1
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Fiedler J, Trottmann F, Ishida K, Ishida-Ito M, Hertweck C. Direct α-Hydroxy Acid Loading onto a Bacterial Thiotemplate Assembly Line via a Multienzyme Gateway. Angew Chem Int Ed Engl 2024; 63:e202405165. [PMID: 38728443 DOI: 10.1002/anie.202405165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/12/2024]
Abstract
Various nonribosomal peptide synthetases (NRPSs) create structural and functional diversity by incorporating α-hydroxy acids into peptide backbones. Trigonic acid, an unusual cyclopropanol-substituted hydroxy acid, is the source of the molecular warhead of malleicyprol, a critical virulence factor of human and animal pathogens of the Burkholderia pseudomallei (BP) group. The process of selecting and loading this building block remained enigmatic as the NRPS module designated for this task is incomplete. Using a combination of bioinformatics, mutational analyses, targeted metabolomics, and in vitro biochemical assays, we show that two trans-acting enzymes are required to load this central building block onto the modular assembly line. An adenylation-thiolation didomain enzyme (BurJ) activates trigonic acid, followed by the translocation of the enzyme-bound α-hydroxy acid thioester by an FkbH-like protein with a mutated phosphatase domain (BurH). This specialized gateway is the first reported direct loading of an α-hydroxy acid onto a bona fide NRPS module in bacteria and expands the synthetic biology toolbox for the site-specific incorporation of non-canonical building blocks. Moreover, insight into the biochemical basis of virulence factor biosynthesis can provide a foundation for developing enzyme inhibitors as anti-virulence therapeutics against BP pathogen infections.
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Affiliation(s)
- Jonas Fiedler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product, Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product, Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product, Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product, Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product, Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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2
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Haq S, Oyler BL, Williams E, Khan MM, Goodlett DR, Bachvaroff T, Place AR. Investigating A Multi-Domain Polyketide Synthase in Amphidinium carterae. Mar Drugs 2023; 21:425. [PMID: 37623706 PMCID: PMC10455422 DOI: 10.3390/md21080425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Dinoflagellates are unicellular organisms that are implicated in harmful algal blooms (HABs) caused by potent toxins that are produced through polyketide synthase (PKS) pathways. However, the exact mechanisms of toxin synthesis are unknown due to a lack of genomic segregation of fat, toxins, and other PKS-based pathways. To better understand the underlying mechanisms, the actions and expression of the PKS proteins were investigated using the toxic dinoflagellate Amphidinium carterae as a model. Cerulenin, a known ketosynthase inhibitor, was shown to reduce acetate incorporation into all fat classes with the toxins amphidinol and sulpho-amphidinol. The mass spectrometry analysis of cerulenin-reacted synthetic peptides derived from ketosynthase domains of A. carterae multimodular PKS transcripts demonstrated a strong covalent bond that could be localized using collision-induced dissociation. One multi-modular PKS sequence present in all dinoflagellates surveyed to date was found to lack an AT domain in toxin-producing species, indicating trans-acting domains, and was shown by Western blotting to be post-transcriptionally processed. These results demonstrate how toxin synthesis in dinoflagellates can be differentiated from fat synthesis despite common underlying pathway.
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Affiliation(s)
- Saddef Haq
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
| | - Benjamin L. Oyler
- University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, MD 21201, USA; (B.L.O.); (M.M.K.)
| | - Ernest Williams
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
| | - Mohd M. Khan
- University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, MD 21201, USA; (B.L.O.); (M.M.K.)
| | - David R. Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8S 1P7, Canada;
| | - Tsvetan Bachvaroff
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
| | - Allen R. Place
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
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3
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Cui F, Fan R, Wang D, Li J, Li T. Research progress on iron uptake pathways and mechanisms of foodborne microorganisms and their application in the food sector. Crit Rev Food Sci Nutr 2023:1-19. [PMID: 37099732 DOI: 10.1080/10408398.2023.2204491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Iron is one of the essential nutrients for almost all microorganisms. Under iron-limited conditions, bacteria can secrete siderophores to the outside world to absorb iron for survival. This process requires the coordinated action of energy-transducing proteins, transporters, and receptors. The spoilage factors of some spoilage bacteria and the pathogenic mechanism of pathogenic bacteria are also closely related to siderophores. Meanwhile, some siderophores have also gradually evolved toward beneficial aspects. First, a variety of siderophores are classified into three aspects. In addition, representative iron uptake systems of Gram-negative and Gram-positive bacteria are described in detail to understand the common and specific pathways of iron uptake by various bacteria. In particular, the causes of siderophore-induced bacterial pathogenicity and the methods and mechanisms of inhibiting bacterial iron absorption under the involvement of siderophores are presented. Then, the application of siderophores in the food sector is mainly discussed, such as improving the food quality of dairy products and meat, inhibiting the attack of pathogenic bacteria on food, improving the plant growth environment, and promoting plant growth. Finally, this review highlights the unresolved fate of siderophores in the iron uptake system and emphasizes further development of siderophore-based substitutes for traditional drugs, new antibiotic-resistance drugs, and vaccines in the food and health sectors.
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Affiliation(s)
- Fangchao Cui
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Rongsen Fan
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Dangfeng Wang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
- College of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianrong Li
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, China
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4
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Basri RS, Rahman RNZRA, Kamarudin NHA, Ali MSM. Carboxylic acid reductases: Structure, catalytic requirements, and applications in biotechnology. Int J Biol Macromol 2023; 240:124526. [PMID: 37080403 DOI: 10.1016/j.ijbiomac.2023.124526] [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: 02/03/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Biocatalysts have been gaining extra attention in recent decades due to their industrial-relevance properties, which may hasten the transition to a cleaner environment. Carboxylic acid reductases (CARs) are large, multi-domain proteins that can catalyze the reduction of carboxylic acids to corresponding aldehydes, with the presence of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). This biocatalytic reaction is of great interest due to the abundance of carboxylic acids in nature and the ability of CAR to convert carboxylic acids to a wide range of aldehydes essentially needed as end products such as vanillin or reaction intermediates for several compounds production such as alcohols, alkanes, and amines. This modular enzyme, found in bacteria and fungi, demands an activation via post-translational modification by the phosphopantetheinyl transferase (PPTase). Recent advances in the characterization and structural studies of CARs revealed valuable information about the enzymes' dynamics, mechanisms, and unique features. In this comprehensive review, we summarize the previous findings on the phylogeny, structural and mechanistic insight of the domains, post-translational modification requirement, strategies for the cofactors regeneration, the extensively broad aldehyde-related industrial application properties of CARs, as well as their recent immobilization approaches.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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5
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Diecker J, Dörner W, Rüschenbaum J, Mootz HD. Unraveling Structural Information of Multi-Domain Nonribosomal Peptide Synthetases by Using Photo-Cross-Linking Analysis with Genetic Code Expansion. Methods Mol Biol 2023; 2670:165-185. [PMID: 37184704 DOI: 10.1007/978-1-0716-3214-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multifunctional enzymes that facilitate the stepwise synthesis of modified peptides, many of which serve as important pharmaceutical products. Typically, NRPSs contain one module for the incorporation of one amino acid into the growing peptide chain. A module consists of the domains required for activation, covalent binding, condensation, termination, and optionally modification of the aminoacyl or peptidyl moiety. We here describe a protocol using genetically encoded photo-cross-linking amino acids to probe the 3D architecture of NRPSs by determining spatial proximity constraints. p-benzoyl-L-phenylalanine (BpF) is incorporated at positions of presumed contact interfaces between domains. The covalent cross-link products are visualized by SDS-PAGE-based methods and precisely mapped by tandem mass spectrometry. Originally intended to study the communication (COM) domains, a special pair of docking domains of unknown structure between two interacting subunits of one NRPS system, this cross-linking approach was also found to be useful to interrogate the spatial proximity of domains that are not connected on the level of the primary structure. The presented photo-cross-linking technique thus provides structural insights complementary to those obtained by protein crystallography and reports on the protein in solution.
