1
|
Paulo BS, Recchia MJJ, Lee S, Fergusson CH, Romanowski SB, Hernandez A, Krull N, Liu DY, Cavanagh H, Bos A, Gray CA, Murphy BT, Linington RG, Eustaquio AS. Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection. Chem Sci 2024:d4sc03594a. [PMID: 39309087 PMCID: PMC11411415 DOI: 10.1039/d4sc03594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024] Open
Abstract
Burkholderiales bacteria have emerged as a promising source of structurally diverse natural products that are expected to play important ecological and industrial roles. This order ranks in the top three in terms of predicted natural product diversity from available genomes, warranting further genome sequencing efforts. However, a major hurdle in obtaining the predicted products is that biosynthetic genes are often 'silent' or poorly expressed. Here we report complementary strain isolation, genomics, metabolomics, and synthetic biology approaches to enable natural product discovery. First, we built a collection of 316 rhizosphere-derived Burkholderiales strains over the course of five years. We then selected 115 strains for sequencing using the mass spectrometry pipeline IDBac to avoid strain redundancy. After predicting and comparing the biosynthetic potential of each strain, a biosynthetic gene cluster that was silent in the native Paraburkholderia megapolitana and Paraburkholderia acidicola producers was cloned and activated by heterologous expression in a Burkholderia sp. host, yielding megapolipeptins A and B. Megapolipeptins are unusual polyketide, nonribosomal peptide, and polyunsaturated fatty acid hybrids that show low structural similarity to known natural products, highlighting the advantage of our Burkholderiales genomics-driven and synthetic biology-enabled pipeline to discover novel natural products.
Collapse
Affiliation(s)
- Bruno S Paulo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | | | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Claire H Fergusson
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Nyssa Krull
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Hannah Cavanagh
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Allyson Bos
- Department of Biological Sciences, University of New Brunswick Saint John New Brunswick E2L 4L5 Canada
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick Saint John New Brunswick E2L 4L5 Canada
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Alessandra S Eustaquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| |
Collapse
|
2
|
Dreckmann TM, Fritz L, Kaiser CF, Bouhired SM, Wirtz DA, Rausch M, Müller A, Schneider T, König GM, Crüsemann M. Biosynthesis of the corallorazines, a widespread class of antibiotic cyclic lipodipeptides. RSC Chem Biol 2024:d4cb00157e. [PMID: 39184525 PMCID: PMC11342130 DOI: 10.1039/d4cb00157e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Corallorazines are cyclic lipodipeptide natural products produced by the myxobacterium Corallococcus coralloides B035. To decipher the basis of corallorazine biosynthesis, the corallorazine nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster crz was identified and analyzed in detail. Here, we present a model of corallorazine biosynthesis, supported by bioinformatic analyses and in vitro investigations on the bimodular NRPS synthesizing the corallorazine core. Corallorazine biosynthesis shows several distinct features, such as the presence of a dehydrating condensation domain, and a unique split adenylation domain on two open reading frames. Using an alternative fatty acyl starter unit, the first steps of corallorazine biosynthesis were characterized in vitro, supporting our biosynthetic model. The dehydrating condensation domain was bioinformatically analyzed in detail and compared to other modifying C domains, revealing unreported specific sequence motives for this domain subfamily. Using global bioinformatics analyses, we show that the crz gene cluster family is widespread among bacteria and encodes notable chemical diversity. Corallorazine A displays moderate antimicrobial activity against selected Gram-positive and Gram-negative bacteria. Mode of action studies comprising whole cell analysis and in vitro test systems revealed that corallorazine A inhibits bacterial transcription by targeting the DNA-dependent RNA polymerase.
Collapse
Affiliation(s)
- Teresa M Dreckmann
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Lisa Fritz
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Christian F Kaiser
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Sarah M Bouhired
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Daniel A Wirtz
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne Bonn Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| |
Collapse
|
3
|
Kostka M, Krug D, Herrmann J, Dickschat JS, Meyer J, Müller R, Schulz S. Identification by Synthesis: Imidacins, Urocanate-Derived Alkaloids from the Myxobacterium Stigmatella aurantiaca. Org Lett 2024; 26:6359-6363. [PMID: 39037587 DOI: 10.1021/acs.orglett.4c02036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Innovative discovery approaches such as genome-mining and metabolomics-inspired methods have reshaped the natural product research field, complementing traditional bioactivity-based screens and allowing hitherto unseen compounds to be uncovered from previously investigated producers. In line with these trends, we report here imidacins, a novel class of secondary metabolites specific to the myxobacterial genus Stigmatella. A combination of secondary metabolome analysis, genome-mining techniques, spectroscopic analysis, and finally total synthesis was used to allow structure elucidation. Imidacins are urocanate-derived aliphatic acids with an adjacent cyclopropane moiety, structural features unprecedented in natural products to date.
Collapse
Affiliation(s)
- Michael Kostka
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jeroen S Dickschat
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julia Meyer
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| |
Collapse
|
4
|
Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
Collapse
Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| |
Collapse
|
5
|
Liu Y, Yamazaki S, Ojika M. Heterologous Biosynthesis of Myxobacterial Antibiotic Miuraenamide A. Molecules 2023; 28:molecules28062815. [PMID: 36985787 PMCID: PMC10051162 DOI: 10.3390/molecules28062815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The hard-to-culture slightly halophilic myxobacterium "Paraliomyxa miuraensis" SMH-27-4 produces antifungal cyclodepsipeptide miuraenamide A (1). Herein, the region (85.9 kbp) containing the biosynthetic gene cluster (BGC) coding the assembly of 1 was identified and heterologously expressed in Myxococcus xanthus. A biosynthetic pathway proposed using in silico analysis was verified through the gene disruption of the heterologous transformant. In addition to the core polyketide synthase (PKS) and nonribosomal peptide synthase (NRPS) genes, tyrosine halogenase and O-methyltransferase genes participated in the biosynthesis of 1 as their gene-disrupted mutants produced a new congener, debromomiuraenamide A (4), and a previously isolated congener, miuraenamide E (3), respectively. Multigene disruption provided a heterologous mutant that produced 1 with the highest yield among the prepared mutants. When fed on 3-bromo-L-tyrosine, this mutant produced more 1 in the yield of 1.21 mg/L, which was 20 times higher than that produced by the initially prepared heterologous transformant. Although this yield was comparable to that of the original producer SMH-27-4 (1 mg/L), the culture time was 4.5 times shorter than that of SMH-27-4, indicating a five-fold efficiency in productivity. The results indicate the great potential of the miuraenamide BGC for the future contribution to drug development through logical gene manipulation.
