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Tehan R, Blount RR, Goold RL, Mattos DR, Spatafora NR, Tabima JF, Gazis R, Wang C, Ishmael JE, Spatafora JW, McPhail KL. Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species. JOURNAL OF NATURAL PRODUCTS 2022; 85:1363-1373. [PMID: 35500108 PMCID: PMC9150700 DOI: 10.1021/acs.jnatprod.2c00153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The genome of entomopathogenic fungus Tolypocladium inflatum Gams encodes 43 putative biosynthetic gene clusters for specialized metabolites, although genotype-phenotype linkages have been reported only for the cyclosporins and fumonisins. T. inflatum was cultured in defined minimal media, supplemented with or without one of nine different amino acids. Acquisition of LC-MS/MS data for molecular networking and manual analysis facilitated annotation of putative known and unknown metabolites. These data led us to target a family of peptaibols and guided the isolation and purification of tolypocladamide H (1), which showed modest antibacterial activity and toxicity to mammalian cells at micromolar concentrations. HRMS/MS, NMR, and advanced Marfey's analysis were used to assign the structure of 1 as a peptaibol containing 4-[(E)-2-butenyl]-4-methyl-l-threonine (Bmt), a hallmark structural motif of the cyclosporins. LC-MS detection of homologous tolypocladamide metabolites and phylogenomic analyses of peptaibol biosynthetic genes in other cultured Tolypocladium species allowed assignment of a putative tolypocladamide nonribosomal peptide synthetase gene.
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Affiliation(s)
- Richard
M. Tehan
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Rheannon R. Blount
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Ryan L. Goold
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Daphne R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nicolas R. Spatafora
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Javier F. Tabima
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
- Department
of Biology, Clark University, Worcester, Massachusetts 01610, United States
| | - Romina Gazis
- Department
of Plant Pathology, Tropical Research and Education Center, University of Florida, Homestead, Florida 33031, United States
| | - 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 200032, People’s Republic
of China
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Joseph W. Spatafora
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
- Tel: +1 541 737 8134. E-mail:
| | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
- Tel: +1 541 737 5808. E-mail:
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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: 49] [Impact Index Per Article: 8.2] [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.
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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
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3
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Tomita H, Katsuyama Y, Minami H, Ohnishi Y. Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis. J Biol Chem 2017; 292:15859-15869. [PMID: 28774961 DOI: 10.1074/jbc.m117.791269] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Rufomycin is a circular heptapeptide with anti-mycobacterial activity and is produced by Streptomyces atratus ATCC 14046. Its structure contains three non-proteinogenic amino acids, N-dimethylallyltryptophan, trans-2-crotylglycine, and 3-nitrotyrosine (3NTyr). Although the rufomycin structure was already reported in the 1960s, its biosynthesis, including 3NTyr generation, remains unclear. To elucidate the rufomycin biosynthetic pathway, we assembled a draft genome sequence of S. atratus and identified the rufomycin biosynthetic gene cluster (ruf cluster), consisting of 20 ORFs (rufA-rufT). We found a putative heptamodular nonribosomal peptide synthetase encoded by rufT, a putative tryptophan N-dimethylallyltransferase encoded by rufP, and a putative trimodular type I polyketide synthase encoded by rufEF Moreover, the ruf cluster contains an apparent operon harboring putative cytochrome P450 (rufO) and nitric oxide synthase (rufN) genes. A similar operon, txtDE, is responsible for the formation of 4-nitrotryptophan in thaxtomin biosynthesis; the cytochrome P450 TxtE catalyzes the 4-nitration of Trp. Therefore, we hypothesized that RufO should catalyze the Tyr 3-nitration. Disruption of rufO abolished rufomycin production by S. atratus, which was restored when 3NTyr was added to the culture medium of the disruptant. Recombinant RufO protein exhibited Tyr 3-nitration activity both in vitro and in vivo Spectroscopic analysis further revealed that RufO recognizes Tyr as the substrate with a dissociation constant of ∼0.1 μm These results indicate that RufO is an unprecedented cytochrome P450 that catalyzes Tyr nitration. Taken together with the results of an in silico analysis of the ruf cluster, we propose a rufomycin biosynthetic pathway in S. atratus.
