51
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Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species. Proc Natl Acad Sci U S A 2018; 115:E4255-E4263. [PMID: 29666226 PMCID: PMC5939090 DOI: 10.1073/pnas.1720941115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Natural products biosynthesized by cryptic gene clusters represent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted by the lack of streamlined genetic tools, especially in nonmodel biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe the discovery of a pair of bacteriophage recombinases and application of recombinase-assisted promoter engineering to rapidly identify and activate several cryptic biosynthetic gene clusters in two Burkholderiales strains that currently lack effective genetic tools. Construction of an efficient genome engineering platform in a natural product producer expedites mining of cryptic BGCs in their native backgrounds, and host melioration for yield or structure optimization. This strategy enables potentially scalable discovery of novel metabolites with intriguing bioactivities from many other bacteria. Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent a largely untapped source of drugs or pesticides. Mining of the cryptic products is limited by the unavailability of streamlined genetic tools in native producers. Precise genome engineering using bacteriophage recombinases is particularly useful for genome mining. However, recombinases are usually host-specific. The genome-guided discovery of novel recombinases and their transient expression could boost cryptic BGC mining. Herein, we reported a genetic system employing Red recombinases from Burkholderiales strain DSM 7029 for efficient genome engineering in several Burkholderiales species that currently lack effective genetic tools. Using specialized recombinases-assisted in situ insertion of functional promoters, we successfully mined five cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, two of which were silent. Two classes of lipopeptides, glidopeptins and rhizomides, were identified through extensive spectroscopic characterization. This recombinase expression strategy offers utility within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities.
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52
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Yan X, Hindra, Ge H, Yang D, Huang T, Crnovcic I, Chang CY, Fang SM, Annaval T, Zhu X, Huang Y, Zhao LX, Jiang Y, Duan Y, Shen B. Discovery of Alternative Producers of the Enediyne Antitumor Antibiotic C-1027 with High Titers. JOURNAL OF NATURAL PRODUCTS 2018; 81:594-599. [PMID: 29345939 PMCID: PMC6261254 DOI: 10.1021/acs.jnatprod.7b01013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The potent cytotoxicity and unique mode of action make the enediyne antitumor antibiotic C-1027 an exquisite drug candidate for anticancer chemotherapy. However, clinical development of C-1027 has been hampered by its low titer from the original producer Streptomyces globisporus C-1027. Here we report three new C-1027 alternative producers, Streptomyces sp. CB00657, CB02329, and CB03608, from The Scripps Research Institute actinomycetes strain collection. Together with the previously disclosed Streptomyces sp. CB02366 strain, four C-1027 alternative producers with C-1027 titers of up to 11-fold higher than the original producer have been discovered. The five C-1027 producers, isolated from distant geographic locations, are distinct Streptomyces strains based on morphology and taxonomy. Pulsed-field gel electrophoresis and Southern analysis of the five C-1027 producers reveal that their C-1027 biosynthetic gene clusters (BGCs) are all located on giant plasmids of varying sizes. The high nucleotide sequence similarity among the five C-1027 BGCs implies that they most likely have evolved from a common ancestor.
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Affiliation(s)
- Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Huiming Ge
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, 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
| | - Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Shi-Ming Fang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Thibault Annaval
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410013, People’s Republic of China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Li-Xing Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic of China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic of China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410013, People’s Republic of China
| | - Ben Shen
- Department of Chemistry, 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
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
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53
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Hoffmann T, Krug D, Bozkurt N, Duddela S, Jansen R, Garcia R, Gerth K, Steinmetz H, Müller R. Correlating chemical diversity with taxonomic distance for discovery of natural products in myxobacteria. Nat Commun 2018; 9:803. [PMID: 29476047 PMCID: PMC5824889 DOI: 10.1038/s41467-018-03184-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 01/24/2018] [Indexed: 01/22/2023] Open
Abstract
Some bacterial clades are important sources of novel bioactive natural products. Estimating the magnitude of chemical diversity available from such a resource is complicated by issues including cultivability, isolation bias and limited analytical data sets. Here we perform a systematic metabolite survey of ~2300 bacterial strains of the order Myxococcales, a well-established source of natural products, using mass spectrometry. Our analysis encompasses both known and previously unidentified metabolites detected under laboratory cultivation conditions, thereby enabling large-scale comparison of production profiles in relation to myxobacterial taxonomy. We find a correlation between taxonomic distance and the production of distinct secondary metabolite families, further supporting the idea that the chances of discovering novel metabolites are greater by examining strains from new genera rather than additional representatives within the same genus. In addition, we report the discovery and structure elucidation of rowithocin, a myxobacterial secondary metabolite featuring an uncommon phosphorylated polyketide scaffold. It is thought that the chances for discovery of novel natural products increase by screening rare organisms. Here the authors analyse metabolites produced by over 2300 myxobacterial strains and, indeed, find a correlation between taxonomic distance and production of distinct secondary metabolite families.