Collapse
Affiliation(s)
- Ying Liu
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Satoshi Yamazaki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Makoto Ojika
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| |
Collapse
|
6
|
Kudo F, Chikuma T, Nambu M, Chisuga T, Sumimoto S, Iwasaki A, Suenaga K, Miyanaga A, Eguchi T. Unique Initiation and Termination Mechanisms Involved in the Biosynthesis of a Hybrid Polyketide-Nonribosomal Peptide Lyngbyapeptin B Produced by the Marine Cyanobacterium Moorena bouillonii. ACS Chem Biol 2023; 18:875-883. [PMID: 36921345 PMCID: PMC10127204 DOI: 10.1021/acschembio.3c00011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Lyngbyapeptin B is a hybrid polyketide-nonribosomal peptide isolated from particular marine cyanobacteria. In this report, we carried out genome sequence analysis of a producer cyanobacterium Moorena bouillonii to understand the biosynthetic mechanisms that generate the unique structural features of lyngbyapeptin B, including the (E)-3-methoxy-2-butenoyl starter unit and the C-terminal thiazole moiety. We identified a putative lyngbyapeptin B biosynthetic (lynB) gene cluster comprising nine open reading frames that include two polyketide synthases (PKSs: LynB1 and LynB2), four nonribosomal peptide synthetases (NRPSs: LynB3, LynB4, LynB5, and LynB6), a putative nonheme diiron oxygenase (LynB7), a type II thioesterase (LynB8), and a hypothetical protein (LynB9). In vitro enzymatic analysis of LynB2 with methyltransferase (MT) and acyl carrier protein (ACP) domains revealed that the LynB2 MT domain (LynB2-MT) catalyzes O-methylation of the acetoacetyl-LynB2 ACP domain (LynB2-ACP) to yield (E)-3-methoxy-2-butenoyl-LynB2-ACP. In addition, in vitro enzymatic analysis of LynB7 revealed that LynB7 catalyzes the oxidative decarboxylation of (4R)-2-methyl-2-thiazoline-4-carboxylic acid to yield 2-methylthiazole in the presence of Fe2+ and molecular oxygen. This result indicates that LynB7 is responsible for the last post-NRPS modification to give the C-terminal thiazole moiety in lyngbyapeptin B biosynthesis. Overall, we identified and characterized a new marine cyanobacterial hybrid PKS-NRPS biosynthetic gene cluster for lyngbyapeptin B production, revealing two unique enzymatic logics.
Collapse
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Takuji Chikuma
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Mizuki Nambu
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Shimpei Sumimoto
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Arihiro Iwasaki
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| |
Collapse
|
7
|
Zeng H, Birkelbach J, Hoffmann J, Popoff A, Volz C, Müller R. Expanding the Ajudazol Cytotoxin Scaffold: Insights from Genome Mining, Biosynthetic Investigations, and Novel Derivatives. JOURNAL OF NATURAL PRODUCTS 2022; 85:2610-2619. [PMID: 36331369 DOI: 10.1021/acs.jnatprod.2c00637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Myxobacteria have proven to be a rich source of natural products, but their biosynthetic potential seems to be underexplored given the high number of biosynthetic gene clusters present in their genomes. In this study, a truncated ajudazol biosynthetic gene cluster in Cystobacter sp. SBCb004 was identified using mutagenesis and metabolomics analyses and a set of novel ajudazols (named ajudazols C-J, 3-10, respectively) were detected and subsequently isolated. Their structures were elucidated using comprehensive HR-MS and NMR spectroscopy. Unlike the known ajudazols A (1) and B (2), which utilize acetyl-CoA as the biosynthetic starter unit, these novel ajudazols were proposed to incorporate 3,3-dimethylacrylyl CoA as the starter. Ajudazols C-J (3-10, respectively) are characterized by varying degrees of hydroxylation, desaturation, and different glycosylation patterns. Two P450-dependent enzymes and one glycosyltransferase are shown to be responsible for the hydroxylation at C-8, the desaturation at C-15 and C-33, and the transfer of a d-β-glucopyranose, respectively, based on mutagenesis results. One of the cytochrome P450-dependent enzymes and the glycosyltransferase were found to be encoded by genes located outside the biosynthetic gene cluster. Ajudazols C-H (3-8, respectively) exhibit cytotoxicity against various cancer cell lines.
Collapse
Affiliation(s)
- Hu Zeng
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Saarland, Germany
| | - Joy Birkelbach
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Saarland, Germany
| | - Judith Hoffmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Saarland, Germany
| | - Alexander Popoff
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Saarland, Germany
| | - Carsten Volz
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Saarland, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Saarland, Germany
| |
Collapse
|
8
|
Bär D, Konetschny B, Kulik A, Xu H, Paccagnella D, Beller P, Ziemert N, Dickschat JS, Gust B. Origin of the 3-methylglutaryl moiety in caprazamycin biosynthesis. Microb Cell Fact 2022; 21:232. [PMID: 36335365 PMCID: PMC9636800 DOI: 10.1186/s12934-022-01955-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Caprazamycins are liponucleoside antibiotics showing bioactivity against Gram-positive bacteria including clinically relevant Mycobacterium tuberculosis by targeting the bacterial MraY-translocase. Their chemical structure contains a unique 3-methylglutaryl moiety which they only share with the closely related liposidomycins. Although the biosynthesis of caprazamycin is understood to some extent, the origin of 3-methylglutaryl-CoA for caprazamycin biosynthesis remains elusive. RESULTS In this work, we demonstrate two pathways of the heterologous producer Streptomyces coelicolor M1154 capable of supplying 3-methylglutaryl-CoA: One is encoded by the caprazamycin gene cluster itself including the 3-hydroxy-3-methylglutaryl-CoA synthase Cpz5. The second pathway is part of primary metabolism of the host cell and encodes for the leucine/isovalerate utilization pathway (Liu-pathway). We could identify the liu cluster in S. coelicolor M1154 and gene deletions showed that the intermediate 3-methylglutaconyl-CoA is used for 3-methylglutaryl-CoA biosynthesis. This is the first report of this intermediate being hijacked for secondary metabolite biosynthesis. Furthermore, Cpz20 and Cpz25 from the caprazamycin gene cluster were found to be part of a common route after both individual pathways are merged together. CONCLUSIONS The unique 3-methylglutaryl moiety in caprazamycin originates both from the caprazamycin gene cluster and the leucine/isovalerate utilization pathway of the heterologous host. Our study enhanced the knowledge on the caprazamycin biosynthesis and points out the importance of primary metabolism of the host cell for biosynthesis of natural products.
Collapse
Affiliation(s)
- Daniel Bär
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Benjamin Konetschny
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Davide Paccagnella
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Patrick Beller
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bertolt Gust
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
| |
Collapse
|
9
|
Cofactor F420, an emerging redox power in biosynthesis of secondary metabolites. Biochem Soc Trans 2022; 50:253-267. [PMID: 35191491 DOI: 10.1042/bst20211286] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 02/07/2023]
Abstract
Cofactor F420 is a low-potential hydride-transfer deazaflavin that mediates important oxidoreductive reactions in the primary metabolism of archaea and a wide range of bacteria. Over the past decade, biochemical studies have demonstrated another essential role for F420 in the biosynthesis of various classes of natural products. These studies have substantiated reports predating the structural determination of F420 that suggested a potential role for F420 in the biosynthesis of several antibiotics produced by Streptomyces. In this article, we focus on this exciting and emerging role of F420 in catalyzing the oxidoreductive transformation of various imine, ketone and enoate moieties in secondary metabolites. Given the extensive and increasing availability of genomic and metagenomic data, these F420-dependent transformations may lead to the discovery of novel secondary metabolites, providing an invaluable and untapped resource in various biotechnological applications.