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Affiliation(s)
- Hiroya Tomita
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657.,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Yohei Katsuyama
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Hiromichi Minami
- the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasuo Ohnishi
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
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Traber R, Kobel H, Loosli HR, Senn H, Rosenwirth B, Lawen A. [Melle4]Cyclosporin, a Novel Natural Cyclosporin with anti-HIV Activity: Structural Elucidation, Biosynthesis and Biological Properties. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500507] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
From fermentations of Tolypocladium niveum supplemented with D-threonine, a novel natural cyclosporin, [Melle4]cyclosporin, was isolated. Its structural elucidation is based on amino acid analysis and spectroscopic data; the amino acid sequence was deduced from two-dimensional NMR investigations applied to the iso-derivative of [Melle4]cyclosporin which, in contrast to the natural product, is present as one homogenous conformation in solution. We show that one of the four N-methyl-L-leucine units of cyclosporin A, namely that in position 4, is replaced by N-methyl-L-isoleucine. The putative mechanism by which D-threonine induces in vivo biosynthesis of [Melle4]cyclosporin is discussed. In vitro biosynthesis of [Melle4]cyclosporin was achieved using the previously described enzymatic system [Lawen and Traber (1993) J Biol Chem268: 20452–20465], thereby demonstrating the high affinity of cyclosporin synthetase for isoleucine in position 4. In a long series of cyclosporins obtained by in vitro and in vivo biosynthesis, [Melle4]cyclosporin represents the first example that is devoid of immunosuppressive efficacy while retaining strong binding to cyclophilin. It exerts potent in vitro anti-HIV-1 activity.
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Affiliation(s)
- R. Traber
- SANDOZ Pharma Ltd, Preclinical Research, CH-4002 Basel, Switzerland
| | - H. Kobel
- SANDOZ Pharma Ltd, Preclinical Research, CH-4002 Basel, Switzerland
| | - H.-R. Loosli
- SANDOZ Pharma Ltd, Preclinical Research, CH-4002 Basel, Switzerland
| | - H. Senn
- SANDOZ Pharma Ltd, Preclinical Research, CH-4002 Basel, Switzerland
| | - B. Rosenwirth
- SANDOZ Forschungsinstitut GmbH, A-1235 Vienna, Austria
| | - A. Lawen
- Institut für Biochemie und Molekulare Biologie, Technische Universität Berlin, Franklinstrasse 29, D-10587 Berlin, Germany and Max-Planck-Gesellschaft zur Förderung der Wissenschaften, AG ‘Enzymologie der Peptidbindung’, Weinbergweg 16a, D-06120 Halle, Germany
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5
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Lawen A. Biosynthesis of cyclosporins and other natural peptidyl prolyl cis/trans isomerase inhibitors. Biochim Biophys Acta Gen Subj 2014; 1850:2111-20. [PMID: 25497210 DOI: 10.1016/j.bbagen.2014.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 01/11/2023]
Abstract
BACKGROUND Peptidyl-prolyl-cis/trans-isomerases (PPIases) are ubiquitously expressed and have been implicated in a wide range of biological functions. Their inhibition is beneficial in immunosuppression, cancer treatment, treatment of autoimmune diseases, protozoan and viral infections. SCOPE OF REVIEW Three classes of PPIases are known, each class having their own specific inhibitors. This review will cover the present knowledge on the biosynthesis of the natural PPIase inhibitors. These include for the cyclophilins: the cyclosporins, the analogues of peptolide SDZ 214-103 and the sanglifehrins; for the FKBPs: ascomycin, rapamycin and FK506 and for the parvulins the naphtoquinone juglone. MAJOR CONCLUSIONS Over the last thirty years much progress has been made in understanding PPIase function and the biosynthesis of natural PPIase inhibitors. Non-immunosuppressive analogues were discovered and served as lead compounds for the development of novel antiviral drugs. There are, however, still unsolved questions which deserve further research into this exciting field. GENERAL SIGNIFICANCE As all the major natural inhibitors of the cyclophilins and FKBPs are synthesized by complex non-ribosomal peptide synthetases and/or polyketide synthases, total chemical synthesis is not a viable option. Thus, fully understanding the modular enzyme systems involved in their biosynthesis may help engineering enzymes capable of synthesizing novel PPIase inhibitors with improved functions for a wide range of conditions. This article is part of a Special Issue entitled Proline-directed Foldases: Cell signaling catalysts and drug targets.
