1
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Im JH, Shin D, Ban YH, Byun WS, Bae ES, Lee D, Du YE, Cui J, Kwon Y, Nam SJ, Cha S, Lee SK, Yoon YJ, Oh DC. Targeted Discovery of an Enediyne-Derived Cycloaromatized Compound, Jejucarboside A, from a Marine Actinomycete. Org Lett 2022; 24:7188-7193. [PMID: 36165456 DOI: 10.1021/acs.orglett.2c02934] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A genomic and spectroscopic signature-based search revealed a cycloaromatized enediyne, jejucarboside A (1), from a marine actinomycete strain. The structure of 1 was determined as a new cyclopenta[a]indene glycoside bearing carbonate functionality by nuclear magnetic resonance, high-resolution mass spectrometry (MS), MS/MS, infrared spectroscopy, and a modified Mosher's method. An iterative enediyne synthase pathway has been proposed for the putative biosynthesis of 1 by genomic analysis. Jejucarboside A exhibited cytotoxicity against the HCT116 colon carcinoma cells.
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Affiliation(s)
- Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Donghoon Lee
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yun Kwon
- Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sangwon Cha
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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2
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Kudo Y, Konoki K, Yotsu-Yamashita M. Mass spectrometry-guided discovery of new analogues of bicyclic phosphotriester salinipostin and evaluation of their monoacylglycerol lipase inhibitory activity. Biosci Biotechnol Biochem 2022; 86:1333-1342. [PMID: 35918181 DOI: 10.1093/bbb/zbac131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022]
Abstract
Natural products containing the highly unusual phosphotriester ring are known to be potent serine hydrolase inhibitors. The long-chain bicyclic enol-phosphotriester salinipostins (SPTs) from the marine actinomycete Salinispora have been identified as selective antimalarial agents. A potential regulatory function has been suggested for phosphotriesters based on their structural relationship with actinomycete signaling molecules and the prevalence of spt-like biosynthetic gene clusters across actinomycetes. In this study, we established a mass spectrometry-guided screening method for phosphotriesters focusing on their characteristic fragment ions. Applying this screening method to the SPT producer Salinispora tropica CNB-440, new SPT analogues (4-6) were discovered and their structures were elucidated by spectroscopic analyses. Previously known and herein-identified SPT analogues inhibited the activity of human monoacylglycerol lipase (MAGL), a key serine hydrolase in the endocannabinoid system, in the nanomolar range. Our method could be applied to the screening of phosphotriesters, potential serine hydrolase inhibitors and signaling molecules.
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Affiliation(s)
- Yuta Kudo
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, Japan.,Graduate School of Agricultural Science, Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, Japan
| | - Keiichi Konoki
- Graduate School of Agricultural Science, Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, Japan
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science, Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, Japan
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3
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Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites. mBio 2021; 12:e0270021. [PMID: 34809466 PMCID: PMC8609351 DOI: 10.1128/mbio.02700-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography–high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames.
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4
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In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov. Antibiotics (Basel) 2021; 10:antibiotics10121447. [PMID: 34943659 PMCID: PMC8698034 DOI: 10.3390/antibiotics10121447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022] Open
Abstract
Micromonospora sp. TP-A0316 and Micromonospora sp. TP-A0468 are producers of arisostatin and kosinostatin, respectively. Micromonospora sp. TP-A0316 showed a 16S rRNA gene sequence similarity of 100% to Micromonosporaoryzae CP2R9-1T whereas Micromonospora sp. TP-A0468 showed a 99.3% similarity to Micromonospora haikouensis 232617T. A phylogenetic analysis based on gyrB sequences suggested that Micromonospora sp. TP-A0316 is closely related to Micromonospora oryzae whereas Micromonospora TP-A0468 is an independent genomospecies. As Micromonospora sp. TP-A0468 showed some phenotypic differences to its closely related species, it was classified as a novel species, for which the name Micromonospora okii sp. nov. is proposed. The type strain is TP-A0468T (= NBRC 110461T). Micromonospora sp. TP-A0316 and M. okii TP-A0468T were both found to harbor 15 gene clusters for secondary metabolites such as polyketides and nonribosomal peptides in their genomes. Arisostatin-biosynthetic gene cluster (BGC) of Micromonospora sp. TP-A0316 closely resembled tetrocarcin A-BGC of Micromonospora chalcea NRRL 11289. A large type-I polyketide synthase gene cluster was present in each genome of Micromonospora sp. TP-A0316 and M. okii TP-A0468T. It was an ortholog of quinolidomicin-BGC of M. chalcea AK-AN57 and widely distributed in the genus Micromonospora.
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5
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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6
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Braesel J, Crnkovic CM, Kunstman KJ, Green SJ, Maienschein-Cline M, Orjala J, Murphy BT, Eustáquio AS. Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete. JOURNAL OF NATURAL PRODUCTS 2018; 81:2057-2068. [PMID: 30110167 PMCID: PMC6174880 DOI: 10.1021/acs.jnatprod.8b00394] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Actinomycete bacteria isolated from freshwater environments are an unexplored source of natural products. Here we report the complete genome of the Great Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to close remaining gaps. All identified biosynthetic gene clusters (BGCs) were manually curated. Five known BGCs were identified encoding desferrioxamine, alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and diazepinomicin, which is currently in phase II clinical trials to treat Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006 is indeed a producer of diazepinomicin and at yields higher than previously reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were transcriptionally active under the culture condition tested. Orphan BGCs include an enediyne polyketide synthase and an uncharacteristically large, 36-module polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in the future. This study is one of the few attempts to report the biosynthetic capacity of a freshwater-derived actinomycete and highlights this resource as a potential reservoir for new natural products.
