51
|
Zhao F, Liu Z, Yang S, Ding N, Gao X. Quinolactacin Biosynthesis Involves Non‐Ribosomal‐Peptide‐Synthetase‐Catalyzed Dieckmann Condensation to Form the Quinolone‐γ‐lactam Hybrid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fanglong Zhao
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Zhiwen Liu
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Shuyuan Yang
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Ning Ding
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
- Department of Bioengineering Rice University Houston TX 77005 USA
| |
Collapse
|
52
|
Oxepinamide F biosynthesis involves enzymatic D-aminoacyl epimerization, 3H-oxepin formation, and hydroxylation induced double bond migration. Nat Commun 2020; 11:4914. [PMID: 33004788 PMCID: PMC7530659 DOI: 10.1038/s41467-020-18713-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
Oxepinamides are derivatives of anthranilyl-containing tripeptides and share an oxepin ring and a fused pyrimidinone moiety. To the best of our knowledge, no studies have been reported on the elucidation of an oxepinamide biosynthetic pathway and conversion of a quinazolinone to a pyrimidinone-fused 1H-oxepin framework by a cytochrome P450 enzyme in fungal natural product biosynthesis. Here we report the isolation of oxepinamide F from Aspergillus ustus and identification of its biosynthetic pathway by gene deletion, heterologous expression, feeding experiments, and enzyme assays. The nonribosomal peptide synthase (NRPS) OpaA assembles the quinazolinone core with D-Phe incorporation. The cytochrome P450 enzyme OpaB catalyzes alone the oxepin ring formation. The flavoenzyme OpaC installs subsequently one hydroxyl group at the oxepin ring, accompanied by double bond migration. The epimerase OpaE changes the D-Phe residue back to L-form, which is essential for the final methylation by OpaF.
Collapse
|
53
|
Hai Y, Jenner M, Tang Y. Fungal siderophore biosynthesis catalysed by an iterative nonribosomal peptide synthetase. Chem Sci 2020; 11:11525-11530. [PMID: 34094397 PMCID: PMC8162485 DOI: 10.1039/d0sc03627g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Siderophores play a vital role in the viability of fungi and are essential for the virulence of many pathogenic fungal species. Despite their importance in fungal physiology and pathogenesis, the programming rule of siderophore assembly by fungal nonribosomal peptide synthetases (NRPSs) remains unresolved. Here, we report the characterization of the bimodular fungal NRPS, SidD, responsible for construction of the extracellular siderophore fusarinine C. The use of intact protein mass spectrometry, together with in vitro biochemical assays of native and dissected enzymes, provided snapshots of individual biosynthetic steps during NPRS catalysis. The adenylation and condensation domain of SidD can iteratively load and condense the amino acid building block cis-AMHO, respectively, to synthesize fusarinine C. Our study showcases the iterative programming features of fungal siderophore-producing NRPSs.
Collapse
Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
| | - Matthew Jenner
- Department of Chemistry, Warwick Integrative Synthetic Biology Center, University of Warwick Coventry UK
- Warwick Integrative Synthetic Biology (WISB) Centre, University of Warwick Coventry UK
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
| |
Collapse
|
54
|
Habib S, Ahmad SA, Wan Johari WL, Abd Shukor MY, Alias SA, Smykla J, Saruni NH, Abdul Razak NS, Yasid NA. Production of Lipopeptide Biosurfactant by a Hydrocarbon-Degrading Antarctic Rhodococcus. Int J Mol Sci 2020; 21:ijms21176138. [PMID: 32858859 PMCID: PMC7504157 DOI: 10.3390/ijms21176138] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/19/2022] Open
Abstract
Rhodococci are renowned for their great metabolic repertoire partly because of their numerous putative pathways for large number of specialized metabolites such as biosurfactant. Screening and genome-based assessment for the capacity to produce surface-active molecules was conducted on Rhodococcus sp. ADL36, a diesel-degrading Antarctic bacterium. The strain showed a positive bacterial adhesion to hydrocarbon (BATH) assay, drop collapse test, oil displacement activity, microplate assay, maximal emulsification index at 45% and ability to reduce water surface tension to < 30 mN/m. The evaluation of the cell-free supernatant demonstrated its high stability across the temperature, pH and salinity gradient although no correlation was found between the surface and emulsification activity. Based on the positive relationship between the assessment of macromolecules content and infrared analysis, the extracted biosurfactant synthesized was classified as a lipopeptide. Prediction of the secondary metabolites in the non-ribosomal peptide synthetase (NRPS) clusters suggested the likelihood of the surface-active lipopeptide production in the strain’s genomic data. This is the third report of surface-active lipopeptide producers from this phylotype and the first from the polar region. The lipopeptide synthesized by ADL36 has the prospect to be an Antarctic remediation tool while furnishing a distinctive natural product for biotechnological application and research.
Collapse
Affiliation(s)
- Syahir Habib
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Wan Lutfi Wan Johari
- Department of Environment, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia;
| | - Mohd Yunus Abd Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, C308 Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Jerzy Smykla
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120 Kraków, Poland;
| | - Nurul Hani Saruni
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Nur Syafiqah Abdul Razak
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
- Correspondence: ; Tel.: +603-9769-8297
| |
Collapse
|
55
|
Zhao F, Liu Z, Yang S, Ding N, Gao X. Quinolactacin Biosynthesis Involves Non-Ribosomal-Peptide-Synthetase-Catalyzed Dieckmann Condensation to Form the Quinolone-γ-lactam Hybrid. Angew Chem Int Ed Engl 2020; 59:19108-19114. [PMID: 32663343 PMCID: PMC10165850 DOI: 10.1002/anie.202005770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Indexed: 12/15/2022]
Abstract
Quinolactacins are novel fungal alkaloids that feature a quinolone-γ-lactam hybrid, which is a potential pharmacophore for the treatment of cancer and Alzheimer's disease. Herein, we report the identification of the quinolactacin A2 biosynthetic gene cluster and elucidate the enzymatic basis for the formation of the quinolone-γ-lactam structure. We reveal an unusual β-keto acid (N-methyl-2-aminobenzoylacetate) precursor that is derived from the primary metabolite l-kynurenine via methylation, oxidative decarboxylation, and amide hydrolysis reactions. In vitro assays reveal two single-module non-ribosomal peptide synthetases (NRPs) that incorporate the β-keto acid and l-isoleucine, followed by Dieckmann condensation, to form the quinolone-γ-lactam. Notably, the bioconversion from l-kynurenine to the β-keto acid is a unique strategy employed by nature to decouple R*-domain-containing NRPS from the polyketide synthase (PKS) machinery, expanding the paradigm for the biosynthesis of quinolone-γ-lactam natural products via Dieckmann condensation.
Collapse
Affiliation(s)
- Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Shuyuan Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Ning Ding
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA.,Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| |
Collapse
|
56
|
Yuan S, Gopal JV, Ren S, Chen L, Liu L, Gao Z. Anticancer fungal natural products: Mechanisms of action and biosynthesis. Eur J Med Chem 2020; 202:112502. [PMID: 32652407 DOI: 10.1016/j.ejmech.2020.112502] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 01/07/2023]
Abstract
Many fungal metabolites show promising anticancer properties both in vitro and in animal models, and some synthetic analogs of those metabolites have progressed into clinical trials. However, currently, there are still no fungi-derived agents approved as anticancer drugs. Two potential reasons could be envisioned: 1) lacking a clear understanding of their anticancer mechanism of action, 2) unable to supply enough materials to support the preclinical and clinic developments. In this review, we will summarize recent efforts on elucidating the anticancer mechanisms and biosynthetic pathways of several promising anticancer fungal natural products.
