci.2013.03.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 03/09/2013] [Accepted: 03/19/2013] [Indexed: 11/27/2022]
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43
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Pathak TP, Miller SJ. Chemical tailoring of teicoplanin with site-selective reactions. J Am Chem Soc 2013; 135:8415-22. [PMID: 23692563 DOI: 10.1021/ja4038998] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Semisynthesis of natural product derivatives combines the power of fermentation with orthogonal chemical reactions. Yet, chemical modification of complex structures represents an unmet challenge, as poor selectivity often undermines efficiency. The complex antibiotic teicoplanin eradicates bacterial infections. However, as resistance emerges, the demand for improved analogues grows. We have discovered chemical reactions that achieve site-selective alteration of teicoplanin. Utilizing peptide-based additives that alter reaction selectivities, certain bromo-teicoplanins are accessible. These new compounds are also scaffolds for selective cross-coupling reactions, enabling further molecular diversification. These studies enable two-step access to glycopeptide analogues not available through either biosynthesis or rapid total chemical synthesis alone. The new compounds exhibit a spectrum of activities, revealing that selective chemical alteration of teicoplanin may lead to analogues with attenuated or enhanced antibacterial properties, in particular against vancomycin- and teicoplanin-resistant strains.
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Affiliation(s)
- Tejas P Pathak
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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44
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Economou NJ, Zentner IJ, Lazo E, Jakoncic J, Stojanoff V, Weeks SD, Grasty KC, Cocklin S, Loll PJ. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:520-33. [PMID: 23519660 PMCID: PMC3606034 DOI: 10.1107/s0907444912050469] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/11/2012] [Indexed: 11/10/2022]
Abstract
Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a D-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein-peptide-antibiotic complex. The 2.05 Å resolution MBP-peptide-teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.
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Affiliation(s)
- Nicoleta J Economou
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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45
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Abstract
Riboflavin-based coenzymes, tightly bound to enzymes catalyzing substrate oxidations and reductions, enable an enormous range of chemical transformations in biosynthetic pathways. Flavoenzymes catalyze substrate oxidations involving amine and alcohol oxidations and desaturations to olefins, the latter setting up Diels-Alder cyclizations in lovastatin and solanapyrone biosyntheses. Both C(4a) and N(5) of the flavin coenzymes are sites for covalent adduct formation. For example, the reactivity of dihydroflavins with molecular oxygen leads to flavin-4a-OOH adducts which then carry out a diverse range of oxygen transfers, including Baeyer-Villiger type ring expansions, olefin epoxidations, halogenations via transient HOCl generation, and an oxidative Favorskii rerrangement during enterocin assembly.
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA.
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46
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Wu HC, Li YS, Liu YC, Lyu SY, Wu CJ, Li TL. Chain elongation and cyclization in type III PKS DpgA. Chembiochem 2012; 13:862-71. [PMID: 22492619 DOI: 10.1002/cbic.201200051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chain elongation and cyclization of precursors of dihydroxyphenylacetyl-CoA (DPA-CoA) catalyzed by the bacterial type III polyketide synthase DpgA were studied. Two labile intermediates, di- and tri-ketidyl-CoA (DK- and TK-CoA), were proposed and chemically synthesized. In the presence of DpgABD, each of these with [(13)C(3)]malonyl-CoA (MA-CoA) was able to form partially (13)C-enriched DPA-CoA. By NMR and MS analysis, the distribution of (13)C atoms in the partially (13)C-enriched DPA-CoA shed light on how the polyketide chain elongates and cyclizes in the DpgA-catalyzed reaction. Polyketone intermediates elongate in a manner different from that which had been believed: two molecules of DK-CoA, or one DK-CoA plus one acetoacetyl-CoA (AA-CoA), but not two molecules of AA-CoA can form one molecule of DPA-CoA. As a result, polyketidyl-CoA serves as both the starter and extender, whereas polyketone-CoA without the terminal carboxyl group can only act as an extender. The terminal carboxyl group is crucial for the cyclization that likely takes place on CoA.
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Affiliation(s)
- Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, PR China
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47
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Peltier-Pain P, Marchillo K, Zhou M, Andes DR, Thorson JS. Natural product disaccharide engineering through tandem glycosyltransferase catalysis reversibility and neoglycosylation. Org Lett 2012; 14:5086-9. [PMID: 22984807 PMCID: PMC3489467 DOI: 10.1021/ol3023374] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A two-step strategy for disaccharide modulation using vancomycin as a model is reported. The strategy relies upon a glycosyltransferase-catalyzed 'reverse' reaction to enable the facile attachment of an alkoxyamine-bearing sugar to the vancomycin core. Neoglycosylation of the corresponding aglycon led to a novel set of vancomycin 1,6-disaccharide variants. While the in vitro antibacterial properties of corresponding vancomycin 1,6-disaccharide analogs were equipotent to the parent antibiotic, the chemoenzymatic method presented is expected to be broadly applicable.
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Affiliation(s)
- Pauline Peltier-Pain
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for Natural Products Research, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
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Huang TH, Peng HJ, Su SN, Liaw SH. Various cross-reactivity of the grass pollen group 4 allergens: crystallographic study of the Bermuda grass isoallergen Cyn d 4. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1303-10. [DOI: 10.1107/s0907444912027552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/18/2012] [Indexed: 11/11/2022]
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Sulfonation of glycopeptide antibiotics by sulfotransferase StaL depends on conformational flexibility of aglycone scaffold. Proc Natl Acad Sci U S A 2012; 109:11824-9. [PMID: 22753479 DOI: 10.1073/pnas.1205377109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although glycopeptide antibiotics (GPAs), including vancomycin and teicoplanin, represent the most important class of anti-infective agents in the treatment of serious gram-positive bacterial infections, their usefulness is threatened by the emergence of resistant strains. GPAs are complex natural products consisting of a heptapeptide skeleton assembled via nonribosomal peptide synthesis and constrained through multiple crosslinks, with diversity resulting from enzymatic modifications by a variety of tailoring enzymes, which can be used to produce GPA analogues that could overcome antibiotic resistance. GPA-modifying sulfotransferases are promising tools for generating the unique derivatives. Despite significant sequence and structural similarities, these sulfotransferases modify distinct side chains on the GPA scaffold. To provide insight into the spatial diversity of modifications, we have determined the crystal structure of the ternary complex of bacterial sulfotransferase StaL with the cofactor product 3'-phosphoadenosine 5'-phosphate and desulfo-A47934 aglycone substrate. Desulfo-A47934 binds with the hydroxyl group on the 4-hydroxyphenylglycine in residue 1 directed toward the 3'-phosphoadenosine 5'-phosphate and hydrogen-bonded to the catalytic His67. Homodimeric StaL can accommodate GPA substrate in only one of the two active sites because of potential steric clashes. Importantly, the aglycone substrate demonstrates a flattened conformation, in contrast to the cup-shaped structures observed previously. Analysis of the conformations of this scaffold showed that despite the apparent rigidity due to crosslinking between the side chains, the aglycone scaffold displays substantial flexibility, important for enzymatic modifications by the GPA-tailoring enzymes. We also discuss the potential of using the current structural information in generating unique GPA derivatives.
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Condurso HL, Bruner SD. Structure guided approaches toward exploiting and manipulating nonribosomal peptide and polyketide biosynthetic pathways. Curr Opin Chem Biol 2012; 16:162-9. [DOI: 10.1016/j.cbpa.2012.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 11/28/2022]
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