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Affiliation(s)
- Julia Diecker
- University of Münster, Institute of Biochemistry, Münster, Germany
| | - Wolfgang Dörner
- University of Münster, Institute of Biochemistry, Münster, Germany
| | | | - Henning D Mootz
- University of Münster, Institute of Biochemistry, Münster, Germany.
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6
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Garvey M. Non-Mammalian Eukaryotic Expression Systems Yeast and Fungi in the Production of Biologics. J Fungi (Basel) 2022; 8:1179. [PMID: 36354946 PMCID: PMC9692369 DOI: 10.3390/jof8111179] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 08/26/2023] Open
Abstract
Biologics have become an important area of medical research generating therapeutics essential for the treatment of many disease states. Biologics are defined as biologically active compounds manufactured by living cells or through biological processes termed bioprocessing. Compared to small molecules which are chemically synthesised they are relatively complex and therapeutically specific molecules. Biologics include hormones, vaccines, blood products, monoclonal antibodies, recombinant therapeutic proteins, enzymes, gene and cellular therapies amongst others. For biologic production prokaryotic and eukaryotic cells (mammalian and non-mammalian) are used as expression systems. Eukaryotic expression systems offer many advantages over prokaryotic based systems. The manufacture of high-quality proteins for human clinical use via recombinant technologies has been achieved in yeast and filamentous fungal systems. Advances in bioprocessing such as genetic engineering, bioreactor design, continuous processing, and quality by design has allowed for increased productivity and higher yield in in these non-mammalian eukaryotic systems with protein translation similar to mammalian systems. The application of eukaryotic expressions systems for the manufacture of biologics of therapeutic importance are described herein.
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Affiliation(s)
- Mary Garvey
- Department of Life Science, Atlantic Technological University, F91 YW50 Sligo, Ireland; ; Tel.: +353-071-9305529
- Centre for Precision Engineering, Materials and Manufacturing Research (PEM), Atlantic Technological University, F91 YW50 Sligo, Ireland
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7
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Richardson SM, Marchetti PM, Herrera MA, Campopiano DJ. Coupled Natural Fusion Enzymes in a Novel Biocatalytic Cascade Convert Fatty Acids to Amines. ACS Catal 2022; 12:12701-12710. [PMID: 36313522 PMCID: PMC9594044 DOI: 10.1021/acscatal.2c02954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/29/2022] [Indexed: 11/28/2022]
Abstract
![]()
Tambjamine YP1 is a pyrrole-containing natural product.
Analysis
of the enzymes encoded in the Pseudoalteromonas tunicata “tam” biosynthetic gene cluster (BGC)
identified a unique di-domain biocatalyst (PtTamH).
Sequence and bioinformatic analysis predicts that PtTamH comprises an N-terminal, pyridoxal 5′-phosphate (PLP)-dependent
transaminase (TA) domain fused to a NADH-dependent C-terminal thioester
reductase (TR) domain. Spectroscopic and chemical analysis revealed
that the TA domain binds PLP, utilizes l-Glu as an amine
donor, accepts a range of fatty aldehydes (C7–C14 with a preference for C12), and produces the
corresponding amines. The previously characterized PtTamA from the “tam” BGC is an ATP-dependent, di-domain
enzyme comprising a class I adenylation domain fused to an acyl carrier
protein (ACP). Since recombinant PtTamA catalyzes
the activation and thioesterification of C12 acid to the holo-ACP domain, we hypothesized that C12 ACP
is the natural substrate for PtTamH. PtTamA and PtTamH were successfully coupled together
in a biocatalytic cascade that converts fatty acids (FAs) to amines
in one pot. Moreover, a structural model of PtTamH
provides insights into how the TA and TR domains are organized. This
work not only characterizes the formation of the tambjamine YP1 tail
but also suggests that PtTamA and PtTamH could be useful biocatalysts for FA to amine functional group
conversion.
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Affiliation(s)
- Shona M. Richardson
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Piera M. Marchetti
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Michael A. Herrera
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Dominic J. Campopiano
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
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8
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Chen H, Zhong L, Zhou H, Sun T, Zhong G, Tu Q, Zhuang Y, Bai X, Wang X, Xu J, Xia L, Shen Y, Zhang Y, Bian X. Biosynthesis of Glidomides and Elucidation of Different Mechanisms for Formation of β-OH Amino Acid Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202203591. [PMID: 35689369 DOI: 10.1002/anie.202203591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/06/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) can incorporate nonproteinogenic amino acids into peptidyl backbones to increase structural diversity. Genome mining of Schlegelella brevitalea led to the identification of a class of linear lipoheptapeptides, glidomides, featuring two unusual residues: threo-β-OH-L-His and threo-β-OH-D-Asp. The β-hydroxylation of Asp and His is catalyzed by the nonheme FeII /α-ketoglutarate-dependent β-hydroxylases GlmD and GlmF, respectively. GlmD independently catalyzes the hydroxylation of L-Asp to primarily produce threo-β-OH-L-Asp on the thiolation domain, and then undergoes epimerization to form threo-β-OH-D-Asp in the final products. However, β-hydroxylation of His requires the concerted action of GlmF and the interface (I) domain, a novel condensation domain family clade. The key sites of I domain for interaction with GlmF were identified, suggesting that the mechanism for hydroxylation of His depends on the collaboration between hydroxylase and NRPS.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yan Zhuang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuemao Shen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
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9
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Chen H, Zhong L, Zhou H, Sun T, Zhong G, Tu Q, Zhuang Y, Bai X, Wang X, Xu J, Xia L, Shen Y, Zhang Y, Bian X. Biosynthesis of Glidomides and Elucidation of Different Mechanisms for Formation of β‐OH Amino Acid Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Yan Zhuang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Xianping Bai
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha 410081 China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha 410081 China
| | - Yuemao Shen
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
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10
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Pedersen TB, Nielsen MR, Kristensen SB, Spedtsberg EML, Sørensen T, Petersen C, Muff J, Sondergaard TE, Nielsen KL, Wimmer R, Gardiner DM, Sørensen JL. Speed dating for enzymes! Finding the perfect phosphopantetheinyl transferase partner for your polyketide synthase. Microb Cell Fact 2022; 21:9. [PMID: 35012550 PMCID: PMC8751348 DOI: 10.1186/s12934-021-01734-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Abstract
The biosynthetic pathways for the fungal polyketides bikaverin and bostrycoidin, from Fusarium verticillioides and Fusarium solani respectively, were reconstructed and heterologously expressed in S. cerevisiae alongside seven different phosphopantetheinyl transferases (PPTases) from a variety of origins spanning bacterial, yeast and fungal origins. In order to gauge the efficiency of the interaction between the ACP-domains of the polyketide synthases (PKS) and PPTases, each were co-expressed individually and the resulting production of target polyketides were determined after 48 h of growth. In co-expression with both biosynthetic pathways, the PPTase from Fusarium verticillioides (FvPPT1) proved most efficient at producing both bikaverin and bostrycoidin, at 1.4 mg/L and 5.9 mg/L respectively. Furthermore, the remaining PPTases showed the ability to interact with both PKS's, except for a single PKS-PPTase combination. The results indicate that it is possible to boost the production of a target polyketide, simply by utilizing a more optimal PPTase partner, instead of the commonly used PPTases; NpgA, Gsp and Sfp, from Aspergillus nidulans, Brevibacillus brevis and Bacillus subtilis respectively.