Collapse
Affiliation(s)
- Siwen Yuan
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jannu Vinay Gopal
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Shuya Ren
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Litong Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| |
Collapse
|
57
|
Yun CS, Nishimoto K, Motoyama T, Shimizu T, Hino T, Dohmae N, Nagano S, Osada H. Unique features of the ketosynthase domain in a nonribosomal peptide synthetase-polyketide synthase hybrid enzyme, tenuazonic acid synthetase 1. J Biol Chem 2020; 295:11602-11612. [PMID: 32565425 DOI: 10.1074/jbc.ra120.013105] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/18/2020] [Indexed: 11/06/2022] Open
Abstract
Many microbial secondary metabolites are produced by multienzyme complexes comprising nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). The ketosynthase (KS) domains of polyketide synthase normally catalyze the decarboxylative Claisen condensation of acyl and malonyl blocks to extend the polyketide chain. However, the terminal KS domain in tenuazonic acid synthetase 1 (TAS1) from the fungus Pyricularia oryzae conducts substrate cyclization. Here, we report on the unique features of the KS domain in TAS1. We observed that this domain is monomeric, not dimeric as is typical for KSs. Analysis of a 1.68-Å resolution crystal structure suggests that the substrate cyclization is triggered via proton abstraction from the active methylene moiety in the substrate by a catalytic His-322 residue. Additionally, we show that TAS1 KS promiscuously accepts aminoacyl substrates and that this promiscuity can be increased by a single amino acid substitution in the substrate-binding pocket of the enzyme. These findings provide insight into a KS domain that accepts the amino acid-containing substrate in an NRPS-PKS hybrid enzyme and provide hints to the substrate cyclization mechanism performed by the KS domain in the biosynthesis of the mycotoxin tenuazonic acid.
Collapse
Affiliation(s)
- Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Kazuki Nishimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| |
Collapse
|
58
|
Yuan B, Liu D, Guan X, Yan Y, Zhang J, Zhang Y, Yang D, Ma M, Lin W. Piperazine ring formation by a single-module NRPS and cleavage by an α-KG-dependent nonheme iron dioxygenase in brasiliamide biosynthesis. Appl Microbiol Biotechnol 2020; 104:6149-6159. [PMID: 32436033 DOI: 10.1007/s00253-020-10678-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/02/2020] [Accepted: 05/10/2020] [Indexed: 10/24/2022]
Abstract
Brasiliamides are a class of piperazine-containing alkaloids produced by Penicillium brasilianum with a range of pharmaceutical activities. The mechanism of brasiliamide biosynthesis, including piperazine ring formation and multiple tailoring modifications, still remains unclear. In this study, the biosynthetic gene cluster of brasiliamides, brs, was identified from the marine-derived fungal strain Penicillium brasilianum WZXY-M122-9. Deletion of a histone deacetylase-encoding gene using a CRISPR/Cas9 gene editing system led to the production of a new compound, namely brasiliamide I (1). The brs-encoded single-module nonribosomal peptide synthetase (NRPS) BrsA is involved in the formation of the piperazine skeleton of brasiliamides. Full-length BrsA protein (113.6 kDa) was purified, and reconstitution of enzymatic activity in vitro confirmed that BrsA stereoselectively accepts L-phenylalanine as the substrate. Multiple deletion of tailoring genes and analysis of purified proteins in vitro enabled us to propose a brasiliamide biosynthetic pathway. In the tailoring steps, an α-ketoglutarate (KG)-dependent nonheme iron dioxygenase, BrsJ, was identified to catalyze piperazine ring cleavage during biosynthesis of brasiliamide A (2). KEY POINTS: The gene cluster encoding brasiliamide biosynthesis, brs, is identified. Deletion of a histone deacetylase-encoding gene produces brasiliamide I. BrsA catalyzes brasiliamide piperazine skeleton formation. BrsJ catalyzes piperazine ring cleavage to produce brasiliamide A. Graphical abstract.
Collapse
Affiliation(s)
- Bochuan Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China
| | - Xin Guan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China
| | - Yunchen Yan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China
| | - Jianping Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China
| | - Yiping Zhang
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, MNR, Xiamen, 361005, People's Republic of China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China.
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, People's Republic of China. .,Institute of Ocean Research, Peking University, Beijing, 100871, People's Republic of China.
| |
Collapse
|
59
|
Della Sala G, Mangoni A, Costantino V, Teta R. Identification of the Biosynthetic Gene Cluster of Thermoactinoamides and Discovery of New Congeners by Integrated Genome Mining and MS-Based Molecular Networking. Front Chem 2020; 8:397. [PMID: 32528927 PMCID: PMC7253712 DOI: 10.3389/fchem.2020.00397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/15/2020] [Indexed: 11/21/2022] Open
Abstract
The putative non-ribosomal peptide synthetase (NRPS) gene cluster encoding the biosynthesis of the bioactive cyclohexapeptide thermoactinoamide A (1) was identified in Thermoactinomyces vulgaris DSM 43016. Based on an in silico prediction, the biosynthetic operon was shown to contain two trimodular NRPSs, designated as ThdA and ThdB, respectively. Chemical analysis of a bacterial crude extract showed the presence of thermoactinoamide A (1), thereby supporting this biosynthetic hypothesis. Notably, integrating genome mining with a LC-HRMS/MS molecular networking-based investigation of the microbial metabolome, we succeeded in the identification of 10 structural variants (2–11) of thermoactinoamide A (1), five of them being new compounds (thermoactinoamides G-K, 7–11). As only one thermoactinoamide operon was found in T. vulgaris, it can be assumed that all thermoactinoamide congeners are assembled by the same multimodular NRPS system. In light of these findings, we suggest that the thermoactinoamide synthetase is able to create chemical diversity, combining the relaxed substrate selectivity of some adenylation domains with the iterative and/or alternative use of specific modules. In the frame of our screening program to discover antitumor natural products, thermoactinoamide A (1) was shown to exert a moderate growth-inhibitory effect in BxPC-3 cancer cells in the low micromolar range, while being inactive in PANC-1 and 3AB-OS solid tumor models.
Collapse
Affiliation(s)
- Gerardo Della Sala
- Laboratory of Pre-clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| | - Valeria Costantino
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| | - Roberta Teta
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| |
Collapse
|
60
|
Niu X, Thaochan N, Hu Q. Diversity of Linear Non-Ribosomal Peptide in Biocontrol Fungi. J Fungi (Basel) 2020; 6:E61. [PMID: 32408496 PMCID: PMC7345191 DOI: 10.3390/jof6020061] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/27/2020] [Accepted: 05/09/2020] [Indexed: 12/16/2022] Open
Abstract
Biocontrol fungi (BFs) play a key role in regulation of pest populations. BFs produce multiple non-ribosomal peptides (NRPs) and other secondary metabolites that interact with pests, plants and microorganisms. NRPs-including linear and cyclic peptides (L-NRPs and C-NRPs)-are small peptides frequently containing special amino acids and other organic acids. They are biosynthesized in fungi through non-ribosomal peptide synthases (NRPSs). Compared with C-NRPs, L-NRPs have simpler structures, with only a linear chain and biosynthesis without cyclization. BFs mainly include entomopathogenic and mycoparasitic fungi, that are used to control insect pests and phytopathogens in fields, respectively. NRPs play an important role of in the interactions of BFs with insects or phytopathogens. On the other hand, the residues of NRPs may contaminate food through BFs activities in the environment. In recent decades, C-NRPs in BFs have been thoroughly reviewed. However, L-NRPs are rarely investigated. In order to better understand the species and potential problems of L-NRPs in BFs, this review lists the L-NRPs from entomopathogenic and mycoparasitic fungi, summarizes their sources, structures, activities and biosynthesis, and details risks and utilization prospects.
Collapse
Affiliation(s)
- Xiaoyan Niu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Narit Thaochan
- Pest Management Biotechnology and Plant Physiology Laboratory, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand;
| | - Qiongbo Hu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| |
Collapse
|
61
|
|
62
|
Li H, Gilchrist CLM, Phan CS, Lacey HJ, Vuong D, Moggach SA, Lacey E, Piggott AM, Chooi YH. Biosynthesis of a New Benzazepine Alkaloid Nanangelenin A from Aspergillus nanangensis Involves an Unusual l-Kynurenine-Incorporating NRPS Catalyzing Regioselective Lactamization. J Am Chem Soc 2020; 142:7145-7152. [PMID: 32182055 DOI: 10.1021/jacs.0c01605] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1-Benzazepine is a pharmaceutically important scaffold but is rare among natural products. Nanangelenin A (1), containing an unprecedented 3,4-dihydro-1-benzazepine-2,5-dione-N-prenyl-N-acetoxy-anthranilamide scaffold, was isolated from a novel species of Australian fungus, Aspergillus nanangensis. Genomic and retrobiosynthetic analyses identified a putative nonribosomal peptide synthetase (NRPS) gene cluster (nan). The detailed biosynthetic pathway to 1 was established by heterologous pathway reconstitution in A. nidulans, which led to biosynthesis of intermediates nanagelenin B-F (2-5 and 7). We demonstrated that the NRPS NanA incorporates anthranilic acid (Ant) and l-kynurenine (l-Kyn), which is supplied by a dedicated indoleamine-2,3-dioxygenase NanC encoded in the gene cluster. Using heterologous in vivo assays and mutagenesis, we demonstrated that the C-terminal condensation (CT) and thiolation (T3) domains of NanA are responsible for the regioselective cyclization of the tethered Ant-l-Kyn dipeptide to form the unusual benzazepine scaffold in 1. We also showed that NanA-CT catalyzes the regioselective cyclization of a surrogate synthetic substrate, Ant-l-Kyn-N-acetylcysteamine, to give the benzazepine scaffold, while spontaneous cyclization of the dipeptide yielded the alternative kinetically favored benzodiazepine scaffold. The discovery of 1 and the characterization of NanA have expanded the chemical and functional diversities of fungal NRPSs.
