1
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Matsuda K, Wakimoto T. Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials. Curr Opin Chem Biol 2024; 80:102465. [PMID: 38759287 DOI: 10.1016/j.cbpa.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
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2
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Qiao S, Cheng Z, Li F. Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization. Beilstein J Org Chem 2024; 20:721-733. [PMID: 38590533 PMCID: PMC10999997 DOI: 10.3762/bjoc.20.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Chemoenzymatic strategies that combine synthetic and enzymatic transformations offer efficient approaches to yield target molecules, which have been increasingly employed in the synthesis of bioactive natural products. In the biosynthesis of macrocyclic nonribosomal peptides, polyketides, and their hybrids, thioesterase (TE) domains play a significant role in late-stage macrocyclization. These domains can accept mimics of native substrates in vitro and exhibit potential for use in total synthesis. This review summarizes the recent advances of TE domains in the chemoenzymatic synthesis for these natural products that aim to address the common issues in classical synthetic approaches and increase synthetic efficiencies, which have the potential to facilitate further pharmaceutical research.
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Affiliation(s)
- Senze Qiao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhongyu Cheng
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Fuzhuo Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Key Laboratory of Smart Drug Delivery (Ministry of Education), State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 201203, China
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3
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Kobayashi M, Onozawa N, Matsuda K, Wakimoto T. Chemoenzymatic tandem cyclization for the facile synthesis of bicyclic peptides. Commun Chem 2024; 7:67. [PMID: 38548970 PMCID: PMC10978974 DOI: 10.1038/s42004-024-01147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Bicyclic peptides exhibit improved metabolic stabilities and target specificities when compared to their linear or mono-cyclic counterparts; however, efficient and straightforward synthesis remains challenging due to their intricate architectures. Here, we present a highly selective and operationally simple one-pot chemoenzymatic tandem cyclization approach to synthesize bicyclic peptides with small to medium ring sizes. Penicillin-binding protein-type thioesterases (PBP-type TEs) efficiently cyclized azide/alkyne-containing peptides in a head-to-tail manner. Successive copper (I)-catalyzed azide-alkyne cycloaddition generated bicyclic peptides in one-pot, thus omitting the purification of monocyclic intermediates. This chemoenzymatic strategy enabled the facile synthesis of bicyclic peptides bearing hexa-, octa-, and undecapeptidyl head-to-tail cyclic scaffolds.
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Affiliation(s)
- Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Naho Onozawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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4
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Paquette AR, Brazeau-Henrie JT, Boddy CN. Thioesterases as tools for chemoenzymatic synthesis of macrolactones. Chem Commun (Camb) 2024; 60:3379-3388. [PMID: 38456624 DOI: 10.1039/d4cc00401a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Macrocycles are a key functional group that can impart unique properties into molecules. Their synthesis has led to the development of many outstanding chemical methodologies and yet still remains challenging. Thioesterase (TE) domains are frequently responsible for macrocyclization in natural product biosynthesis and provide unique strengths for the enzymatic synthesis of macrocycles. In this feature article, we describe our work to characterize the substrate selectivity of TEs and to use these enzymes as biocatalysts. Our efforts have shown that the linear thioester activated substrates are loaded on TEs with limited substrate selectivity to generate acyl-enzyme intermediates. We show that cyclization of the acyl-enzyme intermediates can be highly selective, with competing hydrolysis of the acyl-enzyme intermediates. The mechanisms controlling TE-mediated macrocyclization versus hydrolysis are a significant unsolved problem in TE biochemistry. The potential of TEs as biocatalysts was demonstrated by using them in the chemoenzymatic total synthesis of macrocyclic depsipeptide natural products. This article highlights the strengths and potential of TEs as biocatalysts as well as their limitations, opening exciting research opportunities including TE engineering to optimize these powerful biocatalysts.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
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5
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Konno S, Tanaka M, Mizuguchi T, Toyokai H, Taguchi A, Taniguchi A, Hayashi Y. Peptide mixed phosphonates for covalent complex formation with thioesterases in nonribosomal peptide synthetases. J Pept Sci 2024; 30:e3532. [PMID: 37423887 DOI: 10.1002/psc.3532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023]
Abstract
Natural macrocyclic peptides derived from microorganisms are medicinal resources that are important for the development of new therapeutic agents. Most of these molecules are biosynthesized by a nonribosomal peptide synthetase (NRPS). The thioesterase (TE) domain in NRPS is responsible for the macrocyclization of mature linear peptide thioesters in a final biosynthetic step. NRPS-TEs can cyclize synthetic linear peptide analogs and can be utilized as biocatalysts for the preparation of natural product derivatives. Although the structures and enzymatic activities of TEs have been investigated, the substrate recognition and substrate-TE interaction during the macrocyclization step are still unknown. To understand the TE-mediated macrocyclization, here we report the development of a substrate-based analog with mixed phosphonate warheads, which can react irreversibly with the Ser residue at the active site of TE. We have demonstrated that the tyrocidine A linear peptide (TLP) with a p-nitrophenyl phosphonate (PNP) enables efficient complex formation with tyrocidine synthetase C (TycC)-TE containing tyrocidine synthetase.
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Affiliation(s)
- Sho Konno
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Miyu Tanaka
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tomoe Mizuguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Haruka Toyokai
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
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6
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Yu S, Xu C, Tang T, Zhang Y, Effiong K, Hu J, Bi Y, Xiao X. Down-regulation of iron/zinc ion transport and toxin synthesis in Microcystis aeruginosa exposed to 5,4'-dihydroxyflavone. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132396. [PMID: 37672994 DOI: 10.1016/j.jhazmat.2023.132396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/04/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023]
Abstract
Flavonoids, common natural polyphenolic compounds from plants, have been proposed as highly effective and safe algicides. However, the molecular mechanism of flavonoids inhibiting Microcystis aeruginosa remains unclear. This study aims in exploring the global transcriptional changes and molecular docking in cyanobacterial cells in response to flavonoids. Transcriptomic analysis revealed that 5,4'-dihydroxyflavone (DHF) primarily affected the genes transcription of iron and zinc ion transport, resulting in the blockage of transport for iron (II), iron (III) and zinc (II), which eventually led to a decrease in intracellular iron and zinc content. 5,4'-DHF can also interfere with iron and zinc transport by binding to metal ion transport-related proteins, leading to eliminated biological activities in M. aeruginosa. Meanwhile, 5,4'-DHF inhibit microcystin synthesis and reduce the content of intercellular toxin by inhibiting the transcription of mcyC and binding with McyC protein, implying that 5,4'-DHF have potential to reduce the risk of microcystins in the environment. Moreover, iron starvation and down-regulation of photosynthesis-related genes transcription led to the inhibition of electron transport in photosynthetic system. These results provide more information for the inhibitory mechanism of flavonoids, and the inhibition of flavonoids on metal ion transmembrane transport provides a new perspective for the development of allelochemical algicides.