Collapse
|
10
|
Fortinez CM, Bloudoff K, Harrigan C, Sharon I, Strauss M, Schmeing TM. Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Nat Commun 2022; 13:548. [PMID: 35087027 PMCID: PMC8795117 DOI: 10.1038/s41467-022-28221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
Collapse
Affiliation(s)
- Camille Marie Fortinez
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Connor Harrigan
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Itai Sharon
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Mike Strauss
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
| |
Collapse
|
11
|
Motoyama T, Yun CS, Osada H. Biosynthesis and biological function of secondary metabolites of the rice blast fungus Pyricularia oryzae. J Ind Microbiol Biotechnol 2021; 48:kuab058. [PMID: 34379774 PMCID: PMC8788799 DOI: 10.1093/jimb/kuab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022]
Abstract
Filamentous fungi have many secondary metabolism genes and produce a wide variety of secondary metabolites with complex and unique structures. However, the role of most secondary metabolites remains unclear. Moreover, most fungal secondary metabolism genes are silent or poorly expressed under laboratory conditions and are difficult to utilize. Pyricularia oryzae, the causal pathogen of rice blast disease, is a well-characterized plant pathogenic fungus. P. oryzae also has a large number of secondary metabolism genes and appears to be a suitable organism for analyzing secondary metabolites. However, in case of this fungus, biosynthetic genes for only four groups of secondary metabolites have been well characterized. Among two of the four groups of secondary metabolites, biosynthetic genes were identified by activating secondary metabolism. These secondary metabolites include melanin, a polyketide compound required for rice infection; tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique nonribosomal peptide synthetase-polyketide synthase hybrid enzyme; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi, including plant pathogens and endophytes, and pyriculols, phytotoxic polyketide compounds. This review mainly focuses on the biosynthesis and biological functions of the four groups of P. oryzae secondary metabolites.
Collapse
Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| |
Collapse
|
12
|
Motoyama T. Secondary Metabolites of the Rice Blast Fungus Pyricularia oryzae: Biosynthesis and Biological Function. Int J Mol Sci 2020; 21:E8698. [PMID: 33218033 PMCID: PMC7698770 DOI: 10.3390/ijms21228698] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Plant pathogenic fungi produce a wide variety of secondary metabolites with unique and complex structures. However, most fungal secondary metabolism genes are poorly expressed under laboratory conditions. Moreover, the relationship between pathogenicity and secondary metabolites remains unclear. To activate silent gene clusters in fungi, successful approaches such as epigenetic control, promoter exchange, and heterologous expression have been reported. Pyricularia oryzae, a well-characterized plant pathogenic fungus, is the causal pathogen of rice blast disease. P. oryzae is also rich in secondary metabolism genes. However, biosynthetic genes for only four groups of secondary metabolites have been well characterized in this fungus. Biosynthetic genes for two of the four groups of secondary metabolites have been identified by activating secondary metabolism. This review focuses on the biosynthesis and roles of the four groups of secondary metabolites produced by P. oryzae. These secondary metabolites include melanin, a polyketide compound required for rice infection; pyriculols, phytotoxic polyketide compounds; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi including endophytes and plant pathogens; and tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique NRPS-PKS enzyme.
Collapse
Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| |
Collapse
|
13
|
Lundy TA, Mori S, Garneau-Tsodikova S. A thorough analysis and categorization of bacterial interrupted adenylation domains, including previously unidentified families. RSC Chem Biol 2020; 1:233-250. [PMID: 34458763 PMCID: PMC8341866 DOI: 10.1039/d0cb00092b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022] Open
Abstract
Interrupted adenylation (A) domains are key to the immense structural diversity seen in the nonribosomal peptide (NRP) class of natural products (NPs). Interrupted A domains are A domains that contain within them the catalytic portion of another domain, most commonly a methylation (M) domain. It has been well documented that methylation events occur with extreme specificity on either the backbone (N-) or side chain (O- or S-) of the amino acid (or amino acid-like) building blocks of NRPs. Here, through taxonomic and phylogenetic analyses as well as multiple sequence alignments, we evaluated the similarities and differences between interrupted A domains. We probed their taxonomic distribution amongst bacterial organisms, their evolutionary relatedness, and described conserved motifs of each type of M domain found to be embedded in interrupted A domains. Additionally, we categorized interrupted A domains and the M domains within them into a total of seven distinct families and six different types, respectively. The families of interrupted A domains include two new families, 6 and 7, that possess new architectures. Rather than being interrupted between the previously described a2–a3 or a8–a9 of the ten conserved A domain sequence motifs (a1–a10), family 6 contains an M domain between a6–a7, a previously unknown interruption site. Family 7 demonstrates that di-interrupted A domains exist in Nature, containing an M domain between a2–a3 as well as one between a6–a7, displaying a novel arrangement. These in-depth investigations of amino acid sequences deposited in the NCBI database highlighted the prevalence of interrupted A domains in bacterial organisms, with each family of interrupted A domains having a different taxonomic distribution. They also emphasized the importance of utilizing a broad range of bacteria for NP discovery. Categorization of the families of interrupted A domains and types of M domains allowed for a better understanding of the trends of naturally occurring interrupted A domains, which illuminated patterns and insights on how to harness them for future engineering studies. In-depth study of intriguing bacterial interrupted adenylation domains from seven distinct families and six different types.![]()
Collapse
Affiliation(s)
- Taylor A Lundy
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| | - Shogo Mori
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| |
Collapse
|
14
|
Pang B, Chen Y, Gan F, Yan C, Jin L, Gin JW, Petzold CJ, Keasling JD. Investigation of Indigoidine Synthetase Reveals a Conserved Active-Site Base Residue of Nonribosomal Peptide Synthetase Oxidases. J Am Chem Soc 2020; 142:10931-10935. [PMID: 32510939 DOI: 10.1021/jacs.0c04328] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonribosomal peptide synthetase (NRPS) oxidase (Ox) domains oxidize protein-bound intermediates to install crucial structural motifs in bioactive natural products. The mechanism of this domain remains elusive. Here, by studying indigoidine synthetase, a single-module NRPS involved in the biosynthesis of indigoidine and several other bacterial secondary metabolites, we demonstrate that its Ox domain utilizes an active-site base residue, tyrosine 665, to deprotonate a protein-bound l-glutaminyl residue. We further validate the generality of this active-site residue among NRPS Ox domains. These findings not only resolve the biosynthetic pathway mediated by indigoidine synthetase but enable mechanistic insight into NRPS Ox domains.
Collapse
Affiliation(s)
- Bo Pang
- QB3 Institute, University of California, Berkeley, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Fei Gan
- QB3 Institute, University of California, Berkeley, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Chunsheng Yan
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Liyuan Jin
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jennifer W Gin
- Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D Keasling
- QB3 Institute, University of California, Berkeley, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Chemical & Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK 2970 Horsholm, Denmark.,Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, P. R. China
| |
Collapse
|
15
|
Koomsiri W, Inahashi Y, Leetanasaksakul K, Shiomi K, Takahashi YK, O Mura S, Samborskyy M, Leadlay PF, Wattana-Amorn P, Thamchaipenet A, Nakashima T. Sarpeptins A and B, Lipopeptides Produced by Streptomyces sp. KO-7888 Overexpressing a Specific SARP Regulator. JOURNAL OF NATURAL PRODUCTS 2019; 82:2144-2151. [PMID: 31381320 DOI: 10.1021/acs.jnatprod.9b00074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Whole genome analysis of Streptomyces sp. KO-7888 has revealed various pathway-specific transcriptional regulatory genes associated with silent biosynthetic gene clusters. A Streptomyces antibiotic regulatory protein gene, speR, located adjacent to a novel nonribosomal peptide synthetase (NRPS) gene cluster, was overexpressed in the wild-type strain. The resulting recombinant strain of Streptomyces sp. KO-7888 produced two new lipopeptides, sarpeptins A and B. Their structures were elucidated by high-resolution electrospray ionization mass spectrometry, NMR analysis, and the advanced Marfey's method. The distinct modular sections of the corresponding NRPS biosynthetic gene cluster were characterized, and the assembly line for production of the lipopeptide chain was proposed.