Collapse
Affiliation(s)
| | | | | | - Heather J Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | | | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | | |
Collapse
|
63
|
Bacteria as genetically programmable producers of bioactive natural products. Nat Rev Chem 2020; 4:172-193. [PMID: 37128046 DOI: 10.1038/s41570-020-0176-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2020] [Indexed: 12/17/2022]
Abstract
Next to plants, bacteria account for most of the biomass on Earth. They are found everywhere, although certain species thrive only in specific ecological niches. These microorganisms biosynthesize a plethora of both primary and secondary metabolites, defined, respectively, as those required for the growth and maintenance of cellular functions and those not required for survival but offering a selective advantage for the producer under certain conditions. As a result, bacterial fermentation has long been used to manufacture valuable natural products of nutritional, agrochemical and pharmaceutical interest. The interactions of secondary metabolites with their biological targets have been optimized by millions of years of evolution and they are, thus, considered to be privileged chemical structures, not only for drug discovery. During the last two decades, functional genomics has allowed for an in-depth understanding of the underlying biosynthetic logic of secondary metabolites. This has, in turn, paved the way for the unprecedented use of bacteria as programmable biochemical workhorses. In this Review, we discuss the multifaceted use of bacteria as biological factories in diverse applications and highlight recent advances in targeted genetic engineering of bacteria for the production of valuable bioactive compounds. Emphasis is on current advances to access nature's abundance of natural products.
Collapse
|
64
|
Wang M, Xie Z, Tang S, Chang EL, Tang Y, Guo Z, Cui Y, Wu B, Ye T, Chen Y. Reductase of Mutanobactin Synthetase Triggers Sequential C-C Macrocyclization, C-S Bond Formation, and C-C Bond Cleavage. Org Lett 2020; 22:960-964. [PMID: 31917593 DOI: 10.1021/acs.orglett.9b04501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutanobactins (MUBs) and their congeners that contain a macrocycle and/or a thiazepane ring are lipopeptides from Streptococcus mutans, a major causative agent of dental caries. Here we show that the C-terminal reductase domain of MubD releases the lipohexapeptide intermediates in an aldehyde form, which enables a spontaneous C-C macrocyclization. In the presence of a thiol group, the macrocyclized MUBs can further undergo spontaneous C-S bond formation and C-C bond cleavage to generate diverse MUB congeners.
Collapse
Affiliation(s)
- Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China.,State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics , Peking University Shenzhen Graduate School, Tsinghua University Shenzhen International Graduate School , Shenzhen 518055 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhoujie Xie
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China
| | - Shoubin Tang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics , Peking University Shenzhen Graduate School, Tsinghua University Shenzhen International Graduate School , Shenzhen 518055 , China
| | - Ee Ling Chang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics , Peking University Shenzhen Graduate School, Tsinghua University Shenzhen International Graduate School , Shenzhen 518055 , China
| | - Yue Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China.,State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics , Peking University Shenzhen Graduate School, Tsinghua University Shenzhen International Graduate School , Shenzhen 518055 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yinglu Cui
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China
| | - Bian Wu
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics , Peking University Shenzhen Graduate School, Tsinghua University Shenzhen International Graduate School , Shenzhen 518055 , China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| |
Collapse
|
65
|
Zhang JM, Wang HH, Liu X, Hu CH, Zou Y. Heterologous and Engineered Biosynthesis of Nematocidal Polyketide–Nonribosomal Peptide Hybrid Macrolactone from Extreme Thermophilic Fungi. J Am Chem Soc 2020; 142:1957-1965. [DOI: 10.1021/jacs.9b11410] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jin-Mei Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Hang-Hang Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Xuan Liu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chang-Hua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| |
Collapse
|
66
|
Berry D, Mace W, Grage K, Wesche F, Gore S, Schardl CL, Young CA, Dijkwel PP, Leuchtmann A, Bode HB, Scott B. Efficient nonenzymatic cyclization and domain shuffling drive pyrrolopyrazine diversity from truncated variants of a fungal NRPS. Proc Natl Acad Sci U S A 2019; 116:25614-25623. [PMID: 31801877 PMCID: PMC6926027 DOI: 10.1073/pnas.1913080116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) generate the core peptide scaffolds of many natural products. These include small cyclic dipeptides such as the insect feeding deterrent peramine, which is a pyrrolopyrazine (PPZ) produced by grass-endophytic Epichloë fungi. Biosynthesis of peramine is catalyzed by the 2-module NRPS, PpzA-1, which has a C-terminal reductase (R) domain that is required for reductive release and cyclization of the NRPS-tethered dipeptidyl-thioester intermediate. However, some PpzA variants lack this R domain due to insertion of a transposable element into the 3' end of ppzA We demonstrate here that these truncated PpzA variants utilize nonenzymatic cyclization of the dipeptidyl thioester to a 2,5-diketopiperazine (DKP) to synthesize a range of novel PPZ products. Truncation of the R domain is sufficient to subfunctionalize PpzA-1 into a dedicated DKP synthetase, exemplified by the truncated variant, PpzA-2, which has also evolved altered substrate specificity and reduced N-methyltransferase activity relative to PpzA-1. Further allelic diversity has been generated by recombination-mediated domain shuffling between ppzA-1 and ppzA-2, resulting in the ppzA-3 and ppzA-4 alleles, each of which encodes synthesis of a unique PPZ metabolite. This research establishes that efficient NRPS-catalyzed DKP biosynthesis can occur in vivo through nonenzymatic dipeptidyl cyclization and presents a remarkably clean example of NRPS evolution through recombinant exchange of functionally divergent domains. This work highlights that allelic variants of a single NRPS can result in a surprising level of secondary metabolite diversity comparable to that observed for some gene clusters.
Collapse
Affiliation(s)
- Daniel Berry
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Wade Mace
- Grasslands Research Centre, AgResearch Ltd., Palmerston North 4442, New Zealand
| | - Katrin Grage
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Frank Wesche
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sagar Gore
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | | | | | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Adrian Leuchtmann
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Helge B Bode
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany;
- Buchmann Institute for Molecular Life Sciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
- Landes-Offensive zur Entwicklung Wissenschaftlich-Ökonomischer Exzellenz (LOEWE) Centre for Translational Biodiversity Genomics, 60325 Frankfurt am Main, Germany
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand;
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| |
Collapse
|
67
|
Antitumor astins originate from the fungal endophyte Cyanodermella asteris living within the medicinal plant Aster tataricus. Proc Natl Acad Sci U S A 2019; 116:26909-26917. [PMID: 31811021 DOI: 10.1073/pnas.1910527116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Medicinal plants are a prolific source of natural products with remarkable chemical and biological properties, many of which have considerable remedial benefits. Numerous medicinal plants are suffering from wildcrafting, and thus biotechnological production processes of their natural products are urgently needed. The plant Aster tataricus is widely used in traditional Chinese medicine and contains unique active ingredients named astins. These are macrocyclic peptides showing promising antitumor activities and usually containing the highly unusual moiety 3,4-dichloroproline. The biosynthetic origins of astins are unknown despite being studied for decades. Here we show that astins are produced by the recently discovered fungal endophyte Cyanodermella asteris We were able to produce astins in reasonable and reproducible amounts using axenic cultures of the endophyte. We identified the biosynthetic gene cluster responsible for astin biosynthesis in the genome of C. asteris and propose a production pathway that is based on a nonribosomal peptide synthetase. Striking differences in the production profiles of endophyte and host plant imply a symbiotic cross-species biosynthesis pathway for astin C derivatives, in which plant enzymes or plant signals are required to trigger the synthesis of plant-exclusive variants such as astin A. Our findings lay the foundation for the sustainable biotechnological production of astins independent from aster plants.