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Affiliation(s)
- Tobias Bruun Pedersen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | | | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Celine Petersen
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Jens Muff
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Kåre Lehmann Nielsen
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Donald Max Gardiner
- The University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark.
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11
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Sulpizio A, Crawford CEW, Koweek RS, Charkoudian LK. Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways. J Biol Chem 2021; 296:100328. [PMID: 33493513 PMCID: PMC7949117 DOI: 10.1016/j.jbc.2021.100328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/04/2023] Open
Abstract
Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing 'unnatural natural products.' Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.
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Affiliation(s)
- Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | | | - Rebecca S Koweek
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
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12
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Wang R, Tao W, Liu L, Li C, Bai L, Zhao YL, Shi T. Insights into specificity and catalytic mechanism of amphotericin B/nystatin thioesterase. Proteins 2021; 89:558-568. [PMID: 33389775 DOI: 10.1002/prot.26041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/22/2020] [Accepted: 12/27/2020] [Indexed: 11/12/2022]
Abstract
Polyene polyketides amphotericin B (AMB) and nystatin (NYS) are important antifungal drugs. Thioesterases (TEs), located at the last module of PKS, control the release of polyketides by cyclization or hydrolysis. Intrigued by the tiny structural difference between AMB and NYS, as well as the high sequence identity between AMB TE and NYS TE, we constructed four systems to study the structural characteristics, catalytic mechanism, and product release of AMB TE and NYS TE with combined MD simulations and quantum mechanics/molecular mechanics calculations. The results indicated that compared with AMB TE, NYS TE shows higher specificity on its natural substrate and R26 as well as D186 were proposed to a key role in substrate recognition. The energy barrier of macrocyclization in AMB-TE-Amb and AMB-TE-Nys systems were calculated to be 14.0 and 22.7 kcal/mol, while in NYS-TE-Nys and NYS-TE-Amb systems, their energy barriers were 17.5 and 25.7 kcal/mol, suggesting the cyclization with their natural substrates were more favorable than that with exchanged substrates. At last, the binding free energy obtained with the MM-PBSA.py program suggested that it was easier for natural products to leave TE enzymes after cyclization. And key residues to the departure of polyketide product from the active site were highlighted. We provided a catalytic overview of AMB TE and NYS TE including substrate recognition, catalytic mechanism and product release. These will improve the comprehension of polyene polyketide TEs and benefit for broadening the substrate flexibility of polyketide TEs.
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Affiliation(s)
- Rufan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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13
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Kumar P, Pachisia S, Gupta R. Turn-on detection of assorted phosphates by luminescent chemosensors. Inorg Chem Front 2021. [DOI: 10.1039/d1qi00032b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review illustrates a variety of luminescent chemosensors for the selective detection of assorted phosphates via the “Turn-On” emission mechanism with focus on their design aspects, chemical structures and sensing mechanism.
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Affiliation(s)
- Pramod Kumar
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Sanya Pachisia
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Rajeev Gupta
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
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14
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Hei Y, Zhang H, Tan N, Zhou Y, Wei X, Hu C, Liu Y, Wang L, Qi J, Gao JM. Antimicrobial activity and biosynthetic potential of cultivable actinomycetes associated with Lichen symbiosis from Qinghai-Tibet Plateau. Microbiol Res 2020; 244:126652. [PMID: 33310352 DOI: 10.1016/j.micres.2020.126652] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 01/18/2023]
Abstract
Actinobacteria that inhabit lichen symbionts are considered a promising yet previously underexplored source of novel compounds. Here, for the first time, we conducted a comprehensive investigation with regard to strain isolation and identification of lichen-associated actinobacteria from Tibet Plateau, antimicrobial activity screening, biosynthetic genes detection, bioactive metabolites identification and activity prediction. A large number of culturable actinomycetes were isolated from lichens around Qinghai Lake, in Qinghai-Tibet Plateau. Twenty-seven strains with distinct morphological characteristics were preliminarily studied. 16S rRNA gene identification showed that 13 strains were new species. The PCR-screening of specific biosynthetic genes indicated that these 27 isolates had abundant intrinsic biosynthetic potential. The antimicrobial activity experiment screened out some potential biological control antagonistic bacteria. The metabolites of 13 strains of Streptomyces with antibacterial activity were analyzed by LC-HRMS, and further 18 compounds were identified by NMR and / or LC-HRMS. The identified compounds were mainly pyrrolidine and indole derivatives, as well as anthracyclines. Seven compounds were identified with less biological activity, then predicted and evaluated their biological activity. The predicted results showed that compound 2 had excellent inhibitory activity on HIV-1 reverse transcriptase. Overall, the results indicate actinobacteria isolated from unexploited plateau lichen are promising sources of biological active metabolite, which could provide important bioactive compounds as potential antibiotic drugs.
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Affiliation(s)
- Yueyu Hei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China; College of Innovation and Experiment, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Hongli Zhang
- State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Nana Tan
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, Shaanxi, China
| | - Yuhan Zhou
- College of Innovation and Experiment, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Xin Wei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Chenhao Hu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Yuande Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Le Wang
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, Shaanxi, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China; College of Innovation and Experiment, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China.