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Affiliation(s)
- Jana Braesel
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Camila M. Crnkovic
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
| | - Kevin J. Kunstman
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, IL 60615, USA
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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7
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Heine T, van Berkel WJH, Gassner G, van Pée KH, Tischler D. Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities. BIOLOGY 2018; 7:biology7030042. [PMID: 30072664 PMCID: PMC6165268 DOI: 10.3390/biology7030042] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
Abstract
Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - George Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
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8
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Seghal Kiran G, Ramasamy P, Sekar S, Ramu M, Hassan S, Ninawe A, Selvin J. Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules. Int J Biol Macromol 2018; 112:1278-1288. [DOI: 10.1016/j.ijbiomac.2018.01.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 12/18/2022]
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9
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Chang CY, Lohman JR, Huang T, Michalska K, Bigelow L, Rudolf JD, Jedrzejczak R, Yan X, Ma M, Babnigg G, Joachimiak A, Phillips GN, Shen B. Structural Insights into the Free-Standing Condensation Enzyme SgcC5 Catalyzing Ester-Bond Formation in the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027. Biochemistry 2018. [PMID: 29533601 DOI: 10.1021/acs.biochem.8b00174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
C-1027 is a chromoprotein enediyne antitumor antibiotic, consisting of the CagA apoprotein and the C-1027 chromophore. The C-1027 chromophore features a nine-membered enediyne core appended with three peripheral moieties, including an ( S)-3-chloro-5-hydroxy-β-tyrosine. In a convergent biosynthesis of the C-1027 chromophore, the ( S)-3-chloro-5-hydroxy-β-tyrosine moiety is appended to the enediyne core by the free-standing condensation enzyme SgcC5. Unlike canonical condensation domains from the modular nonribosomal peptide synthetases that catalyze amide-bond formation, SgcC5 catalyzes ester-bond formation, as demonstrated in vitro, between SgcC2-tethered ( S)-3-chloro-5-hydroxy-β-tyrosine and ( R)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core as an acceptor substrate. Here, we report that (i) genes encoding SgcC5 homologues are widespread among both experimentally confirmed and bioinformatically predicted enediyne biosynthetic gene clusters, forming a new clade of condensation enzymes, (ii) SgcC5 shares a similar overall structure with the canonical condensation domains but forms a homodimer in solution, the active site of which is located in a cavity rather than a tunnel typically seen in condensation domains, and (iii) the catalytic histidine of SgcC5 activates the 2-hydroxyl group, while a hydrogen-bond network in SgcC5 prefers the R-enantiomer of the acceptor substrate, accounting for the regio- and stereospecific ester-bond formation between SgcC2-tethered ( S)-3-chloro-5-hydroxy-β-tyrosine and ( R)-1-phenyl-1,2-ethanediol upon acid-base catalysis. These findings expand the catalytic repertoire and reveal new insights into the structure and mechanism of condensation enzymes.
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Affiliation(s)
- Chin-Yuan Chang
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Jeremy R Lohman
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Tingting Huang
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jeffrey D Rudolf
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Xiaohui Yan
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Ming Ma
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States.,Center for Structural Genomics of Infectious Diseases , University of Chicago , Chicago , Illinois 60637 , United States
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States.,Center for Structural Genomics of Infectious Diseases , University of Chicago , Chicago , Illinois 60637 , United States.,Structural Biology Center, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry , Rice University , Houston , Texas 77251 , United States
| | - Ben Shen
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States.,Department of Molecular Medicine , The Scripps Research Institute , Jupiter , Florida 33458 , United States.,Natural Products Library Initiative at The Scripps Research Institute , The Scripps Research Institute , Jupiter , Florida 33458 , United States
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10
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Yamashita S, Terayama K, Ozeki E, Hayashi Y, Hirama M. Synthetic Studies on Presporolide, a Putative Enediyne Precursor of Sporolides. Org Lett 2017; 20:276-279. [DOI: 10.1021/acs.orglett.7b03670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuji Yamashita
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kanae Terayama
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Eri Ozeki
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Yujiro Hayashi
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Masahiro Hirama
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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11
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Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality. Proc Natl Acad Sci U S A 2017; 114:E11121-E11130. [PMID: 29229817 DOI: 10.1073/pnas.1714381115] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown from Salinispora pacifica.
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12
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Ma SY, Xiao YS, Zhang B, Shao FL, Guo ZK, Zhang JJ, Jiao RH, Sun Y, Xu Q, Tan RX, Ge HM. Amycolamycins A and B, Two Enediyne-Derived Compounds from a Locust-Associated Actinomycete. Org Lett 2017; 19:6208-6211. [PMID: 29090939 DOI: 10.1021/acs.orglett.7b03113] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two novel enediyne-derived natural products, amycolamycins A and B (1 and 2), were characterized from a locust-associated actinomycete Amycolatopsis sp. HCa4. Amycolamycins A and B contain a unique 2-(cyclopenta[a]inden-5-yl)oxirane core with suspected enediyne polyketide biosynthetic origin. Sequencing and analysis of the acm biosynthetic gene cluster allowed us to propose the biosynthetic pathway of 1 and 2. Moreover, amycolamycin A (1) was selectively cytotoxic to the M231 breast cancer cell line.