Collapse
|
68
|
Matsuda K, Kuranaga T, Wakimoto T. A New Cyclase Family Catalyzing Head-to-Tail Macrolactamization of Non-ribosomal Peptides. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.1106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
69
|
Steiniger C, Hoffmann S, Süssmuth RD. Probing Exchange Units for Combining Iterative and Linear Fungal Nonribosomal Peptide Synthetases. Cell Chem Biol 2019; 26:1526-1534.e2. [DOI: 10.1016/j.chembiol.2019.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/08/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
|
70
|
Baccile JA, Le HH, Pfannenstiel BT, Bok JW, Gomez C, Brandenburger E, Hoffmeister D, Keller NP, Schroeder FC. Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joshua A. Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
- Present Address: Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA USA
| | - Henry H. Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Brandon T. Pfannenstiel
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Jin Woo Bok
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology Hans-Knöll-Institute Friedrich Schiller University Jena Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology Hans-Knöll-Institute Friedrich Schiller University Jena Germany
| | - Nancy P. Keller
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| |
Collapse
|
71
|
Baccile JA, Le HH, Pfannenstiel BT, Bok JW, Gomez C, Brandenburger E, Hoffmeister D, Keller NP, Schroeder FC. Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains. Angew Chem Int Ed Engl 2019; 58:14589-14593. [PMID: 31342608 PMCID: PMC6764874 DOI: 10.1002/anie.201909052] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 01/08/2023]
Abstract
Cyclization of linear dipeptidyl precursors derived from nonribosomal peptide synthetases (NRPSs) into 2,5-diketopiperazines (DKPs) is a crucial step in the biosynthesis of a large number of bioactive natural products. However, the mechanism of DKP formation in fungi has remained unclear, despite extensive studies of their biosyntheses. Here we show that DKP formation en route to the fungal virulence factor gliotoxin requires a seemingly extraneous couplet of condensation (C) and thiolation (T) domains in the NRPS GliP. In vivo truncation of GliP to remove the CT couplet or just the T domain abrogated production of gliotoxin and all other gli pathway metabolites. Point mutation of conserved active sites in the C and T domains diminished cyclization activity of GliP in vitro and abolished gliotoxin biosynthesis in vivo. Verified NRPSs of other fungal DKPs terminate with similar CT domain couplets, suggesting a conserved strategy for DKP biosynthesis by fungal NRPSs.
Collapse
Affiliation(s)
- Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brandon T Pfannenstiel
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jin Woo Bok
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Nancy P Keller
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
72
|
Hai Y, Jenner M, Tang Y. Complete Stereoinversion of l-Tryptophan by a Fungal Single-Module Nonribosomal Peptide Synthetase. J Am Chem Soc 2019; 141:16222-16226. [PMID: 31573806 DOI: 10.1021/jacs.9b08898] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Single-module nonribosomal peptide synthetases (NRPSs) and NRPS-like enzymes activate and transform carboxylic acids in both primary and secondary metabolism and are of great interest due to their biocatalytic potentials. The single-module NRPS IvoA is essential for fungal pigment biosynthesis. Here, we show that IvoA catalyzes ATP-dependent unidirectional stereoinversion of l-tryptophan to d-tryptophan with complete conversion. While the stereoinversion is catalyzed by the epimerization (E) domain, the terminal condensation (C) domain stereoselectively hydrolyzes d-tryptophanyl-S-phosphopantetheine thioester and thus represents a noncanonical C domain function. Using IvoA, we demonstrate a biocatalytic stereoinversion/deracemization route to access a variety of substituted d-tryptophan analogs in high enantiomeric excess.
Collapse
Affiliation(s)
| | - Matthew Jenner
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , United Kingdom.,Warwick Integrative Synthetic Biology (WISB) Centre , University of Warwick , Coventry CV4 7AL , United Kingdom
| | | |
Collapse
|
73
|
Gulick AM, Aldrich CC. Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes. Nat Prod Rep 2019; 35:1156-1184. [PMID: 30046790 DOI: 10.1039/c8np00044a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to early 2018 The Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) are families of modular enzymes that produce a tremendous diversity of natural products, with antibacterial, antifungal, immunosuppressive, and anticancer activities. Both enzymes utilize a fascinating modular architecture in which the synthetic intermediates are covalently attached to a peptidyl- or acyl-carrier protein that is delivered to catalytic domains for natural product elongation, modification, and termination. An investigation of the structural mechanism therefore requires trapping the often transient interactions between the carrier and catalytic domains. Many novel chemical probes have been produced to enable the structural and functional investigation of multidomain NRPS and PKS structures. This review will describe the design and implementation of the chemical tools that have proven to be useful in biochemical and biophysical studies of these natural product biosynthetic enzymes.
Collapse
Affiliation(s)
- Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 955 Main St, Buffalo, NY 14203, USA.
| | | |
Collapse
|
74
|
Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
Collapse
Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
| | | |
Collapse
|
75
|
Greco C, Pfannenstiel BT, Liu JC, Keller NP. Depsipeptide Aspergillicins Revealed by Chromatin Reader Protein Deletion. ACS Chem Biol 2019; 14:1121-1128. [PMID: 31117395 DOI: 10.1021/acschembio.9b00161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Expression of biosynthetic gene clusters (BGCs) in filamentous fungi is highly regulated by epigenetic remodeling of chromatin structure. Two classes of histone modifying proteins, writers (which place modifications on histone tails) and erasers (which remove the modifications), have been used extensively to activate cryptic BGCs in fungi. Here, for the first time, we present activation of a cryptic BGC by a third category of histone modifying proteins, reader proteins that recognize histone tail modifications and commonly mediate writer and eraser activity. Loss of the reader SntB (Δ sntB) resulted in the synthesis of two cryptic cyclic hexa-depsipeptides, aspergillicin A and aspergillicin F, in the fungus Aspergillus flavus. Liquid chromatography, high resolution mass spectrometry, and NMR analysis coupled with bioinformatic analysis and gene deletion experiments revealed that a six adenylation (A) domain nonribosomal peptide synthetase (NRPS, called AgiA) and O-methyltransferase (AgiB) were required for metabolite formation. A proposed biosynthetic scheme illustrates the requirement for unusual NRPS domains, such as a starting condensation domain and a thiolesterase domain proposed to cyclize the depsipeptides. This latter activity has only been found in bacterial but not fungal NRPS. The agi BGC-unique to A. flavus and some closely related species (e.g., A. oryzae, A. arachidicola)-is located next to a conserved Aspergillus siderophore BGC syntenic to other fungi.
Collapse
Affiliation(s)
- Claudio Greco
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | | | - James C. Liu
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| |
Collapse
|
76
|
Steiniger C, Hoffmann S, Süssmuth RD. Desymmetrization of Cyclodepsipeptides by Assembly Mode Switching of Iterative Nonribosomal Peptide Synthetases. ACS Synth Biol 2019; 8:661-667. [PMID: 30862156 DOI: 10.1021/acssynbio.8b00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nonribosomal peptide synthetases assemble a considerable number of structurally complex peptides of pharmacological importance. This turns them into important biosynthetic machineries for peptide diversification by engineering approaches. To date, manifold reprogramming approaches focus on employing module and domain exchanges, or the engineering of domains responsible for amino acid recognition. In this work, we present an engineering strategy for the manipulation of product assembly modes by fusing iterative fungal cyclodepsipeptide synthetases. The reassignment of terminal condensation domains as canonical condensation domains induces a switch from an exclusively iterative into a mixed linear/iterative peptide assembly mode. In the heterologous host E. coli we thus produced in vivo novel hybrid cyclodepsipeptides with altered structural symmetry. Our findings contribute a new experimental set of nonribosomal peptide synthetase reprogramming to the engineering toolbox for peptide structure diversification.