Collapse
Affiliation(s)
- Wilaiwan Koomsiri
- Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Omics Center for Agriculture, Bioresources, Food and Health , Kasetsart University (OmiKU) , Bangkok 10900 , Thailand
| | - Yuki Inahashi
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Kantinan Leetanasaksakul
- Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Omics Center for Agriculture, Bioresources, Food and Health , Kasetsart University (OmiKU) , Bangkok 10900 , Thailand
| | - Kazuro Shiomi
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Yo Ko Takahashi
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Satoshi O Mura
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Markiyan Samborskyy
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Peter F Leadlay
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry , Kasetsart University , Bangkok 10900 , Thailand
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Omics Center for Agriculture, Bioresources, Food and Health , Kasetsart University (OmiKU) , Bangkok 10900 , Thailand
| | - Takuji Nakashima
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| |
Collapse
|
16
|
Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
Collapse
Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| |
Collapse
|
17
|
Oueis E, Klefisch T, Zaburannyi N, Garcia R, Plaza A, Müller R. Two Biosynthetic Pathways in Jahnella thaxteri for Thaxteramides, Distinct Types of Lipopeptides. Org Lett 2019; 21:5407-5412. [PMID: 31184172 DOI: 10.1021/acs.orglett.9b01524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The structures of five linear lipopeptides, thaxteramides A1, A2, B1, B2, and C isolated from the myxobacterium Jahnella thaxteri, were elucidated. They have a C-terminal common tetrapeptidic Tyr-Gly-β-Ala-Tyr core but differ in the stereochemistry of the tyrosine units, methylations, the remaining amino acids, and the N-terminal polyketide. In silico analysis of the genome sequence complemented with feeding experiments revealed two distinct hybrid PKS/NRPS gene clusters. Three semisynthesized cyclic analogues were found to inhibit the growth of Gram-positive bacteria.
Collapse
Affiliation(s)
- Emilia Oueis
- Department of microbial natural products , Helmholtz-institute for pharmaceutical research Saarland (HIPS), Helmholtz center for infection research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Thorsten Klefisch
- Department of microbial natural products , Helmholtz-institute for pharmaceutical research Saarland (HIPS), Helmholtz center for infection research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Nestor Zaburannyi
- Department of microbial natural products , Helmholtz-institute for pharmaceutical research Saarland (HIPS), Helmholtz center for infection research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Ronald Garcia
- Department of microbial natural products , Helmholtz-institute for pharmaceutical research Saarland (HIPS), Helmholtz center for infection research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,German Centre for Infection Research (DZIF) , Partner Site Hannover , 38124 Braunschweig , Germany
| | - Alberto Plaza
- Department of microbial natural products , Helmholtz-institute for pharmaceutical research Saarland (HIPS), Helmholtz center for infection research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Rolf Müller
- Department of microbial natural products , Helmholtz-institute for pharmaceutical research Saarland (HIPS), Helmholtz center for infection research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,German Centre for Infection Research (DZIF) , Partner Site Hannover , 38124 Braunschweig , Germany
| |
Collapse
|
18
|
Panter F, Krug D, Müller R. Novel Methoxymethacrylate Natural Products Uncovered by Statistics-Based Mining of the Myxococcus fulvus Secondary Metabolome. ACS Chem Biol 2019; 14:88-98. [PMID: 30543288 DOI: 10.1021/acschembio.8b00948] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study reports the uncovering of new myxobacterial natural products through comprehensive analysis of the Myxococcus fulvus secondary metabolome. Statistics-based mining of mass spectrometry data paved the way for full structure elucidation of two new secondary metabolites named fulvuthiacene A and B, and investigation of the underlying biosynthetic pathway revealed an evolutionary link between the fulvuthiacene hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene cluster and the related myxothiazol and melithiazol assembly lines. Detailed characterization of the post-PKS modification enzyme cascade responsible for the fulvuthiacenes' terminal β-methoxy-methyl acrylate moiety was pursued by heterologous expression of these enzymes in the myxothiazol producer Stigmatella aurantiaca DW4/3-1. The discovery of fulvuthiacenes provides new insights into the overall structure-activity relationship picture for the β-methoxyacrylate class of respiratory chain inhibitors and might thus serve as starting point for the development of next-generation β-methoxymethacrylate fungicides.
Collapse
Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover−Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Daniel Krug
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover−Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover−Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
| |
Collapse
|
19
|
Skiba MA, Bivins MM, Schultz JR, Bernard SM, Fiers WD, Dan Q, Kulkarni S, Wipf P, Gerwick WH, Sherman DH, Aldrich CC, Smitha JL. Structural Basis of Polyketide Synthase O-Methylation. ACS Chem Biol 2018; 13:3221-3228. [PMID: 30489068 PMCID: PMC6470024 DOI: 10.1021/acschembio.8b00687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Modular type I polyketide synthases (PKSs) produce some of the most chemically complex metabolites in nature through a series of multienzyme modules. Each module contains a variety of catalytic domains to selectively tailor the growing molecule. PKS O-methyltransferases ( O-MTs) are predicted to methylate β-hydroxyl or β-keto groups, but their activity and structure have not been reported. We determined the domain boundaries and characterized the catalytic activity and structure of the StiD and StiE O-MTs, which methylate opposite β-hydroxyl stereocenters in the myxobacterial stigmatellin biosynthetic pathway. Substrate stereospecificity was demonstrated for the StiD O-MT. Key catalytic residues were identified in the crystal structures and investigated in StiE O-MT via site-directed mutagenesis and further validated with the cyanobacterial CurL O-MT from the curacin biosynthetic pathway. Initial structural and biochemical analysis of PKS O-MTs supplies a new chemoenzymatic tool, with the unique ability to selectively modify hydroxyl groups during polyketide biosynthesis.
Collapse
Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Marissa M. Bivins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - John R. Schultz
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI, 48109, United States
| | - William D. Fiers
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Sarang Kulkarni
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Janet L. Smitha
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| |
Collapse
|
20
|
Son S, Hong YS, Futamura Y, Jang M, Lee JK, Heo KT, Ko SK, Lee JS, Takahashi S, Osada H, Jang JH, Ahn JS. Catenulisporolides, Glycosylated Triene Macrolides from the Chemically Underexploited Actinomycete Catenulispora Species. Org Lett 2018; 20:7234-7238. [DOI: 10.1021/acs.orglett.8b03160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jae Kyoung Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jung Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Korea
| | - Shunji Takahashi
- RIKEN-KRIBB Joint Research Unit, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| |
Collapse
|
21
|
García-Salcedo R, Álvarez-Álvarez R, Olano C, Cañedo L, Braña AF, Méndez C, de la Calle F, Salas JA. Characterization of the Jomthonic Acids Biosynthesis Pathway and Isolation of Novel Analogues in Streptomyces caniferus GUA-06-05-006A. Mar Drugs 2018; 16:md16080259. [PMID: 30065171 PMCID: PMC6117699 DOI: 10.3390/md16080259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 12/20/2022] Open
Abstract
Jomthonic acids (JAs) are a group of natural products (NPs) with adipogenic activity. Structurally, JAs are formed by a modified β-methylphenylalanine residue, whose biosynthesis involves a methyltransferase that in Streptomyces hygroscopicus has been identified as MppJ. Up to date, three JA members (A–C) and a few other natural products containing β-methylphenylalanine have been discovered from soil-derived microorganisms. Herein, we report the identification of a gene (jomM) coding for a putative methyltransferase highly identical to MppJ in the chromosome of the marine actinobacteria Streptomyces caniferus GUA-06-05-006A. In its 5’ region, jomM clusters with two polyketide synthases (PKS) (jomP1, jomP2), a nonribosomal peptide synthetase (NRPS) (jomN) and a thioesterase gene (jomT), possibly conforming a single transcriptional unit. Insertion of a strong constitutive promoter upstream of jomP1 led to the detection of JA A, along with at least two novel JA family members (D and E). Independent inactivation of jomP1, jomN and jomM abolished production of JA A, JA D and JA E, indicating the involvement of these genes in JA biosynthesis. Heterologous expression of the JA biosynthesis cluster in Streptomyces coelicolor M1152 and in Streptomyces albus J1074 led to the production of JA A, B, C and F. We propose a pathway for JAs biosynthesis based on the findings here described.