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
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15
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Wong NK, Zhong S, Li W, Zhou F, Deng Z, Zhou Y. Selective profiling of steviol-catalyzing UDP-glycosyltransferases with a metabolically synthesized probe. Chem Commun (Camb) 2020; 56:12387-12390. [PMID: 32931537 DOI: 10.1039/d0cc04948d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Selective profiling of steviol-catalyzing UDP-glycosyltransferases in plants was accomplished with a probe metabolically synthesized from two substrate-derived components comprising an alkynylated sugar receptor (steviol) module and a diazirine-modified sugar donor (UDP-glucose) module, thereby illustrating a facile approach for harnessing biosynthetic enzymes of natural glycosides in plants for synthetic biology.
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Affiliation(s)
- Nai-Kei Wong
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China.
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16
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Chen N, Liu Y, Li Y, Wang C. Chemical Proteomic Profiling of Protein 4′‐Phosphopantetheinylation in Mammalian Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nan Chen
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yuan Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yuanpei Li
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Chu Wang
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Peking University China
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17
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Chen N, Liu Y, Li Y, Wang C. Chemical Proteomic Profiling of Protein 4′‐Phosphopantetheinylation in Mammalian Cells. Angew Chem Int Ed Engl 2020; 59:16069-16075. [DOI: 10.1002/anie.202004105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Nan Chen
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yuan Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yuanpei Li
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Chu Wang
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Peking University China
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18
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Peng H, Ishida K, Hertweck C. Loss of Single-Domain Function in a Modular Assembly Line Alters the Size and Shape of a Complex Polyketide. Angew Chem Int Ed Engl 2019; 58:18252-18256. [PMID: 31595618 PMCID: PMC6916388 DOI: 10.1002/anie.201911315] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 12/14/2022]
Abstract
The structural wealth of complex polyketide metabolites produced by bacteria results from intricate, highly evolved biosynthetic programs of modular assembly lines, in which the number of modules defines the size of the backbone, and the domain composition controls the degree of functionalization. We report a remarkable case where polyketide chain length and scaffold depend on the function of a single β-keto processing domain: A ketoreductase domain represents a switch between diverging biosynthetic pathways leading either to the antifungal aureothin or to the nematicidal luteoreticulin. By a combination of heterologous expression, mutagenesis, metabolite analyses, and in vitro biotransformation we elucidate the factors governing non-colinear polyketide assembly involving module skipping and demonstrate that a simple point mutation in type I polyketide synthase (PKS) can have a dramatic effect on the metabolic profile. This finding sheds new light on possible evolutionary scenarios and may inspire future synthetic biology approaches.
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Affiliation(s)
- Huiyun Peng
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesChair for Natural Product ChemistryFriedrich Schiller University Jena07743JenaGermany
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19
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Peng H, Ishida K, Hertweck C. Loss of Single‐Domain Function in a Modular Assembly Line Alters the Size and Shape of a Complex Polyketide. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Huiyun Peng
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Biological SciencesChair for Natural Product ChemistryFriedrich Schiller University Jena 07743 Jena Germany
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20
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Khater S, Gupta M, Agrawal P, Sain N, Prava J, Gupta P, Grover M, Kumar N, Mohanty D. SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. Nucleic Acids Res 2019; 45:W72-W79. [PMID: 28460065 PMCID: PMC5570206 DOI: 10.1093/nar/gkx344] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/25/2017] [Indexed: 01/05/2023] Open
Abstract
Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS web-server has been a valuable resource for analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters. We have developed an updated version - SBSPKSv2 which is based on comprehensive analysis of sequence, structure and secondary metabolite chemical structure data from 311 experimentally characterized PKS/NRPS gene clusters with known biosynthetic products. A completely new feature of SBSPKSv2 is the inclusion of features for search in chemical space. It allows the user to compare the chemical structure of a given secondary metabolite to the chemical structures of biosynthetic intermediates and final products. For identification of catalytic domains, SBSPKS now uses profile based searches, which are computationally faster and have high sensitivity. HMM profiles have also been added for a number of new domains and motif information has been used for distinguishing condensation (C), epimerization (E) and cyclization (Cy) domains of NRPS. In summary, the new and updated SBSPKSv2 is a versatile tool for genome mining and analysis of polyketide and non-ribosomal peptide biosynthetic pathways in chemical space. The server is available at: http://www.nii.ac.in/sbspks2.html.
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Affiliation(s)
- Shradha Khater
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Money Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priyesh Agrawal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neetu Sain
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jyoti Prava
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priya Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mansi Grover
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Narendra Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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21
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Nielsen MR, Sondergaard TE, Giese H, Sørensen JL. Advances in linking polyketides and non-ribosomal peptides to their biosynthetic gene clusters in Fusarium. Curr Genet 2019; 65:1263-1280. [DOI: 10.1007/s00294-019-00998-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/24/2022]
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22
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Shemsi AM, Khanday FA, Qurashi A, Khalil A, Guerriero G, Siddiqui KS. Site-directed chemically-modified magnetic enzymes: fabrication, improvements, biotechnological applications and future prospects. Biotechnol Adv 2019; 37:357-381. [DOI: 10.1016/j.biotechadv.2019.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/13/2019] [Accepted: 02/08/2019] [Indexed: 02/08/2023]
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23
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Yan Q, Pfleger BF. Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals. Metab Eng 2019; 58:35-46. [PMID: 31022535 DOI: 10.1016/j.ymben.2019.04.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/20/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023]
Abstract
Microbial production of oleochemicals from renewable feedstocks remains an attractive route to produce high-energy density, liquid transportation fuels and high-value chemical products. Metabolic engineering strategies have been applied to demonstrate production of a wide range of oleochemicals, including free fatty acids, fatty alcohols, esters, olefins, alkanes, ketones, and polyesters in both bacteria and yeast. The majority of these demonstrations synthesized products containing long-chain fatty acids. These successes motivated additional effort to produce analogous molecules comprised of medium-chain fatty acids, molecules that are less common in natural oils and therefore of higher commercial value. Substantial progress has been made towards producing a subset of these chemicals, but significant work remains for most. The other primary challenge to producing oleochemicals in microbes is improving the performance, in terms of yield, rate, and titer, of biocatalysts such that economic large-scale processes are feasible. Common metabolic engineering strategies include blocking pathways that compete with synthesis of oleochemical building blocks and/or consume products, pulling flux through pathways by removing regulatory signals, pushing flux into biosynthesis by overexpressing rate-limiting enzymes, and engineering cells to tolerate the presence of oleochemical products. In this review, we describe the basic fundamentals of oleochemical synthesis and summarize advances since 2013 towards improving performance of heterotrophic microbial cell factories.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