Collapse
Affiliation(s)
- Charlotte Steiniger
- Institut für organische Chemie, Technische Universität Berlin, Strasse des 17. Juni 124/TC2, Berlin, 10623, Germany
| | - Sylvester Hoffmann
- Institut für organische Chemie, Technische Universität Berlin, Strasse des 17. Juni 124/TC2, Berlin, 10623, Germany
| | - Roderich D. Süssmuth
- Institut für organische Chemie, Technische Universität Berlin, Strasse des 17. Juni 124/TC2, Berlin, 10623, Germany
| |
Collapse
|
77
|
Zhou Y, Lin X, Xu C, Shen Y, Wang SP, Liao H, Li L, Deng H, Lin HW. Investigation of Penicillin Binding Protein (PBP)-like Peptide Cyclase and Hydrolase in Surugamide Non-ribosomal Peptide Biosynthesis. Cell Chem Biol 2019; 26:737-744.e4. [PMID: 30905680 DOI: 10.1016/j.chembiol.2019.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/14/2019] [Accepted: 02/11/2019] [Indexed: 11/28/2022]
Abstract
Non-ribosomal peptides (NRPs) are biosynthesized on non-ribosomal peptides synthetase (NRPS) complexes, of which a C-terminal releasing domain commonly offloads the products. Interestingly, a dedicated releasing domain is absent in surugamides (SGM) NRPS, which directs the biosynthesis of cyclic octapeptides, SGM-A to -E, and the linear decapeptide, SGM-F. Here, we confirmed that surE is essential for the production of SGMs via genetic experiments. Biochemical characterization demonstrated that the recombinant enzyme, SurE, can generate the main products SGM-A and -F from the corresponding SNAC substrates, indicating that SurE is a standalone thioesterase-like enzyme. SurE also displays considerable substrate plasticity with expanded ring or different amino acid compositions to produce different cyclopeptides, highlighting the potential of chemoenzymatic applications. Site-directed mutagenesis allowed identification of the key residues of SurE. Finally, bioinformatics analysis suggested that SurE homologs are widely distributed in bacteria, suggesting a general mechanism of NRP release in Nature.
Collapse
Affiliation(s)
- Yongjun Zhou
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao Lin
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Chunmin Xu
- Jiangxi University of Traditional Chinese Medicine, Nanchang 33004, China
| | - Yaoyao Shen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shu-Ping Wang
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hongze Liao
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lei Li
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hai Deng
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| |
Collapse
|
78
|
McErlean M, Overbay J, Van Lanen S. Refining and expanding nonribosomal peptide synthetase function and mechanism. J Ind Microbiol Biotechnol 2019; 46:493-513. [PMID: 30673909 PMCID: PMC6460464 DOI: 10.1007/s10295-018-02130-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are involved in the biosynthesis of numerous peptide and peptide-like natural products that have been exploited in medicine, agriculture, and biotechnology, among other fields. As a consequence, there have been considerable efforts aimed at understanding how NRPSs orchestrate the assembly of these natural products. This review highlights several recent examples that continue to expand upon the fundamental knowledge of NRPS mechanism and includes (1) the discovery of new NRPS substrates and the mechanism by which these sometimes structurally complex substrates are made, (2) the characterization of new NRPS activities and domains that function during the process of peptide assembly, and (3) the various catalytic strategies that are utilized to release the NRPS product. These findings continue to strengthen the predictive power for connecting genes to products, thereby facilitating natural product discovery and development in the Genomics Era.
Collapse
Affiliation(s)
- Matt McErlean
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Jonathan Overbay
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Steven Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA.
| |
Collapse
|
79
|
Resende DISP, Boonpothong P, Sousa E, Kijjoa A, Pinto MMM. Chemistry of the fumiquinazolines and structurally related alkaloids. Nat Prod Rep 2019; 36:7-34. [DOI: 10.1039/c8np00043c] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review covers the isolation, structure elucidation, biological activities, biosynthetic pathways, and synthetic studies of the 77 fumiquinazolines and structurally related alkaloids described up to 2018.
Collapse
Affiliation(s)
- Diana I. S. P. Resende
- Laboratory of Organic and Pharmaceutical Chemistry
- Faculty of Pharmaceutical Sciences
- University of Porto
- 4050-313 Porto
- Portugal
| | - Papichaya Boonpothong
- Laboratory of Organic and Pharmaceutical Chemistry
- Faculty of Pharmaceutical Sciences
- University of Porto
- 4050-313 Porto
- Portugal
| | - Emília Sousa
- Laboratory of Organic and Pharmaceutical Chemistry
- Faculty of Pharmaceutical Sciences
- University of Porto
- 4050-313 Porto
- Portugal
| | - Anake Kijjoa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR)
- Terminal de Cruzeiros do Porto de Leixões
- Matosinhos
- Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar
| | - Madalena M. M. Pinto
- Laboratory of Organic and Pharmaceutical Chemistry
- Faculty of Pharmaceutical Sciences
- University of Porto
- 4050-313 Porto
- Portugal
| |
Collapse
|
80
|
Theobald S, Vesth TC, Rendsvig JK, Nielsen KF, Riley R, de Abreu LM, Salamov A, Frisvad JC, Larsen TO, Andersen MR, Hoof JB. Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication. Sci Rep 2018; 8:17957. [PMID: 30560908 PMCID: PMC6298953 DOI: 10.1038/s41598-018-36561-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 01/01/2023] Open
Abstract
The increased interest in secondary metabolites (SMs) has driven a number of genome sequencing projects to elucidate their biosynthetic pathways. As a result, studies revealed that the number of secondary metabolite gene clusters (SMGCs) greatly outnumbers detected compounds, challenging current methods to dereplicate and categorize this amount of gene clusters on a larger scale. Here, we present an automated workflow for the genetic dereplication and analysis of secondary metabolism genes in fungi. Focusing on the secondary metabolite rich genus Aspergillus, we categorize SMGCs across genomes into SMGC families using network analysis. Our method elucidates the diversity and dynamics of secondary metabolism in section Nigri, showing that SMGC diversity within the section has the same magnitude as within the genus. Using our genome analysis we were able to predict the gene cluster responsible for biosynthesis of malformin, a potentiator of anti-cancer drugs, in 18 strains. To proof the general validity of our predictions, we developed genetic engineering tools in Aspergillus brasiliensis and subsequently verified the genes for biosynthesis of malformin.
Collapse
Affiliation(s)
- Sebastian Theobald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.,The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Tammi C Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Jakob Kræmmer Rendsvig
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.,Chr. Hansen Holding A/S, DK-2970, Hoersholm, Denmark
| | - Robert Riley
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Amyris, Inc., Emeryville, CA, USA
| | | | - Asaf Salamov
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jens Christian Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
| | - Jakob Blæsbjerg Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
| |
Collapse
|
81
|
Bahadoor A, Brauer EK, Bosnich W, Schneiderman D, Johnston A, Aubin Y, Blackwell B, Melanson JE, Harris LJ. Gramillin A and B: Cyclic Lipopeptides Identified as the Nonribosomal Biosynthetic Products of Fusarium graminearum. J Am Chem Soc 2018; 140:16783-16791. [PMID: 30395461 DOI: 10.1021/jacs.8b10017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The virulence and broad host range of Fusarium graminearum is associated with its ability to secrete an arsenal of phytotoxic secondary metabolites, including the regulated mycotoxins belonging to the deoxynivalenol family. The TRI genes responsible for the biosynthesis of deoxynivalenol and related compounds are usually expressed during fungal infection. However, the F. graminearum genome harbors an array of unexplored biosynthetic gene clusters that are also co-induced with the TRI genes, including the nonribosomal peptide synthetase 8 ( NRPS8) gene cluster. Here, we identify two bicyclic lipopeptides, gramillin A (1) and B (2), as the biosynthetic end products of NRPS8. Structural elucidation by high-resolution LC-MS and NMR, including 1H-15N-13C HNCO and HNCA on isotopically enriched compounds, revealed that the gramillins possess a fused bicyclic structure with ring closure of the main peptide macrocycle occurring via an anhydride bond. Through targeted gene disruption, we characterized the GRA1 biosynthetic gene and its transcription factor GRA2 in the NRPS8 gene cluster. Further, we show that the gramillins are produced in planta on maize silks, promoting fungal virulence on maize but have no discernible effect on wheat head infection. Leaf infiltration of the gramillins induces cell death in maize, but not in wheat. Our results show that F. graminearum deploys the gramillins as a virulence agent in maize, but not in wheat, thus displaying host-specific adaptation.