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Affiliation(s)
- Shi Ying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Yong Sheng Xiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Fen Li Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , Hainan 571101, China
| | - Juan Juan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China.,State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine , Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
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13
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Letzel AC, Li J, Amos GCA, Millán-Aguiñaga N, Ginigini J, Abdelmohsen UR, Gaudêncio SP, Ziemert N, Moore BS, Jensen PR. Genomic insights into specialized metabolism in the marine actinomycete Salinispora. Environ Microbiol 2017; 19:3660-3673. [PMID: 28752948 DOI: 10.1111/1462-2920.13867] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 11/28/2022]
Abstract
Comparative genomics is providing new opportunities to address the diversity and distributions of genes encoding the biosynthesis of specialized metabolites. An analysis of 119 genome sequences representing three closely related species of the marine actinomycete genus Salinispora reveals extraordinary biosynthetic diversity in the form of 176 distinct biosynthetic gene clusters (BGCs) of which only 24 have been linked to their products. Remarkably, more than half of the BGCs were observed in only one or two strains, suggesting they were acquired relatively recently in the evolutionary history of the genus. These acquired gene clusters are concentrated in specific genomic islands, which represent hot spots for BGC acquisition. While most BGCs are stable in terms of their chromosomal position, others migrated to different locations or were exchanged with unrelated gene clusters suggesting a plug and play type model of evolution that provides a mechanism to test the relative fitness effects of specialized metabolites. Transcriptome analyses were used to address the relationships between BGC abundance, chromosomal position and product discovery. The results indicate that recently acquired BGCs can be functional and that complex evolutionary processes shape the micro-diversity of specialized metabolism observed in closely related environmental bacteria.
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Affiliation(s)
- Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jing Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Gregory C A Amos
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California 22800, Mexico
| | - Joape Ginigini
- Institute of Applied Sciences, Faculty of Science, Technology and Environment, University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Fiji
| | - Usama R Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Germany.,Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Susana P Gaudêncio
- Department of Chemistry, REQUIMTE, LAQV and UCIBIO, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica 2529-516, Portugal
| | - Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Interfaculty Institute of Microbiology and Infection Medicine Tuübingen, University of Tuübingen, Auf der Morgenstelle 28, Tuübingen 72076, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
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14
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Abstract
The enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 enediynes have been structurally characterized to date. Here we report a genome survey of 3,400 actinomycetes, identifying 81 strains that harbor genes encoding the enediyne polyketide synthase cassettes that could be grouped into 28 distinct clades based on phylogenetic analysis. Genome sequencing of 31 representative strains confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster. A genome neighborhood network allows prediction of new structural features and biosynthetic insights that could be exploited for enediyne discovery. We confirmed one clade as new C-1027 producers, with a significantly higher C-1027 titer than the original producer, and discovered a new family of enediyne natural products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a broad spectrum of cancer cell lines. Our results demonstrate the feasibility of rapid discovery of new enediynes from a large strain collection. Recent advances in microbial genomics clearly revealed that the biosynthetic potential of soil actinomycetes to produce enediynes is underappreciated. A great challenge is to develop innovative methods to discover new enediynes and produce them in sufficient quantities for chemical, biological, and clinical investigations. This work demonstrated the feasibility of rapid discovery of new enediynes from a large strain collection. The new C-1027 producers, with a significantly higher C-1027 titer than the original producer, will impact the practical supply of this important drug lead. The TNMs, with their extremely potent cytotoxicity against various cancer cells and their rapid and complete cancer cell killing characteristics, in comparison with the payloads used in FDA-approved antibody-drug conjugates (ADCs), are poised to be exploited as payload candidates for the next generation of anticancer ADCs. Follow-up studies on the other identified hits promise the discovery of new enediynes, radically expanding the chemical space for the enediyne family.
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15
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Chang CY, Lohman JR, Cao H, Tan K, Rudolf JD, Ma M, Xu W, Bingman CA, Yennamalli RM, Bigelow L, Babnigg G, Yan X, Joachimiak A, Phillips GN, Shen B. Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus. Biochemistry 2016; 55:5142-54. [PMID: 27560143 PMCID: PMC5024704 DOI: 10.1021/acs.biochem.6b00713] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
C-1027
is a chromoprotein enediyne antitumor antibiotic produced
by Streptomyces globisporus. In the last step of
biosynthesis of the (S)-3-chloro-5-hydroxy-β-tyrosine
moiety of the C-1027 enediyne chromophore, SgcE6 and SgcC compose
a two-component monooxygenase that hydroxylates the C-5 position of
(S)-3-chloro-β-tyrosine. This two-component
monooxygenase is remarkable for two reasons. (i) SgcE6 specifically
reacts with FAD and NADH, and (ii) SgcC is active with only the peptidyl
carrier protein (PCP)-tethered substrate. To address the molecular
details of substrate specificity, we determined the crystal structures
of SgcE6 and SgcC at 1.66 and 2.63 Å resolution, respectively.
SgcE6 shares a similar β-barrel fold with the class I HpaC-like
flavin reductases. A flexible loop near the active site of SgcE6 plays
a role in FAD binding, likely by providing sufficient space to accommodate
the AMP moiety of FAD, when compared to that of FMN-utilizing homologues.
SgcC shows structural similarity to a few other known FADH2-dependent monooxygenases and sheds light on some biochemically but
not structurally characterized homologues. The crystal structures
reported here provide insights into substrate specificity, and comparison
with homologues provides a catalytic mechanism of the two-component,
FADH2-dependent monooxygenase (SgcE6 and SgcC) that catalyzes
the hydroxylation of a PCP-tethered substrate.
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Affiliation(s)
- Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Hongnan Cao
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States
| | - Kemin Tan
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Weijun Xu
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Ragothaman M Yennamalli
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States.,Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology , Waknaghat, Himachal Pradesh, India 173234
| | - Lance Bigelow
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - George N Phillips
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
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16
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Huang T, Chang CY, Lohman JR, Rudolf JD, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN, Shen B. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. J Antibiot (Tokyo) 2016; 69:731-740. [PMID: 27406907 PMCID: PMC5083130 DOI: 10.1038/ja.2016.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/30/2016] [Accepted: 06/15/2016] [Indexed: 12/28/2022]
Abstract
Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.