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Affiliation(s)
- Shumiao Yu
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China; Key Laboratory of Marine Ecological Monitoring and Restoration Technologies of the Ministry of Natural Resources of China, Shanghai 201206, China; Donghai Laboratory, Zhoushan, Zhejiang 316021, China
| | - Caicai Xu
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China
| | - Tao Tang
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China
| | - Yiyi Zhang
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China
| | - Kokoette Effiong
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China
| | - Jing Hu
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China
| | - Yonghong Bi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xi Xiao
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang 316021, China; Key Laboratory of Marine Ecological Monitoring and Restoration Technologies of the Ministry of Natural Resources of China, Shanghai 201206, China; Donghai Laboratory, Zhoushan, Zhejiang 316021, China; Key Laboratory of Watershed Non-point Source Pollution Control and Water Eco-security of Ministry of Water Resources, College of Environmental and Resources Sciences, Zhejiang University, Hangzhou 310058, China.
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7
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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8
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Brazeau-Henrie JT, Paquette AR, Boddy CN. In Vitro Biochemical Characterization of Excised Macrocyclizing Thioesterase Domains from Non-ribosomal Peptide Synthetases. Methods Mol Biol 2023; 2670:101-125. [PMID: 37184701 DOI: 10.1007/978-1-0716-3214-7_5] [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
Characterization of thioesterases (TEs) is an important step in understanding natural product biosynthesis. Studying non-ribosomal peptide synthetase (NRPS) TEs presents a unique set of challenges with specific cloning and expression issues as well as the challenging synthesis of the thioester peptides substrate required for characterization of the TE. In this method, we describe the cloning and expression of NRPS TEs, the synthesis of thioester peptides, and the in vitro biochemical characterization of the enzyme.
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Affiliation(s)
| | - André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada.
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9
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Kobayashi M, Fujita K, Matsuda K, Wakimoto T. Chemo-Enzymatic Synthesis of Non-ribosomal Macrolactams by a Penicillin-Binding Protein-Type Thioesterase. Methods Mol Biol 2023; 2670:127-144. [PMID: 37184702 DOI: 10.1007/978-1-0716-3214-7_6] [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
Penicillin-binding protein-type thioesterases (PBP-type TEs) are an emerging family of non-ribosomal peptide cyclases. PBP-type TEs exhibit distinct substrate scopes from the well-exploited ribosomal peptide cyclases and traditional non-ribosomal peptide cyclases. Their unique properties, as well as their stand-alone nature, highlight PBP-type TEs as valuable candidates for development as biocatalysts for peptide macrocyclization. Here in this chapter, we describe the scheme for the chemoenzymatic synthesis of non-ribosomal macrolactam by SurE, a representative member of PBP-type TEs.
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Affiliation(s)
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
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10
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Brazeau-Henrie JT, Paquette AR, O'Rourke AQ, Darnowski MG, Boddy CN. Total and Chemoenzymatic Synthesis of Seongsanamide E. Org Lett 2022; 24:6369-6373. [PMID: 36006794 DOI: 10.1021/acs.orglett.2c02271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The total and chemoenzymatic synthesis of the depsipeptide natural product seongsanamide E, 3, is described. The synthetic C-terminal N-acetylcysteamine thioester of linear natural product 1 was macrolactonized by the excised recombinant purified seongsanamide thioesterase (Sgd-TE) domain, generating 3. Sgd-TE also effects the ring opening of 3. Chemical synthesis provided 3 through a macrolactamization strategy. This work confirms the biosynthesis of 3 and demonstrates the power of Sgd-TE as a biocatalyst.
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Affiliation(s)
- Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - André R Paquette
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Allison Q O'Rourke
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Michael G Darnowski
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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11
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Pardhi DS, Panchal RR, Raval VH, Joshi RG, Poczai P, Almalki WH, Rajput KN. Microbial surfactants: A journey from fundamentals to recent advances. Front Microbiol 2022; 13:982603. [PMID: 35992692 PMCID: PMC9386247 DOI: 10.3389/fmicb.2022.982603] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial surfactants are amphiphilic surface-active substances aid to reduce surface and interfacial tensions by accumulating between two fluid phases. They can be generically classified as low or high molecular weight biosurfactants based on their molecular weight, whilst overall chemical makeup determines whether they are neutral or anionic molecules. They demonstrate a variety of fundamental characteristics, including the lowering of surface tension, emulsification, adsorption, micelle formation, etc. Microbial genera like Bacillus spp., Pseudomonas spp., Candida spp., and Pseudozyma spp. are studied extensively for their production. The type of biosurfactant produced is reliant on the substrate utilized and the pathway pursued by the generating microorganisms. Some advantages of biosurfactants over synthetic surfactants comprise biodegradability, low toxicity, bioavailability, specificity of action, structural diversity, and effectiveness in harsh environments. Biosurfactants are physiologically crucial molecules for producing microorganisms which help the cells to grasp substrates in adverse conditions and also have antimicrobial, anti-adhesive, and antioxidant properties. Biosurfactants are in high demand as a potential product in industries like petroleum, cosmetics, detergents, agriculture, medicine, and food due to their beneficial properties. Biosurfactants are the significant natural biodegradable substances employed to replace the chemical surfactants on a global scale in order to make a cleaner and more sustainable environment.