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Affiliation(s)
- Alfons Lawen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia.
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6
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7
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Walsh CT, O'Brien RV, Khosla C. Nonproteinogenic amino acid building blocks for nonribosomal peptide and hybrid polyketide scaffolds. Angew Chem Int Ed Engl 2013; 52:7098-124. [PMID: 23729217 PMCID: PMC4634941 DOI: 10.1002/anie.201208344] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 12/24/2022]
Abstract
Freestanding nonproteinogenic amino acids have long been recognized for their antimetabolite properties and tendency to be uncovered to reactive functionalities by the catalytic action of target enzymes. By installing them regiospecifically into biogenic peptides and proteins, it may be possible to usher a new era at the interface between small molecule and large molecule medicinal chemistry. Site-selective protein functionalization offers uniquely attractive strategies for posttranslational modification of proteins. Last, but not least, many of the amino acids not selected by nature for protein incorporation offer rich architectural possibilities in the context of ribosomally derived polypeptides. This Review summarizes the biosynthetic routes to and metabolic logic for the major classes of the noncanonical amino acid building blocks that end up in both nonribosomal peptide frameworks and in hybrid nonribosomal peptide-polyketide scaffolds.
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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8
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Walsh CT, O'Brien RV, Khosla C. Nichtproteinogene Aminosäurebausteine für Peptidgerüste aus nichtribosomalen Peptiden und hybriden Polyketiden. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208344] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Survase SA, Kagliwal LD, Annapure US, Singhal RS. Cyclosporin A--a review on fermentative production, downstream processing and pharmacological applications. Biotechnol Adv 2011; 29:418-35. [PMID: 21447377 DOI: 10.1016/j.biotechadv.2011.03.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 03/05/2011] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
In present times, the immunosuppressants have gained considerable importance in the world market. Cyclosporin A (CyA) is a cyclic undecapeptide with a variety of biological activities including immunosuppressive, anti-inflammatory, antifungal and antiparasitic properties. CyA is produced by various types of fermentation techniques using Tolypocladium inflatum. In the present review, we discuss the biosynthetic pathway, fermentative production, downstream processing and pharmacological activities of CyA.
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Affiliation(s)
- Shrikant A Survase
- Food Engineering and Technology Department, Institute of Chemical Technology, Matunga, Mumbai 400019, India
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10
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Wu J, Zhang HB, Xu JL, Cox RJ, Simpson TJ, Zhang LH. 13C labeling reveals multiple amination reactions in the biosynthesis of a novel polyketide polyamine antibiotic zeamine from Dickeya zeae. Chem Commun (Camb) 2009; 46:333-5. [PMID: 20024369 DOI: 10.1039/b916307g] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of zeamine, a novel polyamino-amide antibiotic metabolite of Dickeya zeae has been established by NMR and detailed MS analyses; labelling studies with (13)C-labelled acetates suggest that the repeating secondary amine containing motif may be biosynthesised via a modular PKS containing aminotransferase domains.
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Affiliation(s)
- Jien Wu
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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11
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Wilkinson B, Micklefield J. Chapter 14. Biosynthesis of nonribosomal peptide precursors. Methods Enzymol 2009; 458:353-78. [PMID: 19374990 DOI: 10.1016/s0076-6879(09)04814-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Nonribosomal peptides are natural products typically of bacterial and fungal origin. These highly complex molecules display a broad spectrum of biological activities, and have been exploited for the development of immunosuppressant, antibiotic, anticancer, and other therapeutic agents. The nonribosomal peptides are assembled by nonribosomal peptide synthetase (NRPS) enzymes comprising repeating modules that are responsible for the sequential selection, activation, and condensation of precursor amino acids. In addition to this, fatty acids, alpha-keto acids and alpha-hydroxy acids, as well as polyketide derived units, can also be utilized by NRPS assembly lines. Final tailoring-steps, including glycosylation and prenylation, serve to further decorate the nonribosomal peptides produced. The wide range of experimental methods that are employed in the elucidation of nonribosomal peptide precursor biosynthesis will be discussed, with particularly emphasis on genomics based approaches which have become wide spread over the last 5 years.