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Affiliation(s)
- Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Changsoo Chang
- Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Shonda Clancy
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA
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17
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Nicolaou KC, Wang Y, Lu M, Mandal D, Pattanayak MR, Yu R, Shah AA, Chen JS, Zhang H, Crawford JJ, Pasunoori L, Poudel YB, Chowdari NS, Pan C, Nazeer A, Gangwar S, Vite G, Pitsinos EN. Streamlined Total Synthesis of Uncialamycin and Its Application to the Synthesis of Designed Analogues for Biological Investigations. J Am Chem Soc 2016; 138:8235-46. [DOI: 10.1021/jacs.6b04339] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. C. Nicolaou
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yanping Wang
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| | - Min Lu
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Debashis Mandal
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Manas R. Pattanayak
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ruocheng Yu
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| | - Akshay A. Shah
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| | - Jason S. Chen
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hongjun Zhang
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James J. Crawford
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laxman Pasunoori
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yam B. Poudel
- Bristol-Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Naidu S. Chowdari
- Bristol-Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Chin Pan
- Bristol-Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Ayesha Nazeer
- Bristol-Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Sanjeev Gangwar
- Bristol-Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Gregory Vite
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543-4000, United States
| | - Emmanuel N. Pitsinos
- Department
of Chemistry, BioScience Research Collaborative, Rice University, 6100
Main Street, Houston, Texas 77005, United States
- Laboratory of Natural Products Synthesis & Bioorganic Chemistry, Institute of Nanoscience & Nanotechnology, National Centre of Scientific Research “Demokritos”, Agia Paraskevi GR-15310, Greece
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18
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Rudolf JD, Yan X, Shen B. Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery. J Ind Microbiol Biotechnol 2016; 43:261-76. [PMID: 26318027 PMCID: PMC4753101 DOI: 10.1007/s10295-015-1671-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/09/2015] [Indexed: 01/24/2023]
Abstract
The enediynes are one of the most fascinating families of bacterial natural products given their unprecedented molecular architecture and extraordinary cytotoxicity. Enediynes are rare with only 11 structurally characterized members and four additional members isolated in their cycloaromatized form. Recent advances in DNA sequencing have resulted in an explosion of microbial genomes. A virtual survey of the GenBank and JGI genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains, implying that enediynes are more common than previously thought. Here we report the construction and analysis of an enediyne genome neighborhood network (GNN) as a high-throughput approach to analyze secondary metabolite gene clusters. Analysis of the enediyne GNN facilitated rapid gene cluster annotation, revealed genetic trends in enediyne biosynthetic gene clusters resulting in a simple prediction scheme to determine 9- versus 10-membered enediyne gene clusters, and supported a genomic-based strain prioritization method for enediyne discovery.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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19
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Williams DE, Bottriell H, Davies J, Tietjen I, Brockman MA, Andersen RJ. Unciaphenol, an Oxygenated Analogue of the Bergman Cyclization Product of Uncialamycin Exhibits Anti-HIV Activity. Org Lett 2015; 17:5304-7. [DOI: 10.1021/acs.orglett.5b02664] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David E. Williams
- Departments of Chemistry and Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Helen Bottriell
- Departments of Chemistry and Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Julian Davies
- Life
Sciences Institute, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Ian Tietjen
- Faculty
of Health Sciences and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Mark A. Brockman
- Faculty
of Health Sciences and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
- British
Columbia Centre for Excellence in HIV/AIDS, St. Paul’s Hospital, Vancouver, BC, Canada V6Z 1Y6
| | - Raymond J. Andersen
- Departments of Chemistry and Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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20
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Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation. Antonie van Leeuwenhoek 2015; 108:1075-90. [DOI: 10.1007/s10482-015-0561-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/18/2015] [Indexed: 12/22/2022]
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21
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22
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Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. Nat Prod Rep 2015; 32:738-51. [PMID: 25730728 PMCID: PMC4414829 DOI: 10.1039/c4np00167b] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review covers the initial discovery of the marine actinomycete genus Salinispora through its development as a model for natural product research. A focus is placed on the novel chemical structures reported with reference to their biological activities and the synthetic and biosynthetic studies they have inspired. The time line of discoveries progresses from more traditional bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target the products of specific biosynthetic gene clusters. This overview exemplifies the extraordinary biosynthetic diversity that can emanate from a narrowly defined genus and supports future efforts to explore marine taxa in the search for novel natural products.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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23
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Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. ACTA ACUST UNITED AC 2015; 22:460-471. [PMID: 25865308 DOI: 10.1016/j.chembiol.2015.03.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/26/2015] [Accepted: 03/10/2015] [Indexed: 12/12/2022]
Abstract
Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.
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Affiliation(s)
- Katherine R Duncan
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anna Lechner
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anindita Sarkar
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jie Li
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Paul R Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
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24
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Shen B, Hindra, Yan X, Huang T, Ge H, Yang D, Teng Q, Rudolf JD, Lohman JR. Enediynes: Exploration of microbial genomics to discover new anticancer drug leads. Bioorg Med Chem Lett 2015; 25:9-15. [PMID: 25434000 PMCID: PMC4480864 DOI: 10.1016/j.bmcl.2014.11.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022]
Abstract
The enediyne natural products have been explored for their phenomenal cytotoxicity. The development of enediynes into anticancer drugs has been successfully achieved through the utilization of polymer- and antibody-drug conjugates (ADCs) as drug delivery systems. An increasing inventory of enediynes would benefit current application of ADCs in many oncology programs. Innovations in expanding the enediyne inventory should take advantage of the current knowledge of enediyne biosynthesis and post-genomics technologies. Bioinformatics analysis of microbial genomes reveals that enediynes are underexplored, in particular from Actinomycetales. This digest highlights the emerging opportunities to explore microbial genomics for the discovery of novel enediyne natural products.