Collapse
Affiliation(s)
- Raúl García-Salcedo
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
- Drug Discovery Area, PharmaMar S.A. Avda. de los Reyes 1, 28770 Colmenar Viejo (Madrid), Spain.
| | - Rubén Álvarez-Álvarez
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Carlos Olano
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Librada Cañedo
- Drug Discovery Area, PharmaMar S.A. Avda. de los Reyes 1, 28770 Colmenar Viejo (Madrid), Spain.
| | - Alfredo F Braña
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Carmen Méndez
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Fernando de la Calle
- Drug Discovery Area, PharmaMar S.A. Avda. de los Reyes 1, 28770 Colmenar Viejo (Madrid), Spain.
| | - José A Salas
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| |
Collapse
|
22
|
Sharma G, Subramanian S. Unravelling the Complete Genome of Archangium gephyra DSM 2261T and Evolutionary Insights into Myxobacterial Chitinases. Genome Biol Evol 2018; 9:1304-1311. [PMID: 28379546 PMCID: PMC5441343 DOI: 10.1093/gbe/evx066] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2017] [Indexed: 11/24/2022] Open
Abstract
Family Cystobacteraceae is a group of eubacteria within order Myxococcales and class Deltaproteobacteria that includes more than 20 species belonging to 6 genera, that is, Angiococcus, Archangium, Cystobacter, Hyalangium, Melittangium, and Stigmatella. Earlier these members have been classified based on chitin degrading efficiency such as Cystobacter fuscus and Stigmatella aurantiaca, which are efficient chitin degraders, C. violaceus a partial chitin degrader and Archangium gephyra a chitin nondegrader. Here we report the 12.5 Mbp complete genome of A. gephyra DSM 2261T and compare it with four available genomes within the family Cystobacteraceae. Phylogeny and DNA–DNA hybridization studies reveal that A. gephyra is closest to Angiococcus disciformis, C. violaceus and C. ferrugineus, which are partial chitin degraders of the family Cystobacteraceae. Homology studies reveal the conservation of approximately half of the proteins in these genomes, with about 15% unique proteins in each genome. The total carbohydrate-active enzymes (CAZome) analysis reveals the presence of one GH18 chitinase in the A. gephyra genome whereas eight copies are present in C. fuscus and S. aurantiaca. Evolutionary studies of myxobacterial GH18 chitinases reveal that most of them are likely related to Terrabacteria and Proteobacteria whereas the Archangium GH18 homolog shares maximum similarity with those of chitin nondegrading Acidobacteria.
Collapse
Affiliation(s)
- Gaurav Sharma
- Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Srikrishna Subramanian
- Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, India
| |
Collapse
|
23
|
Miyanaga A, Kudo F, Eguchi T. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat Prod Rep 2018; 35:1185-1209. [DOI: 10.1039/c8np00022k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrids are summarized and discussed.
Collapse
Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tadashi Eguchi
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| |
Collapse
|
24
|
Skiba MA, Sikkema AP, Moss NA, Tran CL, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. A Mononuclear Iron-Dependent Methyltransferase Catalyzes Initial Steps in Assembly of the Apratoxin A Polyketide Starter Unit. ACS Chem Biol 2017; 12:3039-3048. [PMID: 29096064 PMCID: PMC5784268 DOI: 10.1021/acschembio.7b00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural product biosynthetic pathways contain a plethora of enzymatic tools to carry out difficult biosynthetic transformations. Here, we discover an unusual mononuclear iron-dependent methyltransferase that acts in the initiation steps of apratoxin A biosynthesis (AprA MT1). Fe3+-replete AprA MT1 catalyzes one or two methyl transfer reactions on the substrate malonyl-ACP (acyl carrier protein), whereas Co2+, Fe2+, Mn2+, and Ni2+ support only a single methyl transfer. MT1 homologues exist within the "GNAT" (GCN5-related N-acetyltransferase) loading modules of several modular biosynthetic pathways with propionyl, isobutyryl, or pivaloyl starter units. GNAT domains are thought to catalyze decarboxylation of malonyl-CoA and acetyl transfer to a carrier protein. In AprA, the GNAT domain lacks both decarboxylation and acyl transfer activity. A crystal structure of the AprA MT1-GNAT di-domain with bound Mn2+, malonate, and the methyl donor S-adenosylmethionine (SAM) reveals that the malonyl substrate is a bidentate metal ligand, indicating that the metal acts as a Lewis acid to promote methylation of the malonyl α-carbon. The GNAT domain is truncated relative to functional homologues. These results afford an expanded understanding of MT1-GNAT structure and activity and permit the functional annotation of homologous GNAT loading modules both with and without methyltransferases, additionally revealing their rapid evolutionary adaptation in different biosynthetic contexts.
Collapse
Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor MI, 48109
| | - Andrew P. Sikkema
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor MI, 48109
| | - Nathan A. Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Collin L. Tran
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor MI, 48109
| |
Collapse
|
25
|
Li J, Tang X, Awakawa T, Moore BS. Enzymatic C−H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705239] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jie Li
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
| | - Xiaoyu Tang
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
| | - Takayoshi Awakawa
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Bradley S. Moore
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| |
Collapse
|
26
|
Li J, Tang X, Awakawa T, Moore BS. Enzymatic C-H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity. Angew Chem Int Ed Engl 2017; 56:12234-12239. [PMID: 28833969 DOI: 10.1002/anie.201705239] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/28/2017] [Indexed: 11/10/2022]
Abstract
The selective activation of unreactive hydrocarbons by biosynthetic enzymes has inspired new synthetic methods in C-H bond activation. Herein, we report the unprecedented two-step biosynthetic conversion of thiotetromycin to thiotetroamide C involving the tandem oxidation and amidation of an unreactive ethyl group. We detail the genetic and biochemical basis for the terminal amidation in thiotetroamide C biosynthesis, which involves a uniquely adapted cytochrome P450-amidotransferase enzyme pair and highlights the first oxidation-amidation enzymatic cascade reaction leading to the selective formation of a primary amide group from a chemically inert alkyl group. Motivated by the ten-fold increase in antibiotic potency of thiotetroamide C ascribed to the acetamide group and the unusual enzymology involved, we enzymatically interrogated diverse thiolactomycin analogues and prepared an unnatural thiotetroamide C analogue with potentiated bioactivity compared to the parent molecule.