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Affiliation(s)
- Dimple S. Pardhi
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakeshkumar R. Panchal
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Vikram H. Raval
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rushikesh G. Joshi
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- *Correspondence: Peter Poczai,
| | - Waleed H. Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Kiransinh N. Rajput
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
- Kiransinh N. Rajput,
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12
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Guez JS, Coucheney F, Guy J, Béchet M, Fontanille P, Chihib NE, Niehren J, Coutte F, Jacques P. Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Mycosubtilin Isoforms in Bacillus subtilis. Metabolites 2022; 12:metabo12020107. [PMID: 35208182 PMCID: PMC8877110 DOI: 10.3390/metabo12020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Mycosubtilin belongs to the family of lipopeptides. Different isoforms with various antifungal activities can be obtained according to the length and the isomery of the fatty acid. In this work, the activities of the mycosubtilin isoforms were first studied against the pathogen Aspergillus niger, revealing the high activity of the anteiso-C17 isoform. Modification of the mycosubtilin isoform patterns during cultures of the natural strain Bacillus subtilis ATCC 6633 was then investigated through amino acid feeding experiments. In parallel, single-gene knockouts and single-gene overexpression, leading to the overproduction of the anteiso-C15 fatty acid chains, were predicted using informatics tools which provide logical reasoning with formal models of reaction networks. In this way, it was in silico predicted that the single overexpression of the ilvA gene as well as the single knockout of the codY gene may lead to the overproduction of anteiso-C15 fatty acid chains. For the first time, it has been demonstrated that overexpression of ilvA helps to enhance the furniture of odd anteiso fatty acids leading to a favored mycosubtilin anteiso-C17 production pattern (+41%). Alternatively, a knock-out codY mutant led to a higher furniture of even iso fatty acids, leading to a favored mycosubtilin iso-C16 production pattern (+180%). These results showed that increased selective synthesis of particular isoforms of mycosubtilin through metabolic engineering is feasible, disclosing the interest of these approaches for future development of lipopeptide-producing strains.
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Affiliation(s)
- Jean-Sébastien Guez
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Françoise Coucheney
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Joany Guy
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Max Béchet
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Pierre Fontanille
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Nour-Eddine Chihib
- UMR 8207–UMET–Unité Matériaux et Transformations, Centrale Lille, INRAE, CNRS, Université de Lille, F-59000 Lille, France;
| | - Joachim Niehren
- Biocomputing Team, Centre de Recherche en Informatique, Signal et Automatique de Lille CRIStAL, UMR CNRS 9189, Université de Lille, F-59000 Lille, France;
- INRIA, Université de Lille, F-59000 Lille, France
| | - François Coutte
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
- Correspondence: ; Tel.: +33-(0)-328767497
| | - Philippe Jacques
- Équipe Métabolites Spécialisés d’Origine Microbienne, UMRt BioEcoAgro 1158-INRAE, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Université de Liège, B-5030 Gembloux, Belgium;
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13
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Yu J, Song J, Chi C, Liu T, Geng T, Cai Z, Dong W, Shi C, Ma X, Zhang Z, Ma X, Xing B, Jin H, Zhang L, Dong S, Yang D, Ma M. Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zonghui Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Cheng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhongyi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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14
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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15
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Evolutionary and functional analysis of an NRPS condensation domain integrates β-lactam, ᴅ-amino acid, and dehydroamino acid synthesis. Proc Natl Acad Sci U S A 2021; 118:2026017118. [PMID: 33893237 DOI: 10.1073/pnas.2026017118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multidomain biosynthetic enzymes involved in the assembly-line-like synthesis of numerous peptide natural products. Among these are clinically useful antibiotics including three classes of β-lactams: the penicillins/cephalosporins, the monobactams, and the monocyclic nocardicins, as well as the vancomycin family of glycopeptides and the depsipeptide daptomycin. During NRPS synthesis, peptide bond formation is catalyzed by condensation (C) domains, which couple the nascent peptide with the next programmed amino acid of the sequence. A growing number of additional functions are linked to the activity of C domains. In the biosynthesis of the nocardicins, a specialized C domain prepares the embedded β-lactam ring from a serine residue. Here, we examine the evolutionary descent of this unique β-lactam-synthesizing C domain. Guided by its ancestry, we predict and demonstrate in vitro that this C domain alternatively performs peptide bond formation when a single stereochemical change is introduced into its peptide starting material. Remarkably, the function of the downstream thioesterase (TE) domain also changes. Natively, the TE directs C terminus epimerization prior to hydrolysis when the β-lactam is made but catalyzes immediate release of the alternative peptide. In addition, we investigate the roles of C-domain histidine residues in light of clade-specific sequence motifs, refining earlier mechanistic proposals of both β-lactam formation and canonical peptide synthesis. Finally, expanded phylogenetic analysis reveals unifying connections between β-lactam synthesis and allied C domains associated with the appearance of ᴅ-amino acid and dehydroamino acid residues in other NRPS-derived natural products.
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16
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Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
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Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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17
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Qiao L, Fang J, Zhu P, Huang H, Dang C, Pang J, Gao W, Qiu X, Huang L, Li Y. A Novel Chemoenzymatic Approach to Produce Cilengitide Using the Thioesterase Domain from Microcystis aeruginosa Microcystin Synthetase C. Protein J 2020; 38:658-666. [PMID: 31435810 DOI: 10.1007/s10930-019-09864-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Modern organic chemistry faces many difficulties in the reliable production of cyclopeptides, such as poor yields and insufficient regio- and stereoselectivity. Thioesterase (TE) shows impressive stereospecificity, region- and chemoselectivity during the cyclization of peptide substrates. The biocatalytic properties of TE provide high value for industrial applications. Herein, a novel chemoenzymatic method to synthesize cilengitide is described based on the cyclic activity of the TE domain from microcystin synthetase C (McyC) of Microcystis aeruginosa. In addition, a single active site mutation in the McyC TE was engineered to generate a more effective macrocyclization catalyst. Compared to the chemical approach to synthesize cilengitide, this novel enzyme-catalysed methodology exhibits a higher synthetic efficiency with an approximately 3.4-fold higher yield (49.2%).