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24
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Itoh H, Inoue M. Comprehensive Structure–Activity Relationship Studies of Macrocyclic Natural Products Enabled by Their Total Syntheses. Chem Rev 2019; 119:10002-10031. [DOI: 10.1021/acs.chemrev.9b00063] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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25
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Durand GA, Raoult D, Dubourg G. Antibiotic discovery: history, methods and perspectives. Int J Antimicrob Agents 2019; 53:371-382. [DOI: 10.1016/j.ijantimicag.2018.11.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/12/2018] [Accepted: 11/17/2018] [Indexed: 02/08/2023]
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26
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Ohlemacher SI, Xu Y, Kober DL, Malik M, Nix JC, Brett TJ, Henderson JP. YbtT is a low-specificity type II thioesterase that maintains production of the metallophore yersiniabactin in pathogenic enterobacteria. J Biol Chem 2018; 293:19572-19585. [PMID: 30355735 PMCID: PMC6314147 DOI: 10.1074/jbc.ra118.005752] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/23/2018] [Indexed: 12/20/2022] Open
Abstract
Clinical isolates of Yersinia, Klebsiella, and Escherichia coli frequently secrete the small molecule metallophore yersiniabactin (Ybt), which passivates and scavenges transition metals during human infections. YbtT is encoded within the Ybt biosynthetic operon and is critical for full Ybt production in bacteria. However, its biosynthetic function has been unclear because it is not essential for Ybt production by the in vitro reconstituted nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) pathway. Here, we report the structural and biochemical characterization of YbtT. YbtT structures at 1.4-1.9 Å resolution possess a serine hydrolase catalytic triad and an associated substrate chamber with features similar to those previously reported for low-specificity type II thioesterases (TEIIs). We found that YbtT interacts with the two major Ybt biosynthetic proteins, HMWP1 (high-molecular-weight protein 1) and HMWP2 (high-molecular-weight protein 2), and hydrolyzes a variety of aromatic and acyl groups from their phosphopantetheinylated carrier protein domains. In vivo YbtT titration in uropathogenic E. coli revealed a distinct optimum for Ybt production consistent with a tradeoff between clearing both stalled inhibitory intermediates and productive Ybt precursors from HMWP1 and HMWP2. These results are consistent with a model in which YbtT maintains cellular Ybt biosynthesis by removing nonproductive, inhibitory thioesters that form aberrantly at multiple sites on HMWP1 and HMWP2.
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Affiliation(s)
- Shannon I Ohlemacher
- From the Center for Women's Infectious Diseases Research
- Division of Infectious Diseases
- Department of Internal Medicine, and
| | - Yiquan Xu
- From the Center for Women's Infectious Diseases Research
- Division of Infectious Diseases
- Department of Internal Medicine, and
| | - Daniel L Kober
- Department of Internal Medicine, and
- Division of Pulmonary and Critical Care Medicine
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63110 and
| | - Mahnoor Malik
- From the Center for Women's Infectious Diseases Research
- Division of Infectious Diseases
- Department of Internal Medicine, and
| | - Jay C Nix
- the Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Tom J Brett
- Department of Internal Medicine, and
- Division of Pulmonary and Critical Care Medicine
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63110 and
| | - Jeffrey P Henderson
- From the Center for Women's Infectious Diseases Research,
- Division of Infectious Diseases
- Department of Internal Medicine, and
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27
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Auerbach D, Yan F, Zhang Y, Müller R. Characterization of an Unusual Glycerate Esterification Process in Vioprolide Biosynthesis. ACS Chem Biol 2018; 13:3123-3130. [PMID: 30286293 DOI: 10.1021/acschembio.8b00826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria produce a large number of secondary metabolites with extraordinary chemical structures and bioactivities. Vioprolides are promising anticancer and antifungal lead compounds produced by the myxobacterium Cystobacter violaceus Cb vi35, which are initially synthesized as acylated precursors (previoprolides) by nonribosomal peptide synthetases (NRPS). Here, we describe and characterize an unprecedented glycerate esterification process in the biosynthesis of vioprolides. In vitro biochemical investigations revealed that the fatty acyl chain of previoprolides is adenylated by the starting fatty acyl-AMP ligase (FAAL) domain, while the glycerate moiety is incorporated by the FkbH domain. An unusual ester-bond forming condensation domain is shown responsible for the acylation of glycerate. LC-MS analysis and bioactivity assays suggest that the acylation serves for directed membrane transport rather than representing a prodrug mechanism.
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Affiliation(s)
- David Auerbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao, People’s Republic of China
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
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28
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Kim WE, Patel A, Hur GH, Tufar P, Wuo MG, McCammon JA, Burkart MD. Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases. Chembiochem 2018; 20:147-152. [PMID: 30194895 DOI: 10.1002/cbic.201800439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Indexed: 11/12/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the synthesis of a variety of bioactive natural products with clinical and economic significance. Interestingly, these large multimodular enzyme machineries incorporate nonproteinogenic d-amino acids through the use of auxiliary epimerization domains, converting l-amino acids into d-amino acids that impart into the resulting natural products unique bioactivity and resistance to proteases. Due to the large and complex nature of NRPSs, several questions remain unanswered about the mechanism of the catalytic domain reactions. We have investigated the use of mechanism-based crosslinkers to probe the mechanism of an epimerization domain in gramicidin S biosynthesis. In addition, MD simulations were performed, showcasing the possible roles of catalytic residues within the epimerization domain.
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Affiliation(s)
- Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0636, USA
| | - Gene H Hur
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Peter Tufar
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael G Wuo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0636, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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29
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Yan F, Burgard C, Popoff A, Zaburannyi N, Zipf G, Maier J, Bernauer HS, Wenzel SC, Müller R. Synthetic biology approaches and combinatorial biosynthesis towards heterologous lipopeptide production. Chem Sci 2018; 9:7510-7519. [PMID: 30319751 PMCID: PMC6180311 DOI: 10.1039/c8sc02046a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Synthetic biology techniques coupled with heterologous secondary metabolite production offer opportunities for the discovery and optimisation of natural products.
Synthetic biology techniques coupled with heterologous secondary metabolite production offer opportunities for the discovery and optimisation of natural products. Here we developed a new assembly strategy based on type IIS endonucleases and elaborate synthetic DNA platforms, which could be used to seamlessly assemble and engineer biosynthetic gene clusters (BGCs). By applying this versatile tool, we designed and assembled more than thirty different artificial myxochromide BGCs, each around 30 kb in size, and established heterologous expression platforms using a derivative of Myxococcus xanthus DK1622 as a host. In addition to the five native types of myxochromides (A, B, C, D and S), novel lipopeptide structures were produced by combinatorial exchange of nonribosomal peptide synthetase (NRPS) encoding genes from different myxochromide BGCs. Inspired by the evolutionary diversification of the native myxochromide megasynthetases, the ancestral A-type NRPS was engineered by inactivation, deletion, or duplication of catalytic domains and successfully converted into functional B-, C- and D-type megasynthetases. The constructional design approach applied in this study enables combinatorial engineering of complex synthetic BGCs and has great potential for the exploitation of other natural product biosynthetic pathways.