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Affiliation(s)
- Barrie Wilkinson
- Biotica, Chesterford Research Park, Little Chesterford, Essex, United Kingdom
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12
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Felnagle EA, Jackson EE, Chan YA, Podevels AM, Berti AD, McMahon MD, Thomas MG. Nonribosomal peptide synthetases involved in the production of medically relevant natural products. Mol Pharm 2008; 5:191-211. [PMID: 18217713 PMCID: PMC3131160 DOI: 10.1021/mp700137g] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural products biosynthesized wholly or in part by nonribosomal peptide synthetases (NRPSs) are some of the most important drugs currently used clinically for the treatment of a variety of diseases. Since the initial research into NRPSs in the early 1960s, we have gained considerable insights into the mechanism by which these enzymes assemble these natural products. This review will present a brief history of how the basic mechanistic steps of NRPSs were initially deciphered and how this information has led us to understand how nature modified these systems to generate the enormous structural diversity seen in nonribosomal peptides. This review will also briefly discuss how drug development and discovery are being influenced by what we have learned from nature about nonribosomal peptide biosynthesis.
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Affiliation(s)
| | | | | | | | | | | | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison WI 53706
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13
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Hoffmeister D, Keller NP. Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 2007; 24:393-416. [PMID: 17390002 DOI: 10.1039/b603084j] [Citation(s) in RCA: 378] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the literature on the enzymes, genes, and whole gene clusters underlying natural product biosyntheses and their regulation in filamentous fungi. We have included literature references from 1958, yet the majority of citations are between 1995 and the present. A total of 295 references are cited.
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Affiliation(s)
- Dirk Hoffmeister
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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14
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Wu X, Ballard J, Jiang YW. Structure and biosynthesis of the BT peptide antibiotic from Brevibacillus texasporus. Appl Environ Microbiol 2006; 71:8519-30. [PMID: 16332843 PMCID: PMC1317412 DOI: 10.1128/aem.71.12.8519-8530.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated a novel gram-positive bacterium, Brevibacillus texasporus, that produces an antibiotic, BT. BT is a group of related peptides that are produced by B. texasporus cells in response to nutrient limitation. We report here purification and determination of the structure of the most abundant BT isomer, BT1583. Amino acid composition and tandem mass spectrometry experiments yielded a partial BT1583 structure. The presence of ornithine and d-form residues in the partial BT1583 structure indicated that the peptide is synthesized by a nonribosomal peptide synthetase (NRPS). The BT NRPS operon was rapidly and accurately identified by using a novel in silico NRPS operon hunting strategy that involved direct shotgun genomic sequencing rather than the unreliable cosmid library hybridization scheme. Sequence analysis of the BT NRPS operon indicated that it encodes a colinear modular NRPS with a strict correlation between the NRPS modules and the amino acid residues in the peptide. The colinear nature of the BT NRPS enabled us to utilize the genomic information to refine the BT1583 peptide sequence to Me(2)-4-methyl-4-[(E)-2-butenyl]-4,N-methyl-threonine-L-dO-I-V-V-dK-V-dL-K-dY-L-V-CH2OH. In addition, we report the discovery of novel NRPS codons (sets of the substrate specificity-conferring residues in NRPS modules) for valine, lysine, ornithine, and tyrosine.