Collapse
Affiliation(s)
- Adilah Bahadoor
- Metrology , National Research Council Canada , Ottawa , Ontario K1A 0R6 , Canada
| | - Elizabeth K Brauer
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Anne Johnston
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Yves Aubin
- Centre for Biologics Evaluation, Biologics, and Genetic Therapies Directorate , Health Canada , Ottawa , Ontario K1A 0K9 , Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Jeremy E Melanson
- Metrology , National Research Council Canada , Ottawa , Ontario K1A 0R6 , Canada
| | - Linda J Harris
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| |
Collapse
|
82
|
Yang X, Feng P, Yin Y, Bushley K, Spatafora JW, Wang C. Cyclosporine Biosynthesis in Tolypocladium inflatum Benefits Fungal Adaptation to the Environment. mBio 2018; 9:e01211-18. [PMID: 30279281 PMCID: PMC6168864 DOI: 10.1128/mbio.01211-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/22/2018] [Indexed: 12/19/2022] Open
Abstract
The cycloundecapeptide cyclosporin A (CsA) was first isolated from the insect-pathogenic fungus Tolypocladium inflatum for its antifungal activity and later developed as an immunosuppressant drug. However, the full biosynthetic mechanism of CsA remains unknown and has puzzled researchers for decades. In this study, the biosynthetic gene cluster is suggested to include 12 genes encoding enzymes, including the nonribosomal peptide synthetase (NRPS) (SimA) responsible for assembling the 11 amino acid substrates of cyclosporine and a polyketide synthase (PKS) (SimG) to mediate the production of the unusual amino acid (4R)-4-[(E)-2-butenyl]-4-methyl-l-threonine (Bmt). Individual deletion of 10 genes, isolation of intermediates, and substrate feeding experiments show that Bmt is biosynthesized by three enzymes, including SimG, SimI, and SimJ. The substrate d-alanine is catalyzed from l-alanine by alanine racemase SimB. Gene cluster transcription is regulated by a putative basic leucine zipper (bZIP)-type protein encoded by the cluster gene SimL We also found that the cluster cyclophilin (SimC) and transporter (SimD) genes contribute to the tolerance of CsA in the CsA-producing fungus. We also found that cyclosporine production could enable the fungus to outcompete other fungi during cocultivation tests. Deletion of the CsA biosynthetic genes also impaired fungal virulence against insect hosts. Taking all the data together, in addition to proposing a biosynthetic pathway of cyclosporines, the results of this study suggest that CsA produced by this fungus might play important ecological roles in fungal environment interactions.IMPORTANCE The cyclopeptide cyclosporin A was first isolated from the filamentous fungus Tolypocladium inflatum showing antifungal activity and was later developed as an immunosuppressant drug. We report the biosynthetic mechanism of cyclosporines that are mediated by a cluster of genes encoding NRPS and PKS controlled by a bZIP-type transcriptional regulator. The two unusual amino acids Bmt and d-Ala are produced by the PKS pathway and alanine racemase, respectively. The cyclophilin and transporter genes jointly contribute to fungal self-protection against cyclosporines. Cyclosporine confers on T. inflatum the abilities to outcompete other fungi in competitive interactions and to facilitate fungal infection of insect hosts, which therefore benefits fungal adaptations to different environments.
Collapse
Affiliation(s)
- Xiuqing Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Feng
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Yin
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Kathryn Bushley
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| |
Collapse
|
83
|
Kuranaga T, Matsuda K, Sano A, Kobayashi M, Ninomiya A, Takada K, Matsunaga S, Wakimoto T. Total Synthesis of the Nonribosomal Peptide Surugamide B and Identification of a New Offloading Cyclase Family. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Takefumi Kuranaga
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Ayae Sano
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Akihiro Ninomiya
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| |
Collapse
|
84
|
Kuranaga T, Matsuda K, Sano A, Kobayashi M, Ninomiya A, Takada K, Matsunaga S, Wakimoto T. Total Synthesis of the Nonribosomal Peptide Surugamide B and Identification of a New Offloading Cyclase Family. Angew Chem Int Ed Engl 2018; 57:9447-9451. [DOI: 10.1002/anie.201805541] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Takefumi Kuranaga
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Ayae Sano
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Akihiro Ninomiya
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| |
Collapse
|
85
|
Bertrand RL, Abdel-Hameed M, Sorensen JL. Lichen Biosynthetic Gene Clusters. Part I. Genome Sequencing Reveals a Rich Biosynthetic Potential. JOURNAL OF NATURAL PRODUCTS 2018; 81:723-731. [PMID: 29485276 DOI: 10.1021/acs.jnatprod.7b00769] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lichens are symbionts of fungi and algae that produce diverse secondary metabolites with useful properties. Little is known of lichen natural product biosynthesis because of the challenges of working with lichenizing fungi. We describe the first attempt to comprehensively profile the genetic secondary metabolome of a lichenizing fungus. An Illumina platform combined with the Antibiotics and Secondary Metabolites Analysis Shell (FungiSMASH, version 4.0) was used to sequence and annotate assembled contigs of the fungal partner of Cladonia uncialis. Up to 48 putative gene clusters are described comprising type I and type III polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS), hybrid PKS-NRPS, and terpene synthases. The number of gene clusters revealed by this work dwarfs the number of known secondary metabolites from C. uncialis, suggesting that lichenizing fungi have an unexplored biosynthetic potential.
Collapse
Affiliation(s)
- Robert L Bertrand
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - Mona Abdel-Hameed
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - John L Sorensen
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| |
Collapse
|
86
|
de Mattos-Shipley KMJ, Greco C, Heard DM, Hough G, Mulholland NP, Vincent JL, Micklefield J, Simpson TJ, Willis CL, Cox RJ, Bailey AM. The cycloaspeptides: uncovering a new model for methylated nonribosomal peptide biosynthesis. Chem Sci 2018; 9:4109-4117. [PMID: 29780540 PMCID: PMC5941284 DOI: 10.1039/c8sc00717a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/03/2018] [Indexed: 11/21/2022] Open
Abstract
The cycloaspeptide gene cluster includes a pathway-specific N-methyl transferase. Its disruption allowed incorporation of N-methylated amino acids provided in the culture medium, allowing efficient production of cycloaspeptide E and novel related products.
The cycloaspeptides are bioactive pentapeptides produced by various filamentous fungi, which have garnered interest from the agricultural industry due to the reported insecticidal activity of the minor metabolite, cycloaspeptide E. Genome sequencing, bioinformatics and heterologous expression confirmed that the cycloaspeptide gene cluster contains a minimal 5-module nonribosomal peptide synthetase (NRPS) and a new type of trans-acting N-methyltransferase (N-MeT). Deletion of the N-MeT encoding gene and subsequent feeding studies determined that two modules of the NRPS preferentially accept and incorporate N-methylated amino acids. This discovery allowed the development of a system with unprecedented control over substrate supply and thus output, both increasing yields of specific metabolites and allowing the production of novel fluorinated analogues. Furthermore, the biosynthetic pathway to ditryptophenaline, another fungal nonribosomal peptide, was shown to be similar, in that methylated phenylalanine is accepted by the ditryptophenaline NRPS. Again, this allowed the directed biosynthesis of a fluorinated analogue, through the feeding of a mutant strain. These discoveries represent a new paradigm for the production of N-methylated cyclic peptides via the selective incorporation of N-methylated free amino acids.
Collapse
Affiliation(s)
| | - Claudio Greco
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - David M Heard
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - Gemma Hough
- Syngenta Ltd. , Jealott's Hill International Research Centre Bracknell , Berkshire , RG42 6EY , UK
| | - Nicholas P Mulholland
- Syngenta Ltd. , Jealott's Hill International Research Centre Bracknell , Berkshire , RG42 6EY , UK
| | - Jason L Vincent
- Syngenta Ltd. , Jealott's Hill International Research Centre Bracknell , Berkshire , RG42 6EY , UK
| | - Jason Micklefield
- School of Chemistry , University of Manchester , Oxford Road , Manchester , M1 7DN , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - Christine L Willis
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - Russell J Cox
- Institute für Organsche Chemie , Leibniz Universität Hannover , Schneiderberg 1A , 30167 Hannover , Germany.,BMWZ , Leibniz Universität Hannover , Schneiderberg 38 , 30167 Hannover , Germany
| | - Andrew M Bailey
- School of Biological Sciences , University of Bristol , Life Sciences Building, 24 Tyndall Avenue , Bristol , BS8 1TQ , UK .
| |
Collapse
|
87
|
Aspergillus flavus Secondary Metabolites: More than Just Aflatoxins. Food Saf (Tokyo) 2018; 6:7-32. [PMID: 32231944 DOI: 10.14252/foodsafetyfscj.2017024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/09/2018] [Indexed: 11/21/2022] Open
Abstract
Aspergillus flavus is best known for producing the family of potent carcinogenic secondary metabolites known as aflatoxins. However, this opportunistic plant and animal pathogen also produces numerous other secondary metabolites, many of which have also been shown to be toxic. While about forty of these secondary metabolites have been identified from A. flavus cultures, analysis of the genome has predicted the existence of at least 56 secondary metabolite gene clusters. Many of these gene clusters are not expressed during growth of the fungus on standard laboratory media. This presents researchers with a major challenge of devising novel strategies to manipulate the fungus and its genome so as to activate secondary metabolite gene expression and allow identification of associated cluster metabolites. In this review, we discuss the genetic, biochemical and bioinformatic methods that are being used to identify previously uncharacterized secondary metabolite gene clusters and their associated metabolites. It is important to identify as many of these compounds as possible to determine their bioactivity with respect to fungal development, survival, virulence and especially with respect to any potential synergistic toxic effects with aflatoxin.