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Affiliation(s)
- Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Christian Burgard
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Alexander Popoff
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Gregor Zipf
- ATG:biosynthetics GmbH , Weberstraße 40 , 79249 Merzhausen , Germany
| | - Josef Maier
- IStLS - Information Services to Life Sciences , Härlestraße 24/1 , 78727 Oberndorf am Neckar/Boll , Germany
| | - Hubert S Bernauer
- ATG:biosynthetics GmbH , Weberstraße 40 , 79249 Merzhausen , Germany
| | - Silke C Wenzel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
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30
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Abstract
Directed evolution is a powerful technique for generating tailor-made enzymes for a wide range of biocatalytic applications. Following the principles of natural evolution, iterative cycles of mutagenesis and screening or selection are applied to modify protein properties, enhance catalytic activities, or develop completely new protein catalysts for non-natural chemical transformations. This review briefly surveys the experimental methods used to generate genetic diversity and screen or select for improved enzyme variants. Emphasis is placed on a key challenge, namely how to generate novel catalytic activities that expand the scope of natural reactions. Two particularly effective strategies, exploiting catalytic promiscuity and rational design, are illustrated by representative examples of successfully evolved enzymes. Opportunities for extending these approaches to more complex biocatalytic systems are also considered.
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Affiliation(s)
- Cathleen Zeymer
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland;,
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland;,
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31
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A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate. Nat Commun 2018; 9:1780. [PMID: 29725007 PMCID: PMC5934393 DOI: 10.1038/s41467-018-04154-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 02/23/2018] [Indexed: 11/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important family of natural products. Their biosynthesis follows a common scheme in which the leader peptide of a precursor peptide guides the modifications of a single core peptide. Here we describe biochemical studies of the processing of multiple core peptides within a precursor peptide, rare in RiPP biosynthesis. In a cyanobacterial microviridin pathway, an ATP-grasp ligase, AMdnC, installs up to two macrolactones on each of the three core peptides within AMdnA. The enzyme catalysis occurs in a distributive fashion and follows an unstrict N-to-C overall directionality, but a strict order in macrolactonizing each core peptide. Furthermore, AMdnC is catalytically versatile to process unnatural substrates carrying one to four core peptides, and kinetic studies provide insights into its catalytic properties. Collectively, our results reveal a distinct biosynthetic logic of RiPPs, opening up the possibility of modular production via synthetic biology approaches. Microviridins belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, the authors discover a microviridin-synthesizing enzyme in a cyanobacterium that modifies multiple core peptides from a single substrate in a distributive and unstrictly directional manner, an unusual biosynthetic logic for RiPPs.
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32
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Shi T, Liu L, Tao W, Luo S, Fan S, Wang XL, Bai L, Zhao YL. Theoretical Studies on the Catalytic Mechanism and Substrate Diversity for Macrocyclization of Pikromycin Thioesterase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01156] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Lanxuan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Shuobing Fan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Xiao-Lei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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33
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Reimer JM, Haque AS, Tarry MJ, Schmeing TM. Piecing together nonribosomal peptide synthesis. Curr Opin Struct Biol 2018; 49:104-113. [DOI: 10.1016/j.sbi.2018.01.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/08/2018] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
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34
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Chen M, Pang B, Du YN, Zhang YP, Liu W. Characterization of the metallo-dependent amidohydrolases responsible for "auxiliary" leucinyl removal in the biosynthesis of 2,2'-bipyridine antibiotics. Synth Syst Biotechnol 2017; 2:137-146. [PMID: 29062971 PMCID: PMC5636949 DOI: 10.1016/j.synbio.2017.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 01/11/2023] Open
Abstract
2,2'-Bipyridine (2,2'-BiPy) is an attractive core structure present in a number of biologically active natural products, including the structurally related antibiotics caerulomycins (CAEs) and collismycins (COLs). Their biosynthetic pathways share a similar key 2,2'-BiPy-l-leucine intermediate, which is desulfurated or sulfurated at C5, arises from a polyketide synthase/nonribosomal peptide synthetase hybrid assembly line. Focusing on the common off-line modification steps, we here report that the removal of the "auxiliary" l-leucine residue relies on the metallo-dependent amidohydrolase activity of CaeD or ColD. This activity leads to the production of similar 2,2'-BiPy carboxylate products that then receive an oxime functionality that is characteristic for both CAEs and COLs. Unlike many metallo-dependent amidohydrolase superfamily proteins that have been previously reported, these proteins (particularly CaeD) exhibited a strong zinc ion-binding capacity that was proven by site-specific mutagenesis studies to be essential to proteolytic activity. The kinetics of the conversions that respectively involve CaeD and ColD were analyzed, showing the differences in the efficiency and substrate specificity of these two proteins. These findings would generate interest in the metallo-dependent amidohydrolase superfamily proteins that are involved in the biosynthesis of bioactive natural products.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Nature Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Bo Pang
- State Key Laboratory of Bioorganic and Nature Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ya-Nan Du
- State Key Laboratory of Bioorganic and Nature Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yi-Peng Zhang
- State Key Laboratory of Bioorganic and Nature Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Nature Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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35
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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36
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Britton J, Dyer RP, Majumdar S, Raston CL, Weiss GA. Ten-Minute Protein Purification and Surface Tethering for Continuous-Flow Biocatalysis. Angew Chem Int Ed Engl 2017; 56:2296-2301. [PMID: 28133915 PMCID: PMC5480406 DOI: 10.1002/anie.201610821] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/20/2016] [Indexed: 11/07/2022]
Abstract
Nature applies enzymatic assembly lines to synthesize bioactive compounds. Inspired by such capabilities, we have developed a facile method for spatially segregating attached enzymes in a continuous-flow, vortex fluidic device (VFD). Fused Hisn -tags at the protein termini allow rapid bioconjugation and consequent purification through complexation with immobilized metal affinity chromatography (IMAC) resin. Six proteins were purified from complex cell lysates to average homogeneities of 76 %. The most challenging to purify, tobacco epi-aristolochene synthase, was purified in only ten minutes from cell lysate to near homogeneity (>90 %). Furthermore, this "reaction-ready" system demonstrated excellent stability during five days of continuous-flow processing. Towards multi-step transformations in continuous flow, proteins were arrayed as ordered zones on the reactor surface allowing segregation of catalysts. Ordering enzymes into zones opens up new opportunities for continuous-flow biosynthesis.