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Affiliation(s)
- Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Huiming Ge
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Qihui Teng
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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25
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Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A 2014; 111:E1130-9. [PMID: 24616526 DOI: 10.1073/pnas.1324161111] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Access to genome sequence data has challenged traditional natural product discovery paradigms by revealing that the products of most bacterial biosynthetic pathways have yet to be discovered. Despite the insight afforded by this technology, little is known about the diversity and distributions of natural product biosynthetic pathways among bacteria and how they evolve to generate structural diversity. Here we analyze genome sequence data derived from 75 strains of the marine actinomycete genus Salinispora for pathways associated with polyketide and nonribosomal peptide biosynthesis, the products of which account for some of today's most important medicines. The results reveal high levels of diversity, with a total of 124 pathways identified and 229 predicted with continued sequencing. Recent horizontal gene transfer accounts for the majority of pathways, which occur in only one or two strains. Acquired pathways are incorporated into genomic islands and are commonly exchanged within and between species. Acquisition and transfer events largely involve complete pathways, which subsequently evolve by gene gain, loss, and duplication followed by divergence. The exchange of similar pathway types at the precise chromosomal locations in different strains suggests that the mechanisms of integration include pathway-level homologous recombination. Despite extensive horizontal gene transfer there is clear evidence of species-level vertical inheritance, supporting the concept that secondary metabolites represent functional traits that help define Salinispora species. The plasticity of the Salinispora secondary metabolome provides an effective mechanism to maximize population-level secondary metabolite diversity while limiting the number of pathways maintained within any individual genome.
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26
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Dineshkumar K, Aparna V, Madhuri KZ, Hopper W. Biological activity of sporolides A and B from Salinispora tropica: in silico target prediction using ligand-based pharmacophore mapping and in vitro activity validation on HIV-1 reverse transcriptase. Chem Biol Drug Des 2014; 83:350-61. [PMID: 24165098 DOI: 10.1111/cbdd.12252] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/09/2013] [Indexed: 11/29/2022]
Abstract
Sporolides A and B are novel polycyclic macrolides from the obligate marine actinomycetes, Salinispora tropica. The unique and novel structure of sporolides makes them interesting candidates for targeting diverse biological activities. Biological target prediction of sporolides was carried out using ligand-based pharmacophore screening against known inhibitors and drugs. Validation of pharmacophore screening was carried out for the identified hits. New biological targets predicted for sporolides using this method were HIV-1 reverse transcriptase, adenosine A3 receptor, endothelin receptor ET-A, oxytocin receptor, voltage-gated L-type calcium channel α-1C subunit/calcium channel α/Δ subunit 1. Drug-likeness properties were predicted for the selected compounds using QikProp module. Sporolides A and B showed maximum docking score with HIV-1 reverse transcriptase. Structural interaction fingerprints analysis indicated similar binding pattern of the sporolides with the HIV-1 reverse transcriptase. Sporolide B exhibited good inhibitory activity against HIV-1 reverse transcriptase in in vitro fluorescent assay.
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Affiliation(s)
- Kesavan Dineshkumar
- Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, 603203, TamilNadu, India
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Ghosh S, Khamarui S, Gayen KS, Maiti DK. ArCH(OMe)₂--a Pt(IV)-catalyst originator for diverse annulation catalysis. Sci Rep 2013; 3:2987. [PMID: 24136161 PMCID: PMC3798883 DOI: 10.1038/srep02987] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/30/2013] [Indexed: 02/07/2023] Open
Abstract
We discover an important property of a small molecule ArCH(OMe)2 which transforms catalytically inactive PtIIBr2 procatalyst in situ to an powerful catalyst PtIV-species for diverse annulation reaction. The powerful catalytic system enables selective activation of C2-H/N-H and C2-H/C4-H of acetoacetanilide and C = O/C≡C of substituted butyne-1,2-dione for C-C/C-N, C-C/C-C and C-O/C-O bond-forming inter- and intramolecular annulation towards direct syntheses of functionalised 2-pyridones, cyclohexenones and 3(2H)-furanones respectively. In contrast to the common ligand, herein highly labile C-OMe bond of ArCH(OMe)2 is expected to react with PtBr2 towards generation of the high-valent active catalyst. Unlike catalyst promoter or initiator, the reaction does not occur with PtBr2 in the absence of ArCH(OMe)2. In situ generation of PtIV-species and -OMe fragment of ArCH(OMe)2 were confirmed from the UV-vis characteristic peaks about 260 nm and trapping of -OMe group respectively. These observations provide new prospects and perspectives in catalysis for innovative catalyst design.