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Affiliation(s)
- Longliang Qiao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, China
| | - Jian Fang
- College of Medicine, Shaoxing University, Shaoxing, 312000, China
| | - Peng Zhu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, China. .,Ningbo Institute of Oceanography, Ningbo, 315832, China.
| | - Hailong Huang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, China
| | - Chenyang Dang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, China
| | - Jianhu Pang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, China
| | - Weifang Gao
- Ningbo Institute of Oceanography, Ningbo, 315832, China
| | - Xiaoting Qiu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, China
| | - Lili Huang
- Ningbo Institute of Oceanography, Ningbo, 315832, China
| | - Yanrong Li
- Ningbo Institute of Oceanography, Ningbo, 315832, China
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18
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Schmidt JJ, Khatri Y, Brody SI, Zhu C, Pietraszkiewicz H, Valeriote FA, Sherman DH. A Versatile Chemoenzymatic Synthesis for the Discovery of Potent Cryptophycin Analogs. ACS Chem Biol 2020; 15:524-532. [PMID: 31961651 DOI: 10.1021/acschembio.9b00998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cryptophycins are a family of macrocyclic depsipeptide natural products that display exceptionally potent antiproliferative activity against drug-resistant cancers. Unique challenges facing the synthesis and derivatization of this complex group of molecules motivated us to investigate a chemoenzymatic synthesis designed to access new analogs for biological evaluation. The cryptophycin thioesterase (CrpTE) and the cryptophycin epoxidase (CrpE) are a versatile set of enzymes that catalyze macrocyclization and epoxidation of over 20 natural cryptophycin metabolites. Thus, we envisioned a drug development strategy involving their use as standalone biocatalysts for production of unnatural derivatives. Herein, we developed a scalable synthesis of 12 new unit A-B-C-D linear chain elongation intermediates containing heterocyclic aromatic groups as alternatives to the native unit A benzyl group. N-Acetyl cysteamine activated forms of each intermediate were assessed for conversion to macrocyclic products using wild type CrpTE, which demonstrated the exceptional flexibility of this enzyme. Semipreparative scale reactions were conducted for isolation and structural characterization of new cryptophycins. Each was then evaluated as a substrate for CrpE P450 and its ability to generate the epoxidized products from these substrates that possess altered electronics at the unit A styrenyl double bond position. Finally, biological evaluation of the new cryptophycins revealed a des-β-epoxy analog with low picomolar potency, previously limited to cryptophycins bearing epoxide functionality.
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Affiliation(s)
| | | | | | | | - Halina Pietraszkiewicz
- Department of Internal Medicine, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan 48202, United States
| | - Frederick A. Valeriote
- Department of Internal Medicine, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan 48202, United States
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19
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Structural characterization of Kannurin isoforms and evaluation of the role of β-hydroxy fatty acid tail length in functional specificity. Sci Rep 2020; 10:2839. [PMID: 32071421 PMCID: PMC7029025 DOI: 10.1038/s41598-020-59872-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/30/2019] [Indexed: 12/04/2022] Open
Abstract
The novel anti-fungal cyclic lipopeptide ‘Kannurin’ and its three structural variants produced by Bacillus cereus AK1 were previously reported from our laboratory. The present study reports unexplored structural variants of Kannurin those have functional benefits. Due to the difference in β-hydroxy fatty acid tail length, they are designated here as Kannurin A (m/z 994.67 ± 0.015), B (m/z 1008.68 ± 0.017), C (m/z 1022.69 ± 0.021), D (m/z 1036.70 ± 0.01), CL (m/z 1040.71 ± 0.02) and DL (m/z 1054.72 ± 0.01). The isoform A (m/z 994.67 ± 0.015) is the shortest cyclic form of Kannurin identified so far. In addition, CL (m/z 1040.71 ± 0.02) and DL (m/z 1054.72 ± 0.01) are the rare natural linear forms. The results of the antimicrobial assays deduced that the difference in lipid tail length of the isoforms contributes tremendous differences in their antimicrobial properties. The isoforms with short lipid tails (A and B) are more selective and potent towards bacteria, whereas the isoforms with long lipid tails (C and D) are more potent against fungi. The molecular dynamics studies and electron microscopic observations supported with circular dichroic spectroscopy analysis showed the structural confirmation and formation of aggregates of Kannurin in solution. The molecular dynamics simulation studies revealed that a single molecule of Kannurin makes enormous intra-molecular interactions and structural re-arrangements to attain stable lowest energy state in solution. When they reach a particular concentration (CMC) especially in aqueous environment, tends to form structural aggregates called ‘micelles’. With the structural information and activity relationship described in this study, it is trying to point out the sensitive structural entities that can be modified to improve the efficacy and target specificities of lipopeptide class of antibiotics.
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20
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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21
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Guo F, Zhang H, Eltahan R, Zhu G. Molecular and Biochemical Characterization of a Type II Thioesterase From the Zoonotic Protozoan Parasite Cryptosporidium parvum. Front Cell Infect Microbiol 2019; 9:199. [PMID: 31231619 PMCID: PMC6568194 DOI: 10.3389/fcimb.2019.00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/22/2019] [Indexed: 12/05/2022] Open
Abstract
Cryptosporidium parvum is a globally important zoonotic parasite capable of causing severe to deadly diarrhea in humans and animals. Its small genome (~9.1 Mb) encodes not only a highly streamlined metabolism, but also a 25-kb, 3-module fatty acid synthase (CpFAS1) and a 40-kb, 7-module polyketide synthase (CpPKS1). The two megasynthases contain a C-terminal reductase domain to release the final products with predicted chain lengths of ≥C22 for CpFAS1 or C28 to C38 for CpPKS1.The parasite genome also encodes a discrete thioesterase ortholog, suggesting its role to be an alternative tool in releasing the final products from CpFAS1 and/or CpPKS1, or as an editor to remove non-reactive residues or aberrant intermediates, or to control starter units as seen in other parasites. In this study, we have confirmed that this C. parvum thioesterase is a type II thioesterase (thus named as CpTEII). CpTEII contains motifs and a catalytic triad characteristic to the type II thioesterase family. CpTEII is expressed during the entire parasite life cycle stages with the highest levels of expression in the later developmental stages. CpTEII showed the highest hydrolytic activity toward C10:0 decanoyl-CoA, so we speculated that CpTEII may mainly act as an editor to remove non-reactive residues and/or aberrant medium acyl chain from CpFAS1 and/or CpPKS1. However, we cannot rule out the possibility that CpTEII may also participate in the release of final products from CpFAS1 because of its moderate activity on C20:0, C:22:0 and C24:0 acyl-CoA thioesters (i.e., ~20–30% activity vs. decanoyl-CoA).