Collapse
|
88
|
Clevenger KD, Ye R, Bok JW, Thomas PM, Islam MN, Miley GP, Robey MT, Chen C, Yang K, Swyers M, Wu E, Gao P, Wu CC, Keller NP, Kelleher NL. Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity. Biochemistry 2018. [PMID: 29533658 DOI: 10.1021/acs.biochem.8b00076] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The benzodiazepine benzomalvin A/D is a fungally derived specialized metabolite and inhibitor of the substance P receptor NK1, biosynthesized by a three-gene nonribosomal peptide synthetase cluster. Here, we utilize fungal artificial chromosomes with metabolomic scoring (FAC-MS) to perform molecular genetic pathway dissection and targeted metabolomics analysis to assign the in vivo role of each domain in the benzomalvin biosynthetic pathway. The use of FAC-MS identified the terminal cyclizing condensation domain as BenY-CT and the internal C-domains as BenZ-C1 and BenZ-C2. Unexpectedly, we also uncovered evidence suggesting BenY-CT or a yet to be identified protein mediates benzodiazepine formation, representing the first reported benzodiazepine synthase enzymatic activity. This work informs understanding of what defines a fungal CT domain and shows how the FAC-MS platform can be used as a tool for in vivo analyses of specialized metabolite biosynthesis and for the discovery and dissection of new enzyme activities.
Collapse
Affiliation(s)
- Kenneth D Clevenger
- Proteomics Center of Excellence , Northwestern University , Evanston , Illinois 60208 , United States
| | - Rosa Ye
- Intact Genomics, Inc. , St. Louis , Missouri 63132 , United States
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology and Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Paul M Thomas
- Proteomics Center of Excellence , Northwestern University , Evanston , Illinois 60208 , United States.,Department of Molecular Biosciences , Northwestern University , Evanston , Illinois 60201 , United States
| | - Md Nurul Islam
- Intact Genomics, Inc. , St. Louis , Missouri 63132 , United States
| | - Galen P Miley
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Matthew T Robey
- Department of Molecular Biosciences , Northwestern University , Evanston , Illinois 60201 , United States
| | - Cynthia Chen
- Intact Genomics, Inc. , St. Louis , Missouri 63132 , United States
| | - KaHoua Yang
- Department of Medical Microbiology and Immunology and Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Michael Swyers
- Intact Genomics, Inc. , St. Louis , Missouri 63132 , United States
| | - Edward Wu
- Intact Genomics, Inc. , St. Louis , Missouri 63132 , United States
| | - Peng Gao
- Proteomics Center of Excellence , Northwestern University , Evanston , Illinois 60208 , United States
| | - Chengcang C Wu
- Intact Genomics, Inc. , St. Louis , Missouri 63132 , United States
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Neil L Kelleher
- Proteomics Center of Excellence , Northwestern University , Evanston , Illinois 60208 , United States.,Department of Molecular Biosciences , Northwestern University , Evanston , Illinois 60201 , United States.,Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| |
Collapse
|
89
|
Shi YM, Richter C, Challinor VL, Grün P, Girela del Rio A, Kaiser M, Schüffler A, Piepenbring M, Schwalbe H, Bode HB. Georatusin, a Specific Antiparasitic Polyketide–Peptide Hybrid from the Fungus Geomyces auratus. Org Lett 2018; 20:1563-1567. [DOI: 10.1021/acs.orglett.8b00293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Marcel Kaiser
- Swiss Tropical and Public Health Institute Parasite Chemotherapy and University of Basel, 4051 Basel, Switzerland
| | - Anja Schüffler
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 67663 Kaiserslautern, Germany
| | | | | | | |
Collapse
|
90
|
Hai Y, Tang Y. Biosynthesis of Long-Chain N-Acyl Amide by a Truncated Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid Megasynthase in Fungi. J Am Chem Soc 2018; 140:1271-1274. [PMID: 29343058 DOI: 10.1021/jacs.7b13350] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Truncated iterative polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) megasynthases in which only the C domain is present are widespread in fungi, yet nearly all members have unknown functions. Bioinformatics analysis showed that the C domains of such PKS-C enzymes are noncanonical due to substitution at the second histidine in the active site HHxxxDG motif. Here, we used genome mining strategy to characterize a cryptic PKS-C hybrid from Talaromyces wortmanii and discovered the products are reduced long-chain polyketides amidated with a specific ω-amino acid 5-aminopentanoic acid (5PA). The wortmanamides resemble long-chain N-acyl-amide signaling lipids that target diverse receptors including GPCRs. The noncanonical C domain of this PKS-C hybrid was also demonstrated to be a bona fide condensation domain that specifically selects 5PA and catalyzes amidation to release polyketide chain.
Collapse
Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, ‡Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, ‡Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| |
Collapse
|
91
|
De novo design and engineering of non-ribosomal peptide synthetases. Nat Chem 2017; 10:275-281. [PMID: 29461518 DOI: 10.1038/nchem.2890] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/06/2017] [Indexed: 01/20/2023]
Abstract
Peptides derived from non-ribosomal peptide synthetases (NRPSs) represent an important class of pharmaceutically relevant drugs. Methods to generate novel non-ribosomal peptides or to modify peptide natural products in an easy and predictable way are therefore of great interest. However, although the overall modular structure of NRPSs suggests the possibility of adjusting domain specificity and selectivity, only a few examples have been reported and these usually show a severe drop in production titre. Here we report a new strategy for the modification of NRPSs that uses defined exchange units (XUs) and not modules as functional units. XUs are fused at specific positions that connect the condensation and adenylation domains and respect the original specificity of the downstream module to enable the production of the desired peptides. We also present the use of internal condensation domains as an alternative to other peptide-chain-releasing domains for the production of cyclic peptides.
Collapse
|
92
|
A Highly Conserved Basidiomycete Peptide Synthetase Produces a Trimeric Hydroxamate Siderophore. Appl Environ Microbiol 2017; 83:AEM.01478-17. [PMID: 28842536 DOI: 10.1128/aem.01478-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/17/2017] [Indexed: 11/20/2022] Open
Abstract
The model white-rot basidiomycete, Ceriporiopsis (Gelatoporia) subvermispora B, encodes putative natural product biosynthesis genes. Among them is the gene for the seven-domain nonribosomal peptide synthetase CsNPS2. It is a member of the as-yet-uncharacterized fungal type VI siderophore synthetase family, which is highly conserved and widely distributed among the basidiomycetes. These enzymes include only one adenylation (A) domain, i.e., one complete peptide synthetase module, and two thiolation/condensation (T-C) didomain partial modules which together constitute an AT1C1T2C2T3C3 domain setup. The full-length CsNPS2 enzyme (274.5 kDa) was heterologously produced as a polyhistidine fusion in Aspergillus niger as a soluble and active protein. N 5-acetyl-N 5-hydroxy-l-ornithine (l-AHO) and N 5-cis-anhydromevalonyl-N 5 -hydroxy-l-ornithine (l-AMHO) were accepted as the substrates, based on results of an in vitro substrate-dependent [32P]ATP-pyrophosphate radioisotope exchange assay. Full-length holo-CsNPS2 catalyzed amide bond formation between three l-AHO molecules to release the linear l-AHO trimer, called basidioferrin, as the product in vitro, which was verified by liquid chromatography-high-resolution electrospray ionization-mass spectrometry analysis. Phylogenetic analyses suggested that type VI family siderophore synthetases are widespread in mushrooms and evolved in a common ancestor of basidiomycetes.IMPORTANCE The basidiomycete nonribosomal peptide synthetase CsNPS2 represents a member of a widely distributed but previously uninvestigated class (type VI) of fungal siderophore synthetases. Genes orthologous to CsNPS2 are highly conserved across various phylogenetic clades of the basidiomycetes. Hence, our work serves as a broadly applicable model for siderophore biosynthesis and iron metabolism in higher fungi. Also, our results on the amino acid substrate preference of CsNPS2 support a further understanding of the substrate selectivity of fungal adenylation domains. Methodologically, this report highlights the Aspergillus niger/SM-Xpress-based system as a suitable platform to heterologously express multimodular basidiomycete biosynthesis enzymes in the >250-kDa range in soluble and active form.