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Affiliation(s)
- Joshua Britton
- Departments of Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-2025, USA
- Centre for NanoScale Science and Technology, Flinders University, Bedford Park, Adelaide, 5001, Australia
| | - Rebekah P Dyer
- Departments of Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-2025, USA
| | - Sudipta Majumdar
- Departments of Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-2025, USA
| | - Colin L Raston
- Centre for NanoScale Science and Technology, Flinders University, Bedford Park, Adelaide, 5001, Australia
| | - Gregory A Weiss
- Departments of Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-2025, USA
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37
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Britton J, Dyer RP, Majumdar S, Raston CL, Weiss GA. Ten-Minute Protein Purification and Surface Tethering for Continuous-Flow Biocatalysis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joshua Britton
- Departments of Chemistry, Molecular Biology and Biochemistry; University of California; Irvine CA 92697-2025 USA
- Centre for NanoScale Science and Technology; Flinders University; Bedford Park Adelaide 5001 Australia
| | - Rebekah P. Dyer
- Departments of Chemistry, Molecular Biology and Biochemistry; University of California; Irvine CA 92697-2025 USA
| | - Sudipta Majumdar
- Departments of Chemistry, Molecular Biology and Biochemistry; University of California; Irvine CA 92697-2025 USA
| | - Colin L. Raston
- Centre for NanoScale Science and Technology; Flinders University; Bedford Park Adelaide 5001 Australia
| | - Gregory A. Weiss
- Departments of Chemistry, Molecular Biology and Biochemistry; University of California; Irvine CA 92697-2025 USA
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38
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Galea CA, Roberts KD, Zhu Y, Thompson PE, Li J, Velkov T. Functional Characterization of the Unique Terminal Thioesterase Domain from Polymyxin Synthetase. Biochemistry 2017; 56:657-668. [PMID: 28071053 DOI: 10.1021/acs.biochem.6b01139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Polymyxins remain one of the few antibiotics available for treating antibiotic resistant bacteria. Here we describe polymyxin B thioesterase which performs the final step in polymyxin B biosynthesis. Isolated thioesterase catalyzed cyclization of an N-acetylcystamine polymyxin B analogue to form polymyxin B. The thioesterase contained a catalytic cysteine unlike most thioesterases which possess a serine. Supporting this, incubation of polymyxin B thioesterase with reducing agents abolished enzymatic activity, while mutation of the catalytic cysteine to serine significantly decreased activity. NMR spectroscopy demonstrated that uncyclized polymyxin B was disordered in solution, unlike other thioesterase substrates which adopt a transient structure similar to their product. Modeling showed the thioesterase substrate-binding cleft was highly negatively charged, suggesting a mechanism for the cyclization of the substrate. These studies provide new insights into the role of polymyxin thioesterase in polymyxin biosynthesis and highlight its potential use for the chemoenzymatic synthesis of polymyxin lipopeptides.
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Affiliation(s)
| | | | - Yan Zhu
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University , Parkville, Victoria 3800, Australia
| | | | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University , Parkville, Victoria 3800, Australia
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39
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Chen WH, Li K, Guntaka NS, Bruner SD. Interdomain and Intermodule Organization in Epimerization Domain Containing Nonribosomal Peptide Synthetases. ACS Chem Biol 2016; 11:2293-303. [PMID: 27294598 DOI: 10.1021/acschembio.6b00332] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nonribosomal peptide synthetases are large, complex multidomain enzymes responsible for the biosynthesis of a wide range of peptidic natural products. Inherent to synthetase chemistry is the thioester templated mechanism that relies on protein/protein interactions and interdomain dynamics. Several questions related to structure and mechanism remain to be addressed, including the incorporation of accessory domains and intermodule interactions. The inclusion of nonproteinogenic d-amino acids into peptide frameworks is a common and important modification for bioactive nonribosomal peptides. Epimerization domains, embedded in nonribosomal peptide synthetases assembly lines, catalyze the l- to d-amino acid conversion. Here we report the structure of the epimerization domain/peptidyl carrier protein didomain construct from the first module of the cyclic peptide antibiotic gramicidin synthetase. Both holo (phosphopantethiene post-translationally modified) and apo structures were determined, each representing catalytically relevant conformations of the two domains. The structures provide insight into domain-domain recognition, substrate delivery during the assembly line process, in addition to the structural organization of homologous condensation domains, canonical players in all synthetase modules.
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Affiliation(s)
- Wei-Hung Chen
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Kunhua Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Naga Sandhya Guntaka
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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40
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Chen XP, Shi T, Wang XL, Wang J, Chen Q, Bai L, Zhao YL. Theoretical Studies on the Mechanism of Thioesterase-Catalyzed Macrocyclization in Erythromycin Biosynthesis. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01154] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiong-Ping Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ting Shi
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiao-Lei Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jitao Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qihua Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linquan Bai
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yi-Lei Zhao
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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41
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Do we need new antibiotics? Clin Microbiol Infect 2016; 22:408-15. [DOI: 10.1016/j.cmi.2016.03.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/22/2016] [Accepted: 03/13/2016] [Indexed: 01/01/2023]
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42
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Garg S, Rizhsky L, Jin H, Yu X, Jing F, Yandeau-Nelson MD, Nikolau BJ. Microbial production of bi-functional molecules by diversification of the fatty acid pathway. Metab Eng 2016; 35:9-20. [DOI: 10.1016/j.ymben.2016.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
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Sundaram S, Hertweck C. On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems. Curr Opin Chem Biol 2016; 31:82-94. [DOI: 10.1016/j.cbpa.2016.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/21/2015] [Accepted: 01/15/2016] [Indexed: 11/26/2022]
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44
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Nastro RA, Arguelles-Arias A, Ongena M, Di Costanzo A, Trifuoggi M, Guida M, Fickers P. Antimicrobial Activity of Bacillus amyloliquefaciens ANT1 Toward Pathogenic Bacteria and Mold: Effects on Biofilm Formation. Probiotics Antimicrob Proteins 2016; 5:252-8. [PMID: 26783071 DOI: 10.1007/s12602-013-9143-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The intensive use and misuse of antibiotics over the last decades have generated a strong selective pressure for the emergence of multi-resistant strains and nosocomial infections. Biofilm has been demonstrated as a key parameter in spreading infections, especially in hospitals and healthcare units. Therefore, the development of novel anti-biofilm drugs is actually of the upmost importance. Here, the antimicrobial and antibiofilm activities toward pathogenic microorganisms of a set of non-ribosomal synthesized peptides and polyketides isolated from Bacillus amyloliquefaciens ANT1 culture supernatant are presented.