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Affiliation(s)
- Thomas Hoffmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
| | - Nisa Bozkurt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Srikanth Duddela
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Rolf Jansen
- Helmholtz Centre for Infection Research (HZI), Department of Microbial Drugs, 38124, Braunschweig, Germany
| | - Ronald Garcia
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
| | - Klaus Gerth
- Helmholtz Centre for Infection Research (HZI), Department of Microbial Drugs, 38124, Braunschweig, Germany
| | - Heinrich Steinmetz
- Helmholtz Centre for Infection Research (HZI), Department of Microbial Drugs, 38124, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany.
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54
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Hoffmann M, Auerbach D, Panter F, Hoffmann T, Dorrestein PC, Müller R. Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622. ACS Chem Biol 2018; 13:273-280. [PMID: 29185703 DOI: 10.1021/acschembio.7b00816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The fascinating ability of myxobacteria to form multicellular spore filled fruiting bodies under starvation conditions was widely studied as a model for cooperative microbial behavior. The potential of a life cycle induced change of secondary metabolism, as a means to discover novel natural products, remains largely underexplored. We therefore studied the model organism Myxococcus xanthus DK1622 under submersed and solid cultivation conditions to find putatively life-cycle related compounds by applying statistical analysis on analytical data. Utilizing the advantageous characteristics of LC-MS, LC-MS/MS, and MALDI-MSI allowed the identification of compounds unambiguously associated with myxobacterial fruiting bodies. Our screening effort resulted in the purification and structure elucidation of a novel compound, the homospermidine lipid, from cultures that had undergone the fruiting process. A combination of molecular networking and targeted LC-MS/MS in conjunction with our in-house metabolomics database subsequently revealed alternative producers of the respective compound as well as a number of compounds belonging to the same structural class. Three further members of this compound class were isolated from an alternative producer and structurally elucidated by NMR. Insights into the biosynthesis of this novel compound class was gained by feeding of isotopically labeled substrates and in silico analysis.
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Affiliation(s)
- Michael Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - David Auerbach
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Rolf Müller
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
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55
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Improving the discovery of secondary metabolite natural products using ion mobility-mass spectrometry. Curr Opin Chem Biol 2017; 42:160-166. [PMID: 29287234 DOI: 10.1016/j.cbpa.2017.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/30/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
Abstract
Secondary metabolite discovery requires an unbiased, comprehensive workflow to detect unknown unknowns for which little to no molecular knowledge exists. Untargeted mass spectrometry-based metabolomics is a powerful platform, particularly when coupled with ion mobility for high-throughput gas-phase separations to increase peak capacity and obtain gas-phase structural information. Ion mobility data are described by the amount of time an ion spends in the drift cell, which is directly related to an ion's collision cross section (CCS). The CCS parameter describes the size, shape, and charge of a molecule and can be used to characterize unknown metabolomic species. Here, we describe current and emerging applications of ion mobility-mass spectrometry for prioritization, discovery and structure elucidation, and spatial/temporal characterization.
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56
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Adnani N, Chevrette MG, Adibhatla SN, Zhang F, Yu Q, Braun DR, Nelson J, Simpkins SW, McDonald BR, Myers CL, Piotrowski JS, Thompson CJ, Currie CR, Li L, Rajski SR, Bugni TS. Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin. ACS Chem Biol 2017; 12:3093-3102. [PMID: 29121465 DOI: 10.1021/acschembio.7b00688] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Advances in genomics and metabolomics have made clear in recent years that microbial biosynthetic capacities on Earth far exceed previous expectations. This is attributable, in part, to the realization that most microbial natural product (NP) producers harbor biosynthetic machineries not readily amenable to classical laboratory fermentation conditions. Such "cryptic" or dormant biosynthetic gene clusters (BGCs) encode for a vast assortment of potentially new antibiotics and, as such, have become extremely attractive targets for activation under controlled laboratory conditions. We report here that coculturing of a Rhodococcus sp. and a Micromonospora sp. affords keyicin, a new and otherwise unattainable bis-nitroglycosylated anthracycline whose mechanism of action (MOA) appears to deviate from those of other anthracyclines. The structure of keyicin was elucidated using high resolution MS and NMR technologies, as well as detailed molecular modeling studies. Sequencing of the keyicin BGC (within the Micromonospora genome) enabled both structural and genomic comparisons to other anthracycline-producing systems informing efforts to characterize keyicin. The new NP was found to be selectively active against Gram-positive bacteria including both Rhodococcus sp. and Mycobacterium sp. E. coli-based chemical genomics studies revealed that keyicin's MOA, in contrast to many other anthracyclines, does not invoke nucleic acid damage.