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Affiliation(s)
- Xiaofeng Wu
- Department of Medical Biochemistry and Genetics, 428 Reynolds Medical Building, Texas A&M University System Health Science Center, College Station, TX 77843-1114, USA
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15
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Velkov T, Lawen A. Non-ribosomal peptide synthetases as technological platforms for the synthesis of highly modified peptide bioeffectors – Cyclosporin synthetase as a complex example. BIOTECHNOLOGY ANNUAL REVIEW 2003; 9:151-97. [PMID: 14650927 DOI: 10.1016/s1387-2656(03)09002-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Many microbial peptide secondary metabolites possess important medicinal properties, of which the immunosuppressant cyclosporin A is an example. The enormous structural and functional diversity of these low-molecular weight peptides is attributable to their mode of biosynthesis. Peptide secondary metabolites are assembled non-ribosomally by multi-functional enzymes, termed non-ribosomal peptide synthetases. These systems consist of a multi-modular arrangement of the functional domains responsible for the catalysis of the partial reactions of peptide assembly. The extensive homology shared among NRPS systems allows for the generalisation of the knowledge garnered from studies of systems of diverse origins. In this review we shall focus the contemporary knowledge of non-ribosomal peptide biosynthesis on the structure and function of the cyclosporin biosynthetic system, with some emphasis on the re-direction of the biosynthetic potential of this system by combinatorial approaches.
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Affiliation(s)
- Tony Velkov
- Monash University, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, P.O. Box 13D, Melbourne, Victoria 3800, Australia
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von Döhren H, Keller U, Vater J, Zocher R. Multifunctional Peptide Synthetases. Chem Rev 1997; 97:2675-2706. [PMID: 11851477 DOI: 10.1021/cr9600262] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hans von Döhren
- Section Biochemistry and Molecular Biology, Max-Volmer-Institute of Biophysical Chemistry and Biochemistry, Technical University Berlin, Franklinstrasse 29, D-10587 Berlin, Germany
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17
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Carreras CW, Pieper R, Khosla C. The chemistry and biology of fatty acid, polyketide, and nonribosomal peptide biosynthesis. Top Curr Chem (Cham) 1997. [DOI: 10.1007/bfb0119235] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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18
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Offenzeller M, Santer G, Totschnig K, Su Z, Moser H, Traber R, Schneider-Scherzer E. Biosynthesis of the unusual amino acid (4R)-4-[(E)-2-butenyl]-4-methyl-L-threonine of cyclosporin A: enzymatic analysis of the reaction sequence including identification of the methylation precursor in a polyketide pathway. Biochemistry 1996; 35:8401-12. [PMID: 8679598 DOI: 10.1021/bi960224n] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
3(R)-Hydroxy-4(R)-methyl-6(E)-octenoic acid, the C9-backbone of the unusual amino acid (4R)-4-[(E)-2-butenyl]-4-methyl-L-threonine (Bmt), is biosynthesized as a coenzyme A thioester from acetyl-CoA, malonyl-CoA, NADPH, and S-adenosylmethionine via a polyketide pathway. Here we present detailed enzymatic studies about the basic assembly process. After attachment of the activated building units to Bmt polyketide synthase the intermediates remained enzyme-bound throughout the cycle. Premature cutoff of biosynthesis led to the release of the intermediates from the enzyme, either as coenzyme A thioesters or, in the case of reactive C8-intermediates, as lactones. Enzyme-bound 3-oxo-4-hexenoic acid, the condensation product of the second elongation cycle, could be identified as the exclusive substrate for the introduction of the methyl group. Part of the biosynthesis including the first elongation cycle, the second condensation reaction, and the methylation step was shown to follow a processive mechanism. All activated intermediates of this processive part could be introduced into the correct pathway at the respective steps, whereas 2-methyl-3-oxo-4-hexenoyl-CoA and all following methylated intermediates were not able to enter the cycle any more. Obviously, the region of Bmt polyketide synthase responsible for this latter part of the biosynthetic pathway is inaccessible for externally supplied coenzyme A thioesters. Butyryl-CoA was recognized by Bmt polyketide synthase with an efficiency comparable to that of crotonyl-CoA and processed to 3-hydroxy-4-methyloctanoyl-CoA, the saturated analog of the natural basic assembly product, indicating a relaxed specificity of Bmt polyketide synthase with respect to the starter unit.