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Affiliation(s)
- Subhadeep Ghosh
- Department of Chemistry, University of Calcutta, University College of Science, 92 A. P. C. Road, Kolkata-700009, India
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Horsman GP, Lechner A, Ohnishi Y, Moore BS, Shen B. Predictive model for epoxide hydrolase-generated stereochemistry in the biosynthesis of nine-membered enediyne antitumor antibiotics. Biochemistry 2013; 52:5217-24. [PMID: 23844627 DOI: 10.1021/bi400572a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nine-membered enediyne antitumor antibiotics C-1027, neocarzinostatin (NCS), and kedarcidin (KED) possess enediyne cores to which activity-modulating peripheral moieties are attached via (R)- or (S)-vicinal diols. We have previously shown that this stereochemical difference arises from hydrolysis of epoxide precursors by epoxide hydrolases (EHs) with different regioselectivities. The inverting EHs, such as SgcF, hydrolyze an (S)-epoxide substrate to yield an (R)-diol in C-1027 biosynthesis, whereas the retaining EHs, such as NcsF2 and KedF, hydrolyze an (S)-epoxide substrate to yield an (S)-diol in NCS and KED biosynthesis. We now report the characterization of a series of EH mutants and provide a predictive model for EH regioselectivity in the biosynthesis of the nine-membered enediyne antitumor antibiotics. A W236Y mutation in SgcF increased the retaining activity toward (S)-styrene oxide by 3-fold, and a W236Y/Q237M double mutation in SgcF, mimicking NcsF2 and KedF, resulted in a 20-fold increase in the retaining activity. To test the predictive utility of these mutations, two putative enediyne biosynthesis-associated EHs were identified by genome mining and confirmed as inverting enzymes, SpoF from Salinospora tropica CNB-440 and SgrF (SGR_625) from Streptomyces griseus IFO 13350. Finally, phylogenetic analysis of EHs revealed a familial classification according to inverting versus retaining activity. Taken together, these results provide a predictive model for vicinal diol stereochemistry in enediyne biosynthesis and set the stage for further elucidating the origins of EH regioselectivity.
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Affiliation(s)
- Geoffrey P Horsman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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29
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Kersten RD, Lane AL, Nett M, Richter TKS, Duggan BM, Dorrestein PC, Moore BS. Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica. Chembiochem 2013; 14:955-62. [PMID: 23649992 DOI: 10.1002/cbic.201300147] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 12/27/2022]
Abstract
The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.
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Affiliation(s)
- Roland D Kersten
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA
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30
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Lane AL, Nam SJ, Fukuda T, Yamanaka K, Kauffman CA, Jensen PR, Fenical W, Moore BS. Structures and comparative characterization of biosynthetic gene clusters for cyanosporasides, enediyne-derived natural products from marine actinomycetes. J Am Chem Soc 2013; 135:4171-4. [PMID: 23458364 PMCID: PMC3611589 DOI: 10.1021/ja311065v] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyanosporasides are marine bacterial natural products containing a chlorinated cyclopenta[a]indene core of suspected enediyne polyketide biosynthetic origin. Herein, we report the isolation and characterization of novel cyanosporasides C-F (3-6) from the marine actinomycetes Salinispora pacifica CNS-143 and Streptomyces sp. CNT-179, highlighted by the unprecedented C-2' N-acetylcysteamine functionalized hexose group of 6. Cloning, sequencing, and mutagenesis of homologous ~50 kb cyanosporaside biosynthetic gene clusters from both bacteria afforded the first genetic evidence supporting cyanosporaside's enediyne, and thereby p-benzyne biradical, biosynthetic origin and revealed the molecular basis for nitrile and glycosyl functionalization. This study provides new opportunities for bioengineering of enediyne derivatives and expands the structural diversity afforded by enediyne gene clusters.
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Affiliation(s)
- Amy L. Lane
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Sang Jip Nam
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Takashi Fukuda
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Kazuya Yamanaka
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Christopher A. Kauffman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
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Lohman JR, Huang SX, Horsman GP, Dilfer PE, Huang T, Chen Y, Wendt-Pienkowski E, Shen B. Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics. MOLECULAR BIOSYSTEMS 2013; 9:478-91. [PMID: 23360970 DOI: 10.1039/c3mb25523a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enediyne natural product biosynthesis is characterized by a convergence of multiple pathways, generating unique peripheral moieties that are appended onto the distinctive enediyne core. Kedarcidin (KED) possesses two unique peripheral moieties, a (R)-2-aza-3-chloro-β-tyrosine and an iso-propoxy-bearing 2-naphthonate moiety, as well as two deoxysugars. The appendage pattern of these peripheral moieties to the enediyne core in KED differs from the other enediynes studied to date with respect to stereochemical configuration. To investigate the biosynthesis of these moieties and expand our understanding of enediyne core formation, the biosynthetic gene cluster for KED was cloned from Streptoalloteichus sp. ATCC 53650 and sequenced. Bioinformatics analysis of the ked cluster revealed the presence of the conserved genes encoding for enediyne core biosynthesis, type I and type II polyketide synthase loci likely responsible for 2-aza-l-tyrosine and 3,6,8-trihydroxy-2-naphthonate formation, and enzymes known for deoxysugar biosynthesis. Genes homologous to those responsible for the biosynthesis, activation, and coupling of the l-tyrosine-derived moieties from C-1027 and maduropeptin and of the naphthonate moiety from neocarzinostatin are present in the ked cluster, supporting 2-aza-l-tyrosine and 3,6,8-trihydroxy-2-naphthoic acid as precursors, respectively, for the (R)-2-aza-3-chloro-β-tyrosine and the 2-naphthonate moieties in KED biosynthesis.
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Affiliation(s)
- Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
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Jean M, Tomasi S, van de Weghe P. When the nine-membered enediynes play hide and seek. Org Biomol Chem 2012; 10:7453-6. [PMID: 22898710 DOI: 10.1039/c2ob26033f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The lack of stability of the 9-membered enediynes not associated with an apoprotein may explain the low number of isolated natural compounds containing this core. To overcome such a problem, particular attention should be paid during the process of extraction and isolation of secondary metabolites, especially from microorganisms such as actinomycetes in order to identify the non-cycloaromatized derivatives.