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Affiliation(s)
- Fengguang Guo
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Haili Zhang
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Rana Eltahan
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Guan Zhu
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
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22
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Affiliation(s)
- Justin A. Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60201, United States
| | - Yao Lin
- Departments of Chemistry and Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60201, United States
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60201, United States
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23
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Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates. Nat Commun 2017; 8:1045. [PMID: 29051530 PMCID: PMC5648786 DOI: 10.1038/s41467-017-00862-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/02/2017] [Indexed: 01/30/2023] Open
Abstract
Peptide macrocycles are promising therapeutic molecules because they are protease resistant, structurally rigid, membrane permeable, and capable of modulating protein-protein interactions. Here, we report the characterization of the dual function macrocyclase-peptidase enzyme involved in the biosynthesis of the highly toxic amanitin toxin family of macrocycles. The enzyme first removes 10 residues from the N-terminus of a 35-residue substrate. Conformational trapping of the 25 amino-acid peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization. The enzyme rebinds the 25 amino-acid peptide in a different conformation and catalyzes macrocyclization of the N-terminal eight residues. Structures of the enzyme bound to both substrates and biophysical analysis characterize the different binding modes rationalizing the mechanism. Using these insights simpler substrates with only five C-terminal residues were designed, allowing the enzyme to be more effectively exploited in biotechnology.
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24
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Nazari F, Safaie N, Soltani BM, Shams-Bakhsh M, Sharifi M. Bacillus subtilis affects miRNAs and flavanoids production in Agrobacterium-Tobacco interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:98-106. [PMID: 28624685 DOI: 10.1016/j.plaphy.2017.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 05/23/2023]
Abstract
Agrobacterium tumefaciens is a very destructive plant pathogen. Selection of effective biological agents against this pathogen depends on more insight into molecular plant defence responses during the biocontrol agent-pathogen interaction. Auxin as a phytohormone is a key contributor in pathogenesis and plant defence and accumulation of auxin transport carriers are accompanied by increasing in flavonoid and miRNAs concentrations during plant interactions with bacteria. The aim of this research was molecular analysis of Bacillus subtilis (ATCC21332) biocontrol effect against A. tumefaciens (IBRC-M10701) pathogen interacting with Nicotiana tabacum plants. Tobacco plants were either treated with both or one of the challenging bacteria and the expression of miRNAs inside the plants were analysed through qRT-PCR. The results indicated that the bacterial treatments affect expression level of nta-miRNAs. In tobacco plants treated only with A. tumefaciens the expression of nta-miR393 was more than that was recorded for nta-miR167 (3.8 folds, P < 0.05 in 3dpi). While the expression level of nta-miR167 was more than the expression of nta-miR393 in other treatments including tobacco plants treated only with B. subtilis (2.1 folds, P < 0.05) and the plants treated with both of the bacteria (3.9 folds, P < 0.05) in 3 dpi. Also, the composition and concentration of rutin, myrecetin, daidzein and vitexin flavanoid derivatives were detected using HPLC and analysed according the standard curves. All of the tested flavanoid compounds were highly detected in Tobacco plants which were only challenged with A. tumefaciens. The amount of these compounds in the plants which were challenged with the B. subtilis alone, was similar to the amount recorded for the plants challenged with the both bacteria. This study suggests a relationship between the upregulation of nta-miR167, nta-miR393 and accumulation of flavanoid compounds. Overall, the expression of these miRNAs as well as flavonoid derivatives has the potential of being used as biomarkers for the interaction of B. subtilis and A. tumefaciens model system in N. tabacum.
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Affiliation(s)
- Fahimeh Nazari
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Bahram Mohammad Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Masoud Shams-Bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Mohsen Sharifi
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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25
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Abstract
Covering: up to 2017.Natural products are important secondary metabolites produced by bacterial and fungal species that play important roles in cellular growth and signaling, nutrient acquisition, intra- and interspecies communication, and virulence. A subset of natural products is produced by nonribosomal peptide synthetases (NRPSs), a family of large, modular enzymes that function in an assembly line fashion. Because of the pharmaceutical activity of many NRPS products, much effort has gone into the exploration of their biosynthetic pathways and the diverse products they make. Many interesting NRPS pathways have been identified and characterized from both terrestrial and marine bacterial sources. Recently, several NRPS pathways in human commensal bacterial species have been identified that produce molecules with antibiotic activity, suggesting another source of interesting NRPS pathways may be the commensal and pathogenic bacteria that live on the human body. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) have been identified as a significant cause of human bacterial infections that are frequently multidrug resistant. The emerging resistance profile of these organisms has prompted calls from multiple international agencies to identify novel antibacterial targets and develop new approaches to treat infections from ESKAPE pathogens. Each of these species contains several NRPS biosynthetic gene clusters. While some have been well characterized and produce known natural products with important biological roles in microbial physiology, others have yet to be investigated. This review catalogs the NRPS pathways of ESKAPE pathogens. The exploration of novel NRPS products may lead to a better understanding of the chemical communication used by human pathogens and potentially to the discovery of novel therapeutic approaches.
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Affiliation(s)
- Andrew M Gulick
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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26
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 508] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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27
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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28
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Thyagarajan SL, Ramanathan G, Singaravelu S, Kandhasamy S, Perumal P, Sivagnanam UT. Microbial Siderophore as MMP inhibitor:An interactive approach on wound healing application. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.wndm.2016.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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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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Oueis E, Jaspars M, Westwood NJ, Naismith JH. Enzymatic Macrocyclization of 1,2,3-Triazole Peptide Mimetics. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 128:5936-5939. [PMID: 27397939 PMCID: PMC4924595 DOI: 10.1002/ange.201601564] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 11/12/2022]
Abstract
The macrocyclization of linear peptides is very often accompanied by significant improvements in their stability and biological activity. Many strategies are available for their chemical macrocyclization, however, enzyme-mediated methods remain of great interest in terms of synthetic utility. To date, known macrocyclization enzymes have been shown to be active on both peptide and protein substrates. Here we show that the macrocyclization enzyme of the cyanobactin family, PatGmac, is capable of macrocyclizing substrates with one, two, or three 1,4-substituted 1,2,3-triazole moieties. The introduction of non-peptidic scaffolds into macrocycles is highly desirable in tuning the activity and physical properties of peptidic macrocycles. We have isolated and fully characterized nine non-natural triazole-containing cyclic peptides, a further ten molecules are also synthesized. PatGmac has now been shown to be an effective and versatile tool for the ring closure by peptide bond formation.