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Affiliation(s)
- M Offenzeller
- Research and Development, Biochemie GmbH Kundl, Austria
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Kleinkauf H, Von Döhren H. A nonribosomal system of peptide biosynthesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:335-51. [PMID: 8612601 DOI: 10.1111/j.1432-1033.1996.00335.x] [Citation(s) in RCA: 267] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review covers peptide structures originating from the concerted action of enzyme systems without the direct participation of nucleic acids. Biosynthesis proceeds by formation of linear peptidyl intermediates which may be enzymatically modified as well as transformed into specific cyclic structures. The respective enzyme systems are constructed of biosynthetic modules integrated into multienzyme structures. Genetic and DNA-sequence analysis of biosynthetic gene clusters have revealed extensive similarities between prokaryotic and eukaryotic systems, conserved principles of organisation, and a unique mechanism of transport of intermediates during elongation and modification steps involving 4'-phospho-pantetheine. These similarities permit the identification of peptide synthetases and related aminoacyl-ligases and acyl-ligases from sequence data. Similarities to other biosynthetic systems involved in the assembly of polyketide metabolites are discussed.
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Affiliation(s)
- H Kleinkauf
- Institute of Biochemistry and Molecular Biology, Technical University Berlin, Germany
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20
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Lawen A. Biosynthesis and mechanism of action of cyclosporins. PROGRESS IN MEDICINAL CHEMISTRY 1996; 33:53-97. [PMID: 8776941 DOI: 10.1016/s0079-6468(08)70303-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- A Lawen
- Monash University, Department of Biochemistry and Molecular Biology, Clayton, Victoria, Australia
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21
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Pieper R, Luo G, Cane DE, Khosla C. Cell-free synthesis of polyketides by recombinant erythromycin polyketide synthases. Nature 1995; 378:263-6. [PMID: 7477343 DOI: 10.1038/378263a0] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Modular polyketide synthases (PKSs) are complex multi-enzyme proteins that catalyse the bacterial biosynthesis of many pharmaceutically useful polyketides. The PKSs are organized into a series of modules, each containing the active catalytic sites required for one step in the synthesis process. Here we report a method for cell-free enzymatic synthesis of 6-deoxyerythronolide B (6-dEB), the parent molecule of the antibiotic erythromycin A, using recombinant 6-deoxyerythronolide B synthase (DEBS), a modular PKS with at least 28 distinct active sites. We have also synthesized in vitro a triketide lactone by using a truncated mutant of DEBS. The availability of such cell-free synthetic routes will allow direct investigation of the structural and mechanistic basis for the unusual combination of high substrate specificity and tolerance to genetic reprogramming found in this enzyme family.
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Affiliation(s)
- R Pieper
- Department of Chemical Engineering, Stanford University, California 94305-5025, USA
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Weber G, Schörgendorfer K, Schneider-Scherzer E, Leitner E. The peptide synthetase catalyzing cyclosporine production in Tolypocladium niveum is encoded by a giant 45.8-kilobase open reading frame. Curr Genet 1994; 26:120-5. [PMID: 8001164 DOI: 10.1007/bf00313798] [Citation(s) in RCA: 207] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cyclosporin A, a potent and clinically-important immunosuppressive drug (SandimmunR), is synthesized from its precursor amino acids by cyclosporin synthetase, a single multi-functional enzyme. In this study we report the cloning of the corresponding coding region of this synthetase. It contains an open reading frame of 45.8 kb which encodes a peptide with a calculated M(r) of 1,689,243. The predicted gene product contains 11 amino-acid-activating domains that are very similar to one another and to the domains of other peptide synthetases. Seven of these domains harbour N-methyltransferase functions. This is the largest genomic ORF described so far.
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Affiliation(s)
- G Weber
- Biochemie Ges.m.b.H. Kufstein-Schaftenau, Austria
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Hoffmann K, Schneider-Scherzer E, Kleinkauf H, Zocher R. Purification and characterization of eucaryotic alanine racemase acting as key enzyme in cyclosporin biosynthesis. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)99934-5] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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