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Affiliation(s)
- Mickaël Jean
- Université de Rennes 1, UMR 6226, Institut des Sciences Chimiques de Rennes, Equipe PNSCM, UFR Sciences Biologiques et Pharmaceutiques, 2 avenue du Prof Léon Bernard, F-35043 Rennes Cedex, France
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33
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Gerwick WH, Moore BS. Lessons from the past and charting the future of marine natural products drug discovery and chemical biology. ACTA ACUST UNITED AC 2012; 19:85-98. [PMID: 22284357 DOI: 10.1016/j.chembiol.2011.12.014] [Citation(s) in RCA: 405] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 12/31/2022]
Abstract
Marine life forms are an important source of structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents. These success stories have had to overcome difficulties inherent to natural products-derived drugs, such as adequate sourcing of the agent and issues related to structural complexity. Nevertheless, several marine-derived agents are now approved, most as "first-in-class" drugs, with five of seven appearing in the past few years. Additionally, there is a rich pipeline of clinical and preclinical marine compounds to suggest their continued application in human medicine. Understanding of how these agents are biosynthetically assembled has accelerated in recent years, especially through interdisciplinary approaches, and innovative manipulations and re-engineering of some of these gene clusters are yielding novel agents of enhanced pharmaceutical properties compared with the natural product.
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Affiliation(s)
- William H Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92037, USA.
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34
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Abstract
Studies directed towards the synthesis of the architecturally complex marine natural product sporolide B are described. Synthetic analysis suggested advanced hydroquinone and benzodiquinane fragments, which upon elaboration were successfully united via an ester linkage. Macrocyclization studies were then carried out, and although a novel macrocyclization product was obtained, subsequent studies revealed that the tertiary hydroxyls at C(6) and C(10) were sterically encumbered to participate in a successful macrocyclization to furnish sporolide B.
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Abstract
The years 2000 through mid-2010 marked a transformational period in understanding of the biosynthesis of marine natural products. During this decade the field emerged from one largely dominated by chemical approaches to understanding biosynthetic pathways to one incorporating the full force of modern molecular biology and bioinformatics. Fusion of chemical and biological approaches yielded great advances in understanding the genetic and enzymatic basis for marine natural product biosynthesis. Progress was particularly pronounced for marine microbes, especially actinomycetes and cyanobacteria. During this single decade, both the first complete marine microbial natural product biosynthetic gene cluster sequence was released as well as the first entire genome sequence for a secondary metabolite-rich marine microbe. The decade also saw tremendous progress in recognizing the key role of marine microbial symbionts of invertebrates in natural product biosynthesis. Application of genetic and enzymatic knowledge led to genetic engineering of novel “unnatural” natural products during this time, as well as opportunities for discovery of novel natural products through genome mining. The current review highlights selected seminal studies from 2000 through to June 2010 that illustrate breakthroughs in understanding of marine natural product biosynthesis at the genetic, enzymatic, and small-molecule natural product levels. A total of 154 references are cited.
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Affiliation(s)
- Amy L. Lane
- Department of Chemistry, University of North Florida, Jacksonville, FL, 32224, USA.
| | - Bradley S. Moore
- Scripps Institution of Oceanography and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
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36
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Nicolaou KC, Wang J, Tang Y, Botta L. Total synthesis of sporolide B and 9-epi-sporolide B. J Am Chem Soc 2010; 132:11350-63. [PMID: 20698702 DOI: 10.1021/ja1048994] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The total synthesis of the structurally unique secondary metabolite sporolide B (1b) is described. The total synthesis of 1b was developed on the basis of preliminary studies that revealed the reactivity of an appropriate o-quinone as a diene system toward a number of indene derivatives as dienophiles, first in intermolecular and thence intramolecular settings. Thus, substrates were devised (37 and 75) that underwent exquisite intramolecular [4+2] cycloaddition reactions under thermal conditions to provide primitive sporolide-type structures that were subsequently elaborated to a sporolide model system, 9-epi-sporolide B, and 1b. The requisite indene o-quinone precursor 75 was synthesized through a ruthenium-catalyzed [2+2+2] cycloaddition reaction between a propargylic alcohol and a chloroacetylenic cyclopentenyne, followed by elaboration and silver-promoted oxidation of the resulting chloroindene derivative. In addition to the total synthesis of 1b, this work demonstrated, for the first time, the power of the intramolecular hetero [4+2] cycloaddition reaction in the total synthesis of complex molecules and the application of the ruthenium-catalyzed [2+2+2] cycloaddition reaction to highly substituted indene systems possessing a chlorine residue on the aromatic nucleus.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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37
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Gomes PB, Nett M, Dahse HM, Hertweck C. Pitucamycin: structural merger of a phenoxazinone with an epoxyquinone antibiotic. JOURNAL OF NATURAL PRODUCTS 2010; 73:1461-1464. [PMID: 20715808 DOI: 10.1021/np100344u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical profiling of a Streptomyces griseus strain isolated from an old building with moisture damage led to the discovery of two novel phenoxazinones, chandrananimycin D and pitucamycin , along with the known grixazone B. Pitucamycin represents an unprecedented hybrid molecule composed of a phenoxazinone and an enaminomycin-like epoxyquinone moiety.