Collapse
Affiliation(s)
- Jie Li
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA
| | - Xiaoyu Tang
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA
| | - Takayoshi Awakawa
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Bradley S Moore
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| |
Collapse
|
27
|
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
|
28
|
Charousová I, Steinmetz H, Medo J, Javoreková S, Wink J. Soil myxobacteria as a potential source of polyketide-peptide substances. Folia Microbiol (Praha) 2017; 62:305-315. [DOI: 10.1007/s12223-017-0502-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/26/2017] [Indexed: 02/06/2023]
|
29
|
Structural and mutational analysis of the nonribosomal peptide synthetase heterocyclization domain provides insight into catalysis. Proc Natl Acad Sci U S A 2016; 114:95-100. [PMID: 27994138 DOI: 10.1073/pnas.1614191114] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are a family of multidomain, multimodule enzymes that synthesize structurally and functionally diverse peptides, many of which are of great therapeutic or commercial value. The central chemical step of peptide synthesis is amide bond formation, which is typically catalyzed by the condensation (C) domain. In many NRPS modules, the C domain is replaced by the heterocyclization (Cy) domain, a homologous domain that performs two consecutive reactions by using hitherto unknown catalytic mechanisms. It first catalyzes amide bond formation, and then the intramolecular cyclodehydration between a Cys, Ser, or Thr side chain and the backbone carbonyl carbon to form a thiazoline, oxazoline, or methyloxazoline ring. The rings are important for the form and function of the peptide product. We present the crystal structure of an NRPS Cy domain, Cy2 of bacillamide synthetase, at a resolution of 2.3 Å. Despite sharing the same fold, the active sites of C and Cy domains have important differences. The structure allowed us to probe the roles of active-site residues by using mutational analyses in a peptide synthesis assay with intact bacillamide synthetase. The drastically different effects of these mutants, interpreted by using our structural and bioinformatic results, provide insight into the catalytic mechanisms of the Cy domain and implicate a previously unexamined Asp-Thr dyad in catalysis of the cyclodehydration reaction.
Collapse
|
30
|
Biosynthetic Pathway Connects Cryptic Ribosomally Synthesized Posttranslationally Modified Peptide Genes with Pyrroloquinoline Alkaloids. Cell Chem Biol 2016; 23:1504-1514. [PMID: 27866908 DOI: 10.1016/j.chembiol.2016.10.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/09/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022]
Abstract
In an era where natural product biosynthetic gene clusters can be rapidly identified from sequenced genomes, it is unusual for the biosynthesis of an entire natural product class to remain unknown. Yet, the genetic determinates for pyrroloquinoline alkaloid biosynthesis have remained obscure despite their abundance and deceptive structural simplicity. In this work, we have identified the biosynthetic gene cluster for ammosamides A-C, pyrroloquinoline alkaloids from Streptomyces sp. CNR-698. Through direct cloning, heterologous expression and gene deletions we have validated the ammosamide biosynthetic gene cluster and demonstrated that these seemingly simple molecules are derived from a surprisingly complex set of biosynthetic genes that are also found in the biosynthesis of lymphostin, a structurally related pyrroloquinoline alkaloid from Salinispora and Streptomyces. Our results implicate a conserved set of genes driving pyrroloquinoline biosynthesis that consist of genes frequently associated with ribosomal peptide natural product biosynthesis, and whose exact biochemical role remains enigmatic.
Collapse
|
31
|
Ikon N, Ryan RO. On the origin of 3-methylglutaconic acid in disorders of mitochondrial energy metabolism. J Inherit Metab Dis 2016; 39:749-756. [PMID: 27091556 PMCID: PMC4988875 DOI: 10.1007/s10545-016-9933-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/17/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
Abstract
3-methylglutaconic acid (3MGA)-uria occurs in numerous inborn errors of metabolism (IEM) associated with compromised mitochondrial energy metabolism. This organic acid arises from thioester cleavage of 3-methylglutaconyl CoA (3MG CoA), an intermediate in leucine catabolism. In individuals harboring mutations in 3MG CoA hydratase (i.e., primary 3MGA-uria), dietary leucine is the source of 3MGA. In secondary 3MGA-uria, however, no leucine metabolism defects have been reported. While others have suggested 3MGA arises from aberrant isoprenoid shunting from cytosol to mitochondria, an alternative route posits that 3MG CoA arises in three steps from mitochondrial acetyl CoA. Support for this biosynthetic route in IEMs is seen by its regulated occurrence in microorganisms. The fungus, Ustilago maydis, the myxobacterium, Myxococcus xanthus and the marine cyanobacterium, Lyngbya majuscule, generate 3MG CoA (or acyl carrier protein derivative) in the biosynthesis of iron chelating siderophores, iso-odd chain fatty acids and polyketide/nonribosomal peptide products, respectively. The existence of this biosynthetic machinery in these organisms supports a model wherein, under conditions of mitochondrial dysfunction, accumulation of acetyl CoA in the inner mitochondrial space as a result of inefficient fuel utilization drives de novo synthesis of 3MG CoA. Since humans lack the downstream biosynthetic capability of the organisms mentioned above, as 3MG CoA levels rise, thioester hydrolysis yields 3MGA, which is excreted in urine as unspent fuel. Understanding the metabolic origins of 3MGA may increase its utility as a biomarker.
Collapse
Affiliation(s)
- Nikita Ikon
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
| | - Robert O Ryan
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA.
| |
Collapse
|
32
|
Yun CS, Motoyama T, Osada H. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme. Nat Commun 2015; 6:8758. [PMID: 26503170 PMCID: PMC4640141 DOI: 10.1038/ncomms9758] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/28/2015] [Indexed: 12/30/2022] Open
Abstract
Tenuazonic acid (TeA) is a well-known mycotoxin produced by various plant pathogenic fungi. However, its biosynthetic gene has been unknown to date. Here we identify the TeA biosynthetic gene from Magnaporthe oryzae by finding two TeA-inducing conditions of a low-producing strain. We demonstrate that TeA is synthesized from isoleucine and acetoacetyl-coenzyme A by TeA synthetase 1 (TAS1). TAS1 is a unique non-ribosomal peptide synthetase and polyketide synthase (NRPS–PKS) hybrid enzyme that begins with an NRPS module. In contrast to other NRPS/PKS hybrid enzymes, the PKS portion of TAS1 has only a ketosynthase (KS) domain and this domain is indispensable for TAS1 activity. Phylogenetic analysis classifies this KS domain as an independent clade close to type I PKS KS domain. We demonstrate that the TAS1 KS domain conducts the final cyclization step for TeA release. These results indicate that TAS1 is a unique type of NRPS–PKS hybrid enzyme. Tenuazonic acid is a mycotoxin produced by various plant pathogenic fungi but its biosynthetic gene is unknown to date. Here, the authors identify the tenuazonic acid biosynthetic gene encoding a protein with a unique KS domain that conducts cyclization step for tenuazonic acid release in Magnaporthe oryzae.
Collapse
Affiliation(s)
- Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| |
Collapse
|
33
|
Labby KJ, Watsula SG, Garneau-Tsodikova S. Interrupted adenylation domains: unique bifunctional enzymes involved in nonribosomal peptide biosynthesis. Nat Prod Rep 2015; 32:641-53. [PMID: 25622971 DOI: 10.1039/c4np00120f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonribosomal peptides (NRPs) account for a large portion of drugs and drug leads currently available in the pharmaceutical industry. They are one of two main families of natural products biosynthesized on megaenzyme assembly-lines composed of multiple modules that are, in general, each comprised of three core domains and on occasion of accompanying auxiliary domains. The core adenylation (A) domains are known to delineate the identity of the specific chemical components to be incorporated into the growing NRPs. Previously believed to be inactive, A domains interrupted by auxiliary enzymes have recently been proven to be active and capable of performing two distinct chemical reactions. This highlight summarizes current knowledge on A domains and presents the various interrupted A domains found in a number of nonribosomal peptide synthetase (NRPS) assembly-lines, their predicted or proven dual functions, and their potential for manipulation and engineering for chemoenzymatic synthesis of new pharmaceutical agents with increased potency.