Collapse
|
93
|
Steiniger C, Hoffmann S, Mainz A, Kaiser M, Voigt K, Meyer V, Süssmuth RD. Harnessing fungal nonribosomal cyclodepsipeptide synthetases for mechanistic insights and tailored engineering. Chem Sci 2017; 8:7834-7843. [PMID: 29163920 PMCID: PMC5674221 DOI: 10.1039/c7sc03093b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/25/2017] [Indexed: 11/21/2022] Open
Abstract
Hybrid fungal CDP synthetases are constructed from three different origins to produce highly active cyclodepsipeptides up to g L–1 scale.
Nonribosomal peptide synthetases represent potential platforms for the design and engineering of structurally complex peptides. While previous focus has been centred mainly on bacterial systems, fungal synthetases assembling drugs like the antifungal echinocandins, the antibacterial cephalosporins or the anthelmintic cyclodepsipeptide (CDP) PF1022 await in-depth exploitation. As various mechanistic features of fungal CDP biosynthesis are only partly understood, effective engineering of NRPSs has been severely hampered. By combining protein truncation, in trans expression and combinatorial swapping, we assigned important functional segments of fungal CDP synthetases and assessed their in vivo biosynthetic capabilities. Hence, artificial assembly line components comprising of up to three different synthetases were generated. Using Aspergillus niger as a heterologous expression host, we obtained new-to-nature octa-enniatin (4 mg L–1) and octa-beauvericin (10.8 mg L–1), as well as high titers of the hybrid CDP hexa-bassianolide (1.3 g L–1) with an engineered ring size. The hybrid compounds showed up to 12-fold enhanced antiparasitic activity against Leishmania donovani and Trypanosoma cruzi compared to the reference drugs miltefosine and benznidazole, respectively. Our findings thus contribute to a rational engineering of iterative nonribosomal assembly lines.
Collapse
Affiliation(s)
- Charlotte Steiniger
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| | - Sylvester Hoffmann
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| | - Andi Mainz
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| | - Marcel Kaiser
- Parasite Chemotherapy , Medical Parasitology & Infection Biology , Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , Petersplatz 1 , 4003 Basel , Switzerland
| | - Kerstin Voigt
- Jena Microbial Resource Collection (JMRC) , Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie , Hans-Knöll-Institut , Adolf-Reichwein-Straße 23 , 07745 Jena , Germany
| | - Vera Meyer
- Fachgebiet Angewandte und Molekulare Mikrobiologie , Institut für Biotechnologie , Technische Universität Berlin , Gustav-Meyer-Allee 25 , 13355 Berlin , Germany
| | - Roderich D Süssmuth
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| |
Collapse
|
94
|
Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO, Jensen PR, Schulz S, Moore BS, Ziemert N. Function-related replacement of bacterial siderophore pathways. ISME JOURNAL 2017; 12:320-329. [PMID: 28809850 PMCID: PMC5776446 DOI: 10.1038/ismej.2017.137] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/13/2017] [Accepted: 07/14/2017] [Indexed: 01/16/2023]
Abstract
Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive. We previously reported that Salinispora bacteria broadly use the desferrioxamine family of siderophores for iron acquisition. Herein we describe a new and unrelated group of peptidic siderophores called salinichelins from a restricted number of Salinispora strains in which the desferrioxamine biosynthesis genes have been lost. We have reconstructed the evolutionary history of these two different siderophore families and show that the acquisition and retention of the new salinichelin siderophores co-occurs with the loss of the more ancient desferrioxamine pathway. This identical event occurred at least three times independently during the evolution of the genus. We surmise that certain BGCs may be extraneous because of their functional redundancy and demonstrate that the relative evolutionary pace of natural pathway replacement shows high selective pressure against retention of functionally superfluous gene clusters.
Collapse
Affiliation(s)
- Hilke Bruns
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mohammad Alanjary
- German Center for Infection Biology (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, Health and Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nadine Ziemert
- German Center for Infection Biology (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| |
Collapse
|
95
|
Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu CC, Keller NP, Kelleher NL. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol 2017; 13:895-901. [PMID: 28604695 PMCID: PMC5577364 DOI: 10.1038/nchembio.2408] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/13/2017] [Indexed: 12/02/2022]
Abstract
The genomes of filamentous fungi contain up to 90 biosynthetic gene clusters (BGCs) encoding diverse secondary metabolites-an enormous reservoir of untapped chemical potential. However, the recalcitrant genetics, cryptic expression, and unculturability of these fungi prevent scientists from systematically exploiting these gene clusters and harvesting their products. As heterologous expression of fungal BGCs is largely limited to the expression of single or partial clusters, we established a scalable process for the expression of large numbers of full-length gene clusters, called FAC-MS. Using fungal artificial chromosomes (FACs) and metabolomic scoring (MS), we screened 56 secondary metabolite BGCs from diverse fungal species for expression in Aspergillus nidulans. We discovered 15 new metabolites and assigned them with confidence to their BGCs. Using the FAC-MS platform, we extensively characterized a new macrolactone, valactamide A, and its hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS). The ability to regularize access to fungal secondary metabolites at an unprecedented scale stands to revitalize drug discovery platforms with renewable sources of natural products.
Collapse
Affiliation(s)
- Kenneth D Clevenger
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rosa Ye
- Intact Genomics, Inc., St. Louis, Missouri, USA
| | - Galen P Miley
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Maria H Verdan
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Thomas Velk
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - KaHoua Yang
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Peng Gao
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | | | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | | | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, Wisconsin, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| |
Collapse
|
96
|
Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
Collapse
Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| |
Collapse
|
97
|
Decoding and reprogramming fungal iterative nonribosomal peptide synthetases. Nat Commun 2017; 8:15349. [PMID: 28534477 PMCID: PMC5457498 DOI: 10.1038/ncomms15349] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/22/2017] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) assemble a large group of structurally and functionally diverse natural products. While the iterative catalytic mechanism of bacterial NRPSs is known, it remains unclear how fungal NRPSs create products of desired length. Here we show that fungal iterative NRPSs adopt an alternate incorporation strategy. Beauvericin and bassianolide synthetases have the same C1-A1-T1-C2-A2-MT-T2a-T2b-C3 domain organization. During catalysis, C3 and C2 take turns to incorporate the two biosynthetic precursors into the growing depsipeptide chain that swings between T1 and T2a/T2b with C3 cyclizing the chain when it reaches the full length. We reconstruct the total biosynthesis of beauvericin in vitro by reacting C2 and C3 with two SNAC-linked precursors and present a domain swapping approach to reprogramming these enzymes for peptides with altered lengths. These findings highlight the difference between bacterial and fungal NRPS mechanisms and provide a framework for the enzymatic synthesis of non-natural nonribosomal peptides. Nonribosomal peptides are important bioactive molecules that are synthetized by enzymes containing several catalytic domains. Here the authors describe the catalytic mechanism of fungal nonribosomal peptide synthetases and present an approach to modify these enzymes to produce specific nonribosomal peptides.
Collapse
|
98
|
Bloudoff K, Schmeing TM. Structural and functional aspects of the nonribosomal peptide synthetase condensation domain superfamily: discovery, dissection and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1587-1604. [PMID: 28526268 DOI: 10.1016/j.bbapap.2017.05.010] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes, each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes. This review discusses some of the important insights into the structure, catalytic mechanism, specificity, and gatekeeping functions of C domains revealed since their discovery. In addition, C domains are the archetypal members of the C domain superfamily, which includes several other members that also function as NRPS domains. The other family members can replace the C domain in NRP synthesis, can work in concert with a C domain, or can fulfill diverse and novel functions. These domains include the epimerization (E) domain, the heterocyclization (Cy) domain, the ester-bond forming C domain, the fungal NRPS terminal C domain (CT), the β-lactam ring forming C domain, and the X domain. We also discuss structural and function insight into C, E, Cy, CT and X domains, to present a holistic overview of historical and current knowledge of the C domain superfamily. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
Collapse
Affiliation(s)
- Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada.
| |
Collapse
|
99
|
Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
Collapse
Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| |
Collapse
|
100
|
Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
Collapse
Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| |
Collapse
|