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Affiliation(s)
- Emilia Oueis
- Biomedical Science Research ComplexUniversity of St Andrews, BSRCNorth HaughSt AndrewsKY16 9STUK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of ChemistryUniversity of AberdeenOld AberdeenAB24 3UEUK
| | - Nicholas J. Westwood
- Biomedical Science Research ComplexUniversity of St Andrews, BSRCNorth HaughSt AndrewsKY16 9STUK
| | - James H. Naismith
- Biomedical Science Research ComplexUniversity of St Andrews, BSRCNorth HaughSt AndrewsKY16 9STUK
- State Key Laboratory of BiotherapySichuan UniversityChina
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Oueis E, Jaspars M, Westwood NJ, Naismith JH. Enzymatic Macrocyclization of 1,2,3-Triazole Peptide Mimetics. Angew Chem Int Ed Engl 2016; 55:5842-5. [PMID: 27059105 PMCID: PMC4924597 DOI: 10.1002/anie.201601564] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 11/20/2022]
Abstract
The macrocyclization of linear peptides is very often accompanied by significant improvements in their stability and biological activity. Many strategies are available for their chemical macrocyclization, however, enzyme-mediated methods remain of great interest in terms of synthetic utility. To date, known macrocyclization enzymes have been shown to be active on both peptide and protein substrates. Here we show that the macrocyclization enzyme of the cyanobactin family, PatGmac, is capable of macrocyclizing substrates with one, two, or three 1,4-substituted 1,2,3-triazole moieties. The introduction of non-peptidic scaffolds into macrocycles is highly desirable in tuning the activity and physical properties of peptidic macrocycles. We have isolated and fully characterized nine non-natural triazole-containing cyclic peptides, a further ten molecules are also synthesized. PatGmac has now been shown to be an effective and versatile tool for the ring closure by peptide bond formation.
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Affiliation(s)
- Emilia Oueis
- Biomedical Science Research Complex, University of St Andrews, BSRC, North Haugh, St Andrews, KY16 9ST, UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE, UK
| | - Nicholas J Westwood
- Biomedical Science Research Complex, University of St Andrews, BSRC, North Haugh, St Andrews, KY16 9ST, UK
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews, BSRC, North Haugh, St Andrews, KY16 9ST, UK.
- State Key Laboratory of Biotherapy, Sichuan University, China.
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Yun CS, Motoyama T, Osada H. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme. Nat Commun 2015; 6:8758. [PMID: 26503170 PMCID: PMC4640141 DOI: 10.1038/ncomms9758] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/28/2015] [Indexed: 12/30/2022] Open
Abstract
Tenuazonic acid (TeA) is a well-known mycotoxin produced by various plant pathogenic fungi. However, its biosynthetic gene has been unknown to date. Here we identify the TeA biosynthetic gene from Magnaporthe oryzae by finding two TeA-inducing conditions of a low-producing strain. We demonstrate that TeA is synthesized from isoleucine and acetoacetyl-coenzyme A by TeA synthetase 1 (TAS1). TAS1 is a unique non-ribosomal peptide synthetase and polyketide synthase (NRPS–PKS) hybrid enzyme that begins with an NRPS module. In contrast to other NRPS/PKS hybrid enzymes, the PKS portion of TAS1 has only a ketosynthase (KS) domain and this domain is indispensable for TAS1 activity. Phylogenetic analysis classifies this KS domain as an independent clade close to type I PKS KS domain. We demonstrate that the TAS1 KS domain conducts the final cyclization step for TeA release. These results indicate that TAS1 is a unique type of NRPS–PKS hybrid enzyme. Tenuazonic acid is a mycotoxin produced by various plant pathogenic fungi but its biosynthetic gene is unknown to date. Here, the authors identify the tenuazonic acid biosynthetic gene encoding a protein with a unique KS domain that conducts cyclization step for tenuazonic acid release in Magnaporthe oryzae.
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Affiliation(s)
- Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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Vater J, Niu B, Dietel K, Borriss R. Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1548-1558. [PMID: 26100395 DOI: 10.1007/s13361-015-1130-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/18/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Paenibacillus polymyxa-M1 is a potent producer of bioactive compounds, such as lipopeptides, polyketides, and lantibiotics of biotechnological and medical interest. Genome sequencing revealed nine gene clusters for nonribosomal biosynthesis of such agents. Here we report on the investigation of the fusaricidins, a complex of cyclic lipopeptides containing 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid component by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). More than 20 variants of these compounds were detected and characterized in detail. Mass spectrometric sequence analysis was performed by MALDI-LIFT-TOF/TOF fragment analysis. The obtained product ion spectra show a specific processing in the fatty acid part. GHPD is cleaved between the α- and ß-position yielding two fragments a and b, one bearing the end-standing guanidine group and another one comprising the residual two C-atoms of GHPD with the attached peptide moiety. The complete sequence of all fusaricidins was derived from sets of bn- and yn-ions. The fusaricidin complex can be divided into four lipopeptide families, three of them showing variations of the amino acid in position 3, Val or Ile for the first and Tyr or Phe for families 2 and 3, respectively. A collection of novel fusaricidins was detected differing from those of families 1-3 by an additional residue of 71 Da (family 4). LIFT-TOF/TOF fragment spectra of these species imply that in their peptide moiety, an Ala-residue is attached by an ester bond to the free hydroxyl group of Thr4. More than 10 novel fusaricidins were characterized mass spectrometrically.