Collapse
Affiliation(s)
- Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI 53511, USA
| | | | | |
Collapse
|
34
|
Sigrist R, da Costa BZ, Marsaioli AJ, de Oliveira LG. Nature-inspired enzymatic cascades to build valuable compounds. Biotechnol Adv 2015; 33:394-411. [PMID: 25795056 DOI: 10.1016/j.biotechadv.2015.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/09/2015] [Indexed: 11/30/2022]
Abstract
Biocatalysis currently is focusing on enzymatic and multi-enzymatic cascade processes instead of single steps imbedded into chemical pathways. Alongside this scientific revolution, this review provides an overview on multi-enzymatic cascades that are responsible for the biosynthesis of some terpenes, alkaloids and polyethers, which are important classes of natural products. Herein, we illustrate the development of studies inspired by multi- and chemo-enzymatic approaches to build the core moieties of polyethers, polypeptide alkaloids, piperidines and pyrrolidines promoted by the joint action of oxidoreductases, hydrolases, cyclases, transaminases and imine reductases.
Collapse
Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Bruna Zucoloto da Costa
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Anita Jocelyne Marsaioli
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil.
| |
Collapse
|
35
|
Oßwald C, Zaburannyi N, Burgard C, Hoffmann T, Wenzel SC, Müller R. A highly unusual polyketide synthase directs dawenol polyene biosynthesis in Stigmatella aurantiaca. J Biotechnol 2014; 191:54-63. [DOI: 10.1016/j.jbiotec.2014.07.447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/17/2014] [Accepted: 07/25/2014] [Indexed: 01/29/2023]
|
36
|
Al-Mestarihi AH, Villamizar G, Fernández J, Zolova OE, Lombó F, Garneau-Tsodikova S. Adenylation and S-methylation of cysteine by the bifunctional enzyme TioN in thiocoraline biosynthesis. J Am Chem Soc 2014; 136:17350-4. [PMID: 25409494 DOI: 10.1021/ja510489j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The antitumor agent thiocoraline is a nonribosomally biosynthesized bisintercalator natural product, which contains in its peptidic backbone two S-methylated l-cysteine residues. S-Methylation occurs very rarely in nature, and is observed extremely rarely in nonribosomal peptide scaffolds. We have proposed that during thiocoraline biosynthesis, TioN, a stand-alone adenylation domain interrupted by the S-adenosyl-l-methionine binding region of a methyltransferase enzyme, is capable of performing two functions: the adenylation and S-methylation of l-cysteine. Herein, by preparation of knockouts of TioN and its MbtH-like protein partner TioT, we confirmed their role in thiocoraline biosynthesis. We also co-expressed recombinant TioN and TioT and biochemically investigated three potential pathways involving activation, methylation, and loading of l-cysteine onto the TioN partner thiolation domain, TioS(T4). The valuable insights gained into the pathway(s) followed for the production of S-Me-l-Cys-S-TioS(T4) will serve as a guide for the development of novel engineered interrupted adenylation enzymes for combinatorial biosynthesis.
Collapse
Affiliation(s)
- Ahmad H Al-Mestarihi
- Department of Pharmaceutical Sciences, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | |
Collapse
|
37
|
Abstract
Covering: up to the end of 2013. Myxobacteria produce a vast range of structurally diverse natural products with prominent biological activities. Here, we provide a detailed description and judge the potential of all antibiotically active myxobacterial compounds as lead structures, pointing out their particularities and, if known, their mode of action. Thus, the review provides an overview of the potential of specific compounds, suitable for future investigations and possible clinical applications.
Collapse
Affiliation(s)
- Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | | | | | | |
Collapse
|
38
|
Schieferdecker S, Exner TE, Gross H, Roth M, Nett M. New myxothiazols from the predatory bacterium Myxococcus fulvus. J Antibiot (Tokyo) 2014; 67:519-25. [DOI: 10.1038/ja.2014.31] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/14/2014] [Accepted: 03/05/2014] [Indexed: 11/09/2022]
|
39
|
Gomes ES, Schuch V, de Macedo Lemos EG. Biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. Braz J Microbiol 2014; 44:1007-34. [PMID: 24688489 PMCID: PMC3958165 DOI: 10.1590/s1517-83822013000400002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
The discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. In fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the “goose that laid the golden egg,” the potential of this wealth is still inexorable: simply adjust the focus from “micro” to “nano”, that means changing the look from microorganisms to nanograms of DNA. Then, the search for new drugs, driven by genetic engineering combined with metagenomic strategies, shows us a way to bypass the barriers imposed by methodologies limited to isolation and culturing. However, we are far from solving the problem of supplying new molecules that are effective against the plasticity of multi- or pan-drug-resistant pathogens. Although the first advances in genetic engineering date back to 1990, there is still a lack of high-throughput methods to speed up the screening of new genes and design new molecules by recombination of pathways. In addition, it is necessary an increase in the variety of heterologous hosts and improvements throughout the full drug discovery pipeline. Among numerous studies focused on this subject, those on polyketide antibiotics stand out for the large technical-scientific efforts that established novel solutions for the transfer/engineering of major metabolic pathways using transposons and other episomes, overcoming one of the main methodological constraints for the heterologous expression of major pathways. In silico prediction analysis of three-dimensional enzymatic structures and advances in sequencing technologies have expanded access to the metabolic potential of microorganisms.
Collapse
Affiliation(s)
- Elisângela Soares Gomes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Campus de Jaboticabal, Jaboticabal, SP, Brazil
| | - Viviane Schuch
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Campus de Jaboticabal, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Campus de Jaboticabal, Jaboticabal, SP, Brazil
| |
Collapse
|
40
|
Fuchs SW, Grundmann F, Kurz M, Kaiser M, Bode HB. Fabclavines: bioactive peptide-polyketide-polyamino hybrids from Xenorhabdus. Chembiochem 2014; 15:512-6. [PMID: 24532262 DOI: 10.1002/cbic.201300802] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/12/2022]
Abstract
The structure of the fabclavines-unique mixtures of nonribosomally derived peptide-polyketide hybrids connected to an unusual polyamino moiety-has been solved by detailed NMR and MS methods. These compounds have been identified in two different entomopathogenic Xenorhabdus strains, thereby leading also to the identification of the fabclavine biosynthesis gene cluster. Detailed analysis of these clusters and initial mutagenesis experiments allowed the prediction of a biosynthesis pathway in which the polyamino moiety is derived from an unusual type of fatty acid synthase that is normally involved in formation of polyunsaturated fatty acids. As fabclavines show broad-spectrum activity against bacteria, fungi, and other eukaryotic cells, they might act as "protection factors" against all kinds of food competitors during the complex life cycle of Xenorhabdus, its nematode host, and their insect prey.