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Affiliation(s)
- Navid Adnani
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Marc G. Chevrette
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53705, United States
- Department
of Genetics, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Srikar N. Adibhatla
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Fan Zhang
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Qing Yu
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Justin Nelson
- Bioinformatics
and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Scott W. Simpkins
- Bioinformatics
and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Bradon R. McDonald
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Chad L. Myers
- Bioinformatics
and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department
of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | | | | | - Cameron R. Currie
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Scott R. Rajski
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
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57
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Cheng C, Othman EM, Stopper H, Edrada-Ebel R, Hentschel U, Abdelmohsen UR. Isolation of Petrocidin A, a New Cytotoxic Cyclic Dipeptide from the Marine Sponge-Derived Bacterium Streptomyces sp. SBT348. Mar Drugs 2017; 15:md15120383. [PMID: 29211005 PMCID: PMC5742843 DOI: 10.3390/md15120383] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/06/2017] [Accepted: 11/16/2017] [Indexed: 01/22/2023] Open
Abstract
A new cyclic dipeptide, petrocidin A (1), along with three known compounds-2,3-dihydroxybenzoic acid (2), 2,3-dihydroxybenzamide (3), and maltol (4)-were isolated from the solid culture of Streptomyces sp. SBT348. The strain Streptomyces sp. SBT348 had been prioritized in a strain collection of 64 sponge-associated actinomycetes based on its distinct metabolomic profile using liquid chromatography/high-resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR). The absolute configuration of all α-amino acids was determined by HPLC analysis after derivatization with Marfey's reagent and comparison with commercially available reference amino acids. Structure elucidation was pursued in the presented study by mass spectrometry and NMR spectral data. Petrocidin A (1) and 2,3-dihydroxybenzamide (3) exhibited significant cytotoxicity towards the human promyelocytic HL-60 and the human colon adenocarcinoma HT-29 cell lines. These results demonstrated the potential of sponge-associated actinomycetes for the discovery of novel and pharmacologically active natural products.
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Affiliation(s)
- Cheng Cheng
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany.
| | - Eman M Othman
- Department of Toxicology, University of Würzburg, Versbacher Str. 9, D-97078 Würzburg, Germany.
- Department of Analytical Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt.
| | - Helga Stopper
- Department of Toxicology, University of Würzburg, Versbacher Str. 9, D-97078 Würzburg, Germany.
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, 27 Taylor Street, Glasgow G4 0NR, UK.
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany.
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology, and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105 Kiel, Germany.
| | - Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany.
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt.
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58
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Hillman ET, Readnour LR, Solomon KV. Exploiting the natural product potential of fungi with integrated -omics and synthetic biology approaches. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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59
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Ohlemacher SI, Giblin DE, d'Avignon DA, Stapleton AE, Trautner BW, Henderson JP. Enterobacteria secrete an inhibitor of Pseudomonas virulence during clinical bacteriuria. J Clin Invest 2017; 127:4018-4030. [PMID: 28945201 DOI: 10.1172/jci92464] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/02/2017] [Indexed: 11/17/2022] Open
Abstract
Escherichia coli and other Enterobacteriaceae are among the most common pathogens of the human urinary tract. Among the genetic gains of function associated with urinary E. coli isolates is the Yersinia high pathogenicity island (HPI), which directs the biosynthesis of yersiniabactin (Ybt), a virulence-associated metallophore. Using a metabolomics approach, we found that E. coli and other Enterobacteriaceae expressing the Yersinia HPI also secrete escherichelin, a second metallophore whose chemical structure matches a known synthetic inhibitor of the virulence-associated pyochelin siderophore system in Pseudomonas aeruginosa. We detected escherichelin during clinical E. coli urinary tract infection (UTI) and experimental human colonization with a commensal, potentially probiotic E. coli bacteriuria strain. Escherichelin production by colonizing enterobacteria may help human hosts resist opportunistic infections by Pseudomonas and other pyochelin-expressing bacteria. This siderophore-based mechanism of microbial antagonism may be one of many elements contributing to the protective effects of the human microbiome. Future UTI-preventive probiotic strains may benefit by retaining the escherichelin biosynthetic capacity of the Yersinia HPI while eliminating the Ybt biosynthetic capacity.
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Affiliation(s)
- Shannon I Ohlemacher
- Center for Women's Infectious Diseases Research.,Division of Infectious Diseases.,Department of Internal Medicine, and
| | - Daryl E Giblin
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - D André d'Avignon
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Ann E Stapleton
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Barbara W Trautner
- The Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA.,Section of Infectious Diseases, Departments of Medicine and Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Diseases Research.,Division of Infectious Diseases.,Department of Internal Medicine, and
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60
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Hüttel S, Testolin G, Herrmann J, Planke T, Gille F, Moreno M, Stadler M, Brönstrup M, Kirschning A, Müller R. Entdeckung und Totalsynthese von natürlichen Cystobactamid‐Derivaten mit herausragender Aktivität gegen Gram‐negative Pathogene. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705913] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Stephan Hüttel
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung Universitätscampus E8 1 66123 Saarbrücken Deutschland
- Abteilung Mikrobielle Wirkstoffe Helmholtz-Zentrum für Infektionsforschung Inhoffenstraße 7 38124 Braunschweig Deutschland
- Deutsches Zentrum für Infektionsforschung, DZIF Standort Hannover-Braunschweig Deutschland
| | - Giambattista Testolin
- Abteilung Chemische Biologie Helmholtz-Zentrum für Infektionsforschung Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Jennifer Herrmann
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung Universitätscampus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung, DZIF Standort Hannover-Braunschweig Deutschland
| | - Therese Planke
- Institut für Organische Chemie Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
| | - Franziska Gille
- Institut für Organische Chemie Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
| | - Maria Moreno
- Institut für Organische Chemie Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
| | - Marc Stadler
- Abteilung Mikrobielle Wirkstoffe Helmholtz-Zentrum für Infektionsforschung Inhoffenstraße 7 38124 Braunschweig Deutschland
- Deutsches Zentrum für Infektionsforschung, DZIF Standort Hannover-Braunschweig Deutschland
| | - Mark Brönstrup
- Deutsches Zentrum für Infektionsforschung, DZIF Standort Hannover-Braunschweig Deutschland
- Abteilung Chemische Biologie Helmholtz-Zentrum für Infektionsforschung Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Andreas Kirschning
- Institut für Organische Chemie Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung Universitätscampus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung, DZIF Standort Hannover-Braunschweig Deutschland
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61
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Hüttel S, Testolin G, Herrmann J, Planke T, Gille F, Moreno M, Stadler M, Brönstrup M, Kirschning A, Müller R. Discovery and Total Synthesis of Natural Cystobactamid Derivatives with Superior Activity against Gram-Negative Pathogens. Angew Chem Int Ed Engl 2017; 56:12760-12764. [PMID: 28730677 DOI: 10.1002/anie.201705913] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Indexed: 11/07/2022]
Abstract
Antibiotic discovery and development is challenging as chemical scaffolds of synthetic origin often lack the required pharmaceutical properties, and the discovery of novel ones from natural sources is tedious. Herein, we report the discovery of new cystobactamids with a significantly improved antibacterial profile in a detailed screening of myxobacterial producer strains. Some of these new derivatives display antibacterial activities in the low-μg mL-1 range against Gram-negative pathogens, including clinical isolates of Klebsiella oxytoca, Pseudomonas aeruginosa, and fluoroquinolone-resistant Enterobacteriaceae, which were not observed for previously reported cystobactamids. Our findings provide structure-activity relationships and show how pathogen resistance can be overcome by natural scaffold diversity. The most promising derivative 861-2 was prepared by total synthesis, enabling further chemical optimization of this privileged scaffold.
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Affiliation(s)
- Stephan Hüttel
- Abteilung Mikrobielle Naturstoffe, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,Abteilung Mikrobielle Wirkstoffe, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
| | - Giambattista Testolin
- Abteilung Chemische Biologie, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jennifer Herrmann
- Abteilung Mikrobielle Naturstoffe, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
| | - Therese Planke
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Franziska Gille
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Maria Moreno
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Marc Stadler
- Abteilung Mikrobielle