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Affiliation(s)
- Joachim Vater
- Institut für Chemie, Technische Universität Berlin, Mueller-Breslau-Straße 10, 10623, Berlin, Germany,
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Butelase 1 is an Asx-specific ligase enabling peptide macrocyclization and synthesis. Nat Chem Biol 2014; 10:732-8. [PMID: 25038786 DOI: 10.1038/nchembio.1586] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 06/13/2014] [Indexed: 01/29/2023]
Abstract
Proteases are ubiquitous in nature, whereas naturally occurring peptide ligases, enzymes catalyzing the reverse reactions of proteases, are rare occurrences. Here we describe the discovery of butelase 1, to our knowledge the first asparagine/aspartate (Asx) peptide ligase to be reported. This highly efficient enzyme was isolated from Clitoria ternatea, a cyclic peptide-producing medicinal plant. Butelase 1 shares 71% sequence identity and the same catalytic triad with legumain proteases but does not hydrolyze the protease substrate of legumain. Instead, butelase 1 cyclizes various peptides of plant and animal origin with yields greater than 95%. With Kcat values of up to 17 s(-1) and catalytic efficiencies as high as 542,000 M(-1) s(-1), butelase 1 is the fastest peptide ligase known. Notably, butelase 1 also displays broad specificity for the N-terminal amino acids of the peptide substrate, thus providing a new tool for C terminus-specific intermolecular peptide ligations.
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Sequence characterization and computational analysis of the non-ribosomal peptide synthetases controlling biosynthesis of lipopeptides, fengycins and bacillomycin D, from Bacillus amyloliquefaciens Q-426. Biotechnol Lett 2013; 35:2155-63. [PMID: 24068498 DOI: 10.1007/s10529-013-1320-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
Lipopeptides secreted by bacteria attract interest because of their uses in biomedicine, biotechnology and food technology; however, harnessing their megasynthases (non-ribosomal peptide synthetases, NRPSs) has met with some difficulties in heterologous expression and crystallization. Here, we used similarity and phylogenetic analysis of NRPS sequences, including the fengycin and iturin family synthetases from Bacillus spp., and have developed a novel approach for delineating the length and boundaries of NRPS domains from Bacillus amyloliquefaciens strain Q-426. The sequences were further characterized (including specific residues and conserved motifs) that gave insight into the basis of the substrate specificity. Data from the prediction of the NRPS domains, obtained by the self-optimized prediction method with Alignment program, showed they are all structurally unstable, making it difficult to determine their crystal structures.
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Wyatt MA, Mok MCY, Junop M, Magarvey NA. Heterologous expression and structural characterisation of a pyrazinone natural product assembly line. Chembiochem 2012; 13:2408-15. [PMID: 23070851 DOI: 10.1002/cbic.201200340] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 11/07/2022]
Abstract
Through a number of strategies nonribosomal peptide assembly lines give rise to a metabolic diversity not possible by ribosomal synthesis. One distinction within nonribosomal assembly is that products are elaborated on an enzyme-tethered substrate, and their release is enzyme catalysed. Reductive release by NAD(P)H-dependent catalysts is one observed nonribosomal termination and release strategy. Here we probed the selectivity of a terminal reductase domain by using a full-length heterologously expressed nonribosomal peptide synthetase for the dipeptide aureusimine and were able to generate 17 new analogues. Further, we generated an X-ray structure of aureusimine terminal reductase to gain insight into the structural details associated with this enzymatic domain.
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Affiliation(s)
- Morgan A Wyatt
- Michael G. Degroote Institute for Infectious Disease Research, McMaster University, 1200 Main St. W, Hamilton ON, L8N 3Z5, Canada
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Saha R, Saha N, Donofrio RS, Bestervelt LL. Microbial siderophores: a mini review. J Basic Microbiol 2012; 53:303-17. [PMID: 22733623 DOI: 10.1002/jobm.201100552] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 01/20/2012] [Indexed: 01/22/2023]
Abstract
Iron is one of the major limiting factors and essential nutrients of microbial life. Since in nature it is not readily available in the preferred form, microorganisms produce small high affinity chelating molecules called siderophores for its acquisition. Microorganisms produce a wide variety of siderophores controlled at the molecular level by different genes to accumulate, mobilize and transport iron for metabolism. Siderophores also play a critical role in the expression of virulence and development of biofilms by different microbes. Apart from maintaining microbial life, siderophores can be harnessed for the sustainability of human, animals and plants. With the advent of modern molecular tools, a major breakthrough is taking place in the understanding of the multifaceted role of siderophores in nature. This mini review is intended to provide a general overview on siderophore along with its role and applications.
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Affiliation(s)
- Ratul Saha
- Department of Microbiology and Molecular Biology, NSF International, Ann Arbor, MI, USA.
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40
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Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 298] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
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41
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Bowers AA. Biochemical and biosynthetic preparation of natural product-like cyclic peptide libraries. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20068f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural product gene clusters are increasingly being used to compliment biochemical methods for production of cyclic peptide libraries.
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Affiliation(s)
- Albert A. Bowers
- Purdue University
- Dept. of Medicinal Chemistry and Molecular Pharmacology
- West Lafayette
- USA
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Xu W, Li L, Du L, Tan N. Various mechanisms in cyclopeptide production from precursors synthesized independently of non-ribosomal peptide synthetases. Acta Biochim Biophys Sin (Shanghai) 2011; 43:757-62. [PMID: 21764803 DOI: 10.1093/abbs/gmr062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An increasing number of cyclopeptides have been discovered as products of ribosomal synthetic pathway. The biosynthetic study of these cyclopeptides has revealed interesting new mechanisms for cyclization. This review highlighted the recent discoveries in cyclization mechanisms for cyclopeptides synthesized independently of non-ribosomal peptide synthetases, including endopeptidase-catalyzed cyclization, intein-mediated cyclization, and peptide synthetase-catalyzed cyclization. This information may help to design hybrid ribosomal and non-ribosomal biosynthetic systems to produce novel cyclopeptides with various bioactivities.