Collapse
Affiliation(s)
- Sebastian W Fuchs
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany)
| | | | | | | | | |
Collapse
|
41
|
Bunet R, Riclea R, Laureti L, Hôtel L, Paris C, Girardet JM, Spiteller D, Dickschat JS, Leblond P, Aigle B. A single Sfp-type phosphopantetheinyl transferase plays a major role in the biosynthesis of PKS and NRPS derived metabolites in Streptomyces ambofaciens ATCC23877. PLoS One 2014; 9:e87607. [PMID: 24498152 PMCID: PMC3909215 DOI: 10.1371/journal.pone.0087607] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/20/2013] [Indexed: 01/31/2023] Open
Abstract
The phosphopantetheinyl transferases (PPTases) are responsible for the activation of the carrier protein domains of the polyketide synthases (PKS), non ribosomal peptide synthases (NRPS) and fatty acid synthases (FAS). The analysis of the Streptomyces ambofaciens ATCC23877 genome has revealed the presence of four putative PPTase encoding genes. One of these genes appears to be essential and is likely involved in fatty acid biosynthesis. Two other PPTase genes, samT0172 (alpN) and samL0372, are located within a type II PKS gene cluster responsible for the kinamycin production and an hybrid NRPS-PKS cluster involved in antimycin production, respectively, and their products were shown to be specifically involved in the biosynthesis of these secondary metabolites. Surprisingly, the fourth PPTase gene, which is not located within a secondary metabolite gene cluster, appears to play a pleiotropic role. Its product is likely involved in the activation of the acyl- and peptidyl-carrier protein domains within all the other PKS and NRPS complexes encoded by S. ambofaciens. Indeed, the deletion of this gene affects the production of the spiramycin and stambomycin macrolide antibiotics and of the grey spore pigment, all three being PKS-derived metabolites, as well as the production of the nonribosomally produced compounds, the hydroxamate siderophore coelichelin and the pyrrolamide antibiotic congocidine. In addition, this PPTase seems to act in concert with the product of samL0372 to activate the ACP and/or PCP domains of the antimycin biosynthesis cluster which is also responsible for the production of volatile lactones.
Collapse
Affiliation(s)
- Robert Bunet
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
- INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
| | - Ramona Riclea
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Luisa Laureti
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
- INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
| | - Laurence Hôtel
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
- INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
| | - Cédric Paris
- Université de Lorraine, Laboratoire d’Ingénierie des Biomolécules, Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires, Vandœuvre-lès-Nancy, France
| | - Jean-Michel Girardet
- Université de Lorraine, Unité de Recherche Animal et Fonctionnalités des Produits Animaux (URAFPA), Vandœuvre-lès-Nancy Cedex, France
- INRA,URAFPA, USC 340, Vandœuvre-lès-Nancy, France
| | - Dieter Spiteller
- Department of Biology, Chemical Ecology/Biological Chemistry, University of Konstanz, Konstanz, Germany
| | | | - Pierre Leblond
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
- INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
| | - Bertrand Aigle
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
- INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, France
- * E-mail:
| |
Collapse
|
42
|
Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
Collapse
Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | | | | | | | | |
Collapse
|
43
|
KtzJ-dependent serine activation and O-methylation by KtzH for kutznerides biosynthesis. J Antibiot (Tokyo) 2013; 67:59-64. [DOI: 10.1038/ja.2013.98] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 12/11/2022]
|
44
|
Desriac F, Jégou C, Balnois E, Brillet B, Le Chevalier P, Fleury Y. Antimicrobial peptides from marine proteobacteria. Mar Drugs 2013; 11:3632-60. [PMID: 24084784 PMCID: PMC3826127 DOI: 10.3390/md11103632] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 01/03/2023] Open
Abstract
After years of inadequate use and the emergence of multidrug resistant (MDR) strains, the efficiency of "classical" antibiotics has decreased significantly. New drugs to fight MDR strains are urgently needed. Bacteria hold much promise as a source of unusual bioactive metabolites. However, the potential of marine bacteria, except for Actinomycetes and Cyanobacteria, has been largely underexplored. In the past two decades, the structures of several antimicrobial compounds have been elucidated in marine Proteobacteria. Of these compounds, polyketides (PKs), synthesised by condensation of malonyl-coenzyme A and/or acetyl-coenzyme A, and non-ribosomal peptides (NRPs), obtained through the linkage of (unusual) amino acids, have recently generated particular interest. NRPs are good examples of naturally modified peptides. Here, we review and compile the data on the antimicrobial peptides isolated from marine Proteobacteria, especially NRPs.
Collapse
Affiliation(s)
- Florie Desriac
- University of Brest, LUBEM EA 3882, SFR 148, Quimper 29000, France.
| | | | | | | | | | | |
Collapse
|
45
|
Müller R, Wink J. Future potential for anti-infectives from bacteria - how to exploit biodiversity and genomic potential. Int J Med Microbiol 2013; 304:3-13. [PMID: 24119567 DOI: 10.1016/j.ijmm.2013.09.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The early stages of antibiotic development include the identification of novel hit compounds. Since actinomycetes and myxobacteria are still the most important natural sources of active metabolites, we provide an overview on these producers and discuss three of the most promising approaches toward finding novel anti-infectives from microorganisms. These are defined as the use of biodiversity to find novel producers, the variation of culture conditions and induction of silent genes, and the exploitation of the genomic potential of producers via "genome mining". Challenges that exist beyond compound discovery are outlined in the last section.
Collapse
Affiliation(s)
- Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), P.O. Box 151150, 66041 Saarbrücken, Germany; Helmholtz Centre for Infectious Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Joachim Wink
- Helmholtz Centre for Infectious Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany.
| |
Collapse
|
46
|
Li Y, Luxenburger E, Müller R. An alternative isovaleryl CoA biosynthetic pathway involving a previously unknown 3-methylglutaconyl CoA decarboxylase. Angew Chem Int Ed Engl 2012; 52:1304-8. [PMID: 23225771 DOI: 10.1002/anie.201207984] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Yanyan Li
- Helmholtz Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie, Universität des Saarlandes, 66041 Saarbrücken, Germany
| | | | | |
Collapse
|
47
|
Li Y, Luxenburger E, Müller R. Ein alternativer Isovaleryl-CoA-Biosyntheseweg: Beteiligung einer bisher unbekannten 3-Methylglutaconyl-CoA-Decarboxylase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
48
|
Brachmann AO, Reimer D, Lorenzen W, Augusto Alonso E, Kopp Y, Piel J, Bode HB. Reciprocal Cross Talk between Fatty Acid and Antibiotic Biosynthesis in a Nematode Symbiont. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
49
|
Brachmann AO, Reimer D, Lorenzen W, Augusto Alonso E, Kopp Y, Piel J, Bode HB. Reciprocal Cross Talk between Fatty Acid and Antibiotic Biosynthesis in a Nematode Symbiont. Angew Chem Int Ed Engl 2012; 51:12086-9. [DOI: 10.1002/anie.201205384] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Indexed: 11/06/2022]
|
50
|
Synthetic biotechnology to study and engineer ribosomal bottromycin biosynthesis. ACTA ACUST UNITED AC 2012; 19:1278-87. [PMID: 23021914 DOI: 10.1016/j.chembiol.2012.08.013] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/03/2012] [Accepted: 08/09/2012] [Indexed: 12/23/2022]
Abstract
Bottromycins represent a promising class of antibiotics binding to the therapeutically unexploited A-site of the bacterial ribosome. By inhibiting translation they are active against clinically important pathogens, such as vancomycin-resistant Enterococci. Structurally, bottromycins are heavily modified peptides exhibiting various unusual biosynthetic features. To set the stage for compound modification and yield optimization, we identified the biosynthetic gene cluster, used synthetic biotechnology approaches to establish and improve heterologous production, and generated analogs by pathway genetic engineering. We unambiguously identified three radical SAM methyltransferase-encoding genes required for various methylations at unactivated carbons yielding tert-butyl valine, methyl-proline, and β-methyl-phenylalanine residues, plus a gene involved in aspartate methyl-ester formation. Evidence for the formation of the exo-thiazole unit and for a macrocyclodehydration mechanism leading to amidine ring formation is provided.
Collapse
|