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Affiliation(s)
- Rosa Anna Nastro
- Department of Sciences for the Environment, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy.
| | - Anthony Arguelles-Arias
- Centre d'Ingenierie des Proteines, Bacterial Physiology and Genetics, Allée de la chimie, Université de Liège, Bat. B6, 4000, Liège, Belgium
| | - Marc Ongena
- Unité de Bio-Industrie, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés, 5030, Gembloux, Belgium
| | - Amelia Di Costanzo
- Department of Biology, University Federico II of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 5, 80126, Naples, Italy
| | - Marco Trifuoggi
- Department of Chemical Sciences, University Federico II of Naples, Complesso Universitario di Monte Sant'Angelo, Ed.4, Via Cinthia 5, 80126, Naples, Italy
| | - Marco Guida
- Department of Biology, University Federico II of Naples, Complesso Universitario di Monte Sant'Angelo, Ed.7, Via Cinthia 5, 80126, Naples, Italy.
| | - Patrick Fickers
- Unité de Biotechnologies et Bioprocédés, Université Libre de Bruxelles, Av F.-D. Roosevelt, 50, CP165/61, 1050, Brussels, Belgium.
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45
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Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis. J Antibiot (Tokyo) 2015; 69:353-61. [PMID: 26648120 DOI: 10.1038/ja.2015.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/01/2015] [Indexed: 11/09/2022]
Abstract
Although most clinically used antibiotics are derived from natural products, identifying new antibacterial molecules from natural product extracts is difficult due to the complexity of these extracts and the limited tools to correlate biological activity with specific molecules. Here, we show that bacterial cytological profiling (BCP) provides a rapid method for mechanism of action determination on plates and in complex natural product extracts and for activity-guided purification. We prepared an extract from Bacillus subtilis 3610 that killed the Escherichia coli lptD mutant and used BCP to observe two types of bioactivities in the unfractionated extract: inhibition of translation and permeablization of the cytoplasmic membrane. We used BCP to guide purification of the molecules responsible for each activity, identifying the translation inhibitors bacillaene and bacillaene B (glycosylated bacillaene) and demonstrating that two molecules contribute to cell permeabilitization, the bacteriocin subtilosin and the cyclic peptide sporulation killing factor. Our results suggest that bacillaene mediates translational arrest, and show that bacillaene B has a minimum inhibitory concentration 10 × higher than unmodified bacillaene. Finally, we show that BCP can be used to screen strains on an agar plate without the need for extract preparation, greatly saving time and improving throughput. Thus, BCP simplifies the isolation of novel natural products, by identifying strains, crude extracts and fractions with interesting bioactivities even when multiple activities are present, allowing investigators to focus labor-intensive steps on those with desired activities.
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46
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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47
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Luhavaya H, Dias MVB, Williams SR, Hong H, de Oliveira LG, Leadlay PF. Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis. ACTA ACUST UNITED AC 2015; 127:13826-13829. [PMID: 27587902 PMCID: PMC4988243 DOI: 10.1002/ange.201507090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/25/2023]
Abstract
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+β barrel fold proteins.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-000, São Paulo-SP (Brazil)
| | - Simon R Williams
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana G de Oliveira
- Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas-SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
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48
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Luhavaya H, Dias MVB, Williams SR, Hong H, de Oliveira LG, Leadlay PF. Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13622-5. [PMID: 26377145 PMCID: PMC4648038 DOI: 10.1002/anie.201507090] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 02/06/2023]
Abstract
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+β barrel fold proteins.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-000, São Paulo-SP (Brazil)
| | - Simon R Williams
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana G de Oliveira
- Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas-SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK).
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49
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Sucipto H, Sahner JH, Prusov E, Wenzel SC, Hartmann RW, Koehnke J, Müller R. In vitro reconstitution of α-pyrone ring formation in myxopyronin biosynthesis. Chem Sci 2015; 6:5076-5085. [PMID: 29308173 PMCID: PMC5724707 DOI: 10.1039/c5sc01013f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/14/2015] [Indexed: 12/22/2022] Open
Abstract
Myxopyronins are α-pyrone antibiotics produced by the terrestrial bacterium Myxococcus fulvus Mx f50 and possess antibacterial activity against Gram-positive and Gram-negative pathogens. They target the bacterial RNA polymerase (RNAP) "switch region" as non-competitive inhibitors and display no cross-resistance to the established RNAP inhibitor rifampicin. Recent analysis of the myxopyronin biosynthetic pathway led to the hypothesis that this secondary metabolite is produced from two separate polyketide parts, which are condensed by the stand-alone ketosynthase MxnB. Using in vitro assays we show that MxnB catalyzes a unique condensation reaction forming the α-pyrone ring of myxopyronins from two activated acyl chains in form of their β-keto intermediates. MxnB is able to accept thioester substrates coupled to either N-acetylcysteamine (NAC) or a specific carrier protein (CP). The turnover rate of MxnB for substrates bound to CP was 12-fold higher than for NAC substrates, demonstrating the importance of protein-protein interactions in polyketide synthase (PKS) systems. The crystal structure of MxnB reveals the enzyme to be an unusual member of the ketosynthase group capable of binding and condensing two long alkyl chains bound to carrier proteins. The geometry of the two binding tunnels supports the biochemical data and allows us to propose an order of reaction, which is supported by the identification of novel myxopyronin congeners in the extract of the producer strain. Insights into the mechanism of this unique condensation reaction do not only expand our knowledge regarding the thiolase enzyme family but also opens up opportunities for PKS bioengineering to achieve directed structural modifications.
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Affiliation(s)
- H Sucipto
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 3 , 66123 Saarbrücken , Germany .
| | - J H Sahner
- Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland , Pharmaceutical and Medicinal Chemistry , Saarland University , Building C2 3 , 66123 Saarbrücken , Germany
| | - E Prusov
- Helmholtz Centre for Infection Research , Inhoffenstrasse 7 , 38124 Braunschweig , Germany
| | - S C Wenzel
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 3 , 66123 Saarbrücken , Germany .
| | - R W Hartmann
- Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland , Pharmaceutical and Medicinal Chemistry , Saarland University , Building C2 3 , 66123 Saarbrücken , Germany
| | - J Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 2 , 66123 Saarbrücken , Germany .
| | - R Müller
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 3 , 66123 Saarbrücken , Germany .
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50
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Ding W, Li Y, Zhang Q. Substrate-Controlled Stereochemistry in Natural Product Biosynthesis. ACS Chem Biol 2015; 10:1590-8. [PMID: 25844528 DOI: 10.1021/acschembio.5b00104] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Enzymes are generally believed to be highly regio- and stereoselective catalysts that strictly control the reaction coordinates and dominate the final catalytic outcomes. However, recent studies have started to suggest that substrates sometimes play key roles in determining the product selectivity in enzyme catalysis. Here, we highlight several enzymatic reactions in which the stereoselectivity is, at least in large part, governed by the intrinsic properties of the substrate rather than by characteristics of the enzyme. These reactions are involved in the biosynthesis of different classes of natural products, including lanthipeptides, sactipeptides, and polyketides. Understanding the mechanism of substrate-controlled stereospecificity may not only expand our knowledge of enzyme catalysis and enzyme evolution but also guide bioengineering efforts to produce novel valuable products.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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