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Affiliation(s)
- Wenyan Xu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, China
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Characterization of the N-Methyltransferase Activities of the Multifunctional Polypeptide Cyclosporin Synthetase. ACTA ACUST UNITED AC 2011; 18:464-75. [DOI: 10.1016/j.chembiol.2011.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 01/10/2011] [Accepted: 01/24/2011] [Indexed: 11/18/2022]
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44
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Harmrolfs K, Brünjes M, Dräger G, Floss HG, Sasse F, Taft F, Kirschning A. Cyclization of synthetic seco-proansamitocins to ansamitocin macrolactams by Actinosynnema pretiosum as biocatalyst. Chembiochem 2011; 11:2517-20. [PMID: 21077088 DOI: 10.1002/cbic.201000422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kirsten Harmrolfs
- Institut für Organische Chemie und Biomolekulares, Wirkstoffzentrum (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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Roongsawang N, Washio K, Morikawa M. Diversity of nonribosomal peptide synthetases involved in the biosynthesis of lipopeptide biosurfactants. Int J Mol Sci 2010; 12:141-72. [PMID: 21339982 PMCID: PMC3039948 DOI: 10.3390/ijms12010141] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/03/2010] [Accepted: 12/10/2010] [Indexed: 12/02/2022] Open
Abstract
Lipopeptide biosurfactants (LPBSs) consist of a hydrophobic fatty acid portion linked to a hydrophilic peptide chain in the molecule. With their complex and diverse structures, LPBSs exhibit various biological activities including surface activity as well as anti-cellular and anti-enzymatic activities. LPBSs are also involved in multi-cellular behaviors such as swarming motility and biofilm formation. Among the bacterial genera, Bacillus (Gram-positive) and Pseudomonas (Gram-negative) have received the most attention because they produce a wide range of effective LPBSs that are potentially useful for agricultural, chemical, food, and pharmaceutical industries. The biosynthetic mechanisms and gene regulation systems of LPBSs have been extensively analyzed over the last decade. LPBSs are generally synthesized in a ribosome-independent manner with megaenzymes called nonribosomal peptide synthetases (NRPSs). Production of active-form NRPSs requires not only transcriptional induction and translation but also post-translational modification and assemblage. The accumulated knowledge reveals the versatility and evolutionary lineage of the NRPSs system. This review provides an overview of the structural and functional diversity of LPBSs and their different biosynthetic mechanisms in Bacillus and Pseudomonas, including both typical and unique systems. Finally, successful genetic engineering of NRPSs for creating novel lipopeptides is also discussed.
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Affiliation(s)
- Niran Roongsawang
- Microbial Cell Factory Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
- Authors to whom correspondence should be addressed; E-Mails: (N.R.); (M.M.); Tel.: +66-2564-6700 (N.R.); +81-11-706-2253 (M.M.); Fax: +66-2564-6707 (N.R.); +81-11-706-2253 (M.M.)
| | - Kenji Washio
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan; E-Mail:
| | - Masaaki Morikawa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (N.R.); (M.M.); Tel.: +66-2564-6700 (N.R.); +81-11-706-2253 (M.M.); Fax: +66-2564-6707 (N.R.); +81-11-706-2253 (M.M.)
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Li Y, Giulionatti M, Houghten RA. Macrolactonization of peptide thioesters catalyzed by imidazole and its application in the synthesis of kahalalide B and analogues. Org Lett 2010; 12:2250-3. [PMID: 20426464 DOI: 10.1021/ol100596p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The macrolactonization of peptide thioester to yield cyclic depsipeptides was developed using imidazole as a catalyst. This strategy was applied to the synthesis of kahalalide B and its analogues.
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Affiliation(s)
- Yangmei Li
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, USA
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Surveys of non-ribosomal peptide and polyketide assembly lines in fungi and prospects for their analysis in vitro and in vivo. Fungal Genet Biol 2010; 48:49-61. [PMID: 20601041 DOI: 10.1016/j.fgb.2010.06.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/02/2010] [Accepted: 06/21/2010] [Indexed: 12/16/2022]
Abstract
With many bioactive non-ribosomal peptides and polyketides produced in fungi, studies of their biosyntheses are an active area of research. Practical limitations of working with mega-dalton synthetases including cell lysis and protein extraction to recombinant gene and pathway expression has slowed understanding of many secondary metabolic processes relative to bacterial counterparts. Recent advances in accessing fungal biosynthetic machinery are beginning to change this. Here we describe the successes of some studies of thiotemplate biosynthesis in fungal systems, along with very recent advances in chemical tagging and mass spectrometric strategies to selectively study biosynthetic conveyer belts in isolation, and within a few years, in endogenous fungal proteomes.
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48
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Mulyani S, Egel E, Kittel C, Turkanovic S, Wohlleben W, Süssmuth RD, van Pée KH. The thioesterase Bhp is involved in the formation of beta-hydroxytyrosine during balhimycin biosynthesis in Amycolatopsis balhimycina. Chembiochem 2010; 11:266-71. [PMID: 19998400 DOI: 10.1002/cbic.200900600] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The putative hydrolase gene bhp from the balhimycin biosynthetic gene cluster has been cloned and overexpressed in Escherichia coli. The corresponding enzyme Bhp was purified to homogeneity by nickel-chelating chromatography and characterized. Although Bhp has sequence similarities to hydrolases with "haloperoxidase"/perhydrolase activity, it did not show any enzymatic activity with standard "haloperoxidase"/perhydrolase substrates (e.g., monochlorodimedone and phenol red), nonspecific esterase substrates (such as p-nitrophenyl acetate, p-nitrophenyl phosphate and S-thiophenyl acetate) or the model lactonase substrate dihydrocoumarin. However, Bhp could be shown to catalyse the hydrolysis of S-beta-hydroxytyrosyl-N-acetyl cysteamine thioester (beta-OH-Tyr-SNAC) with 15 times the efficiency of S-L-tyrosyl-N-acetyl cysteamine thioester (L-Tyr-SNAC). This is in agreement with the suggestion that Bhp is involved in balhimycin biosynthesis, during which it was supposed to catalyse the hydrolysis of beta-OH-Tyr-S-PCP (PCP=peptidyl carrier protein) to free beta-hydroxytyrosine (beta-OH-Tyr) and strongly suggests that Bhp is a thioesterase with high substrate specificity for PCP-bound beta-OH-Tyr and not a "haloperoxidase"/perhydrolase or nonspecific esterase.
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Affiliation(s)
- Sri Mulyani
- Biochemistry, TU Dresden, 01062 Dresden, Germany
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49
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Velkov T, Thompson PE, Nation RL, Li J. Structure--activity relationships of polymyxin antibiotics. J Med Chem 2010; 53:1898-916. [PMID: 19874036 DOI: 10.1021/jm900999h] [Citation(s) in RCA: 509] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tony Velkov
- School of Medicine, Deakin University, Pigdons Road, Geelong 3217, Victoria, Australia.
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50
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