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Affiliation(s)
- Patrícia Bezerra Gomes
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse, 07745 Jena, Germany
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Sequence-based analysis of secondary-metabolite biosynthesis in marine actinobacteria. Appl Environ Microbiol 2010; 76:2487-99. [PMID: 20154113 DOI: 10.1128/aem.02852-09] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A diverse collection of 60 marine-sediment-derived Actinobacteria representing 52 operational taxonomic units was screened by PCR for genes associated with secondary-metabolite biosynthesis. Three primer sets were employed to specifically target adenylation domains associated with nonribosomal peptide synthetases (NRPSs) and ketosynthase (KS) domains associated with type I modular, iterative, hybrid, and enediyne polyketide synthases (PKSs). In total, two-thirds of the strains yielded a sequence-verified PCR product for at least one of these biosynthetic types. Genes associated with enediyne biosynthesis were detected in only two genera, while 88% of the ketosynthase sequences shared greatest homology with modular PKSs. Positive strains included representatives of families not traditionally associated with secondary-metabolite production, including the Corynebacteriaceae, Gordoniaceae, Intrasporangiaceae, and Micrococcaceae. In four of five cases where phylogenetic analyses of KS sequences revealed close evolutionary relationships to genes associated with experimentally characterized biosynthetic pathways, secondary-metabolite production was accurately predicted. Sequence clustering patterns were used to provide an estimate of PKS pathway diversity and to assess the biosynthetic richness of individual strains. The detection of highly similar KS sequences in distantly related strains provided evidence of horizontal gene transfer, while control experiments designed to amplify KS sequences from Salinispora arenicola strain CNS-205, for which a genome sequence is available, led to the detection of 70% of the targeted PKS pathways. The results provide a bioinformatic assessment of secondary-metabolite biosynthetic potential that can be applied in the absence of fully assembled pathways or genome sequences. The rapid identification of strains that possess the greatest potential to produce new secondary metabolites along with those that produce known compounds can be used to improve the process of natural-product discovery by providing a method to prioritize strains for fermentation studies and chemical analysis.
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39
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Liang ZX. Complexity and simplicity in the biosynthesis of enediyne natural products. Nat Prod Rep 2010; 27:499-528. [DOI: 10.1039/b908165h] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Blunt JW, Copp BR, Munro MHG, Northcote PT, Prinsep MR. Marine natural products. Nat Prod Rep 2010; 27:165-237. [DOI: 10.1039/b906091j] [Citation(s) in RCA: 322] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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41
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Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 2009; 26:1362-84. [PMID: 19844637 PMCID: PMC3063060 DOI: 10.1039/b817069j] [Citation(s) in RCA: 543] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The phylum Actinobacteria hosts diverse high G + C, Gram-positive bacteria that have evolved a complex chemical language of natural product chemistry to help navigate their fascinatingly varied lifestyles. To date, 71 Actinobacteria genomes have been completed and annotated, with the vast majority representing the Actinomycetales, which are the source of numerous antibiotics and other drugs from genera such as Streptomyces, Saccharopolyspora and Salinispora . These genomic analyses have illuminated the secondary metabolic proficiency of these microbes – underappreciated for years based on conventional isolation programs – and have helped set the foundation for a new natural product discovery paradigm based on genome mining. Trends in the secondary metabolomes of natural product-rich actinomycetes are highlighted in this review article, which contains 199 references.
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Affiliation(s)
- Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Sagamihara, Kanagawa, 228-8555, Japan.
| | - Bradley S. Moore
- Scripps Institution of Oceanography and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
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42
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Li P, Menche D. Cycloadditions in the Total Synthesis of Sporolide B. Angew Chem Int Ed Engl 2009; 48:5078-80. [DOI: 10.1002/anie.200901894] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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44
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Abstract
An ocean of discovery: The first total synthesis of the highly oxygenated, marine-derived, natural product sporolide B has been achieved through a convergent strategy. The key steps involve a ruthenium-catalyzed [2+2+2] cycloaddition to assemble the indene structural motif and a thermally induced Diels-Alder-type reaction to forge the macrocycle (see scheme).
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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45
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Gulder TAM, Moore BS. Chasing the treasures of the sea - bacterial marine natural products. Curr Opin Microbiol 2009; 12:252-60. [PMID: 19481972 DOI: 10.1016/j.mib.2009.05.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 05/06/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
Abstract
Bacterial marine natural products are an important source of novel lead structures for drug discovery. The cytotoxic properties of many of these secondary metabolites are of particular interest for the development of new anticancer agents. Tremendous advances in marine molecular biology, genome sequencing, and bioinformatics have paved the way to fully exploit the biomedical potential of marine bacterial products. In addition, unique biosynthetic enzymes discovered from bacteria from the sea have begun to emerge as powerful biocatalysts in medicinal chemistry and total synthesis. The increasingly interdisciplinary field of marine natural product chemistry thus strongly impacts future developments in medicine, chemistry, and biology.
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Affiliation(s)
- Tobias A M Gulder
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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46
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Exploration and engineering of biosynthetic pathways in the marine actinomycete Salinispora tropica. PURE APPL CHEM 2009. [DOI: 10.1351/pac-con-08-08-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In recent years, members of the marine actinomycete genus Salinispora have proven to be a precious source of structurally diverse secondary metabolites, including the potent anticancer agent salinosporamide A and the enediyne-derived sporolides. The tremendous potential of these marine-dwelling microbes for natural products biosynthesis, however, was not fully realized until sequencing of the Salinispora tropica genome revealed the presence of numerous orphan biosynthetic loci besides a plethora of rare metabolic pathways. This contribution summarizes the biochemical exploration of this prolific organism, highlighting studies in which genome-based information was exploited for the discovery of new enzymatic processes and the engineering of unnatural natural products. Inactivation of key genes within the salinosporamide pathway has expanded its inherent metabolic plasticity and enabled access to various salinosporamide derivatives by mutasynthesis. New insights into the biosynthesis of the sporolides allowed us to increase production titers of these structurally complex molecules, thereby providing the means to search for the DNA cleaving presporolide enediyne.
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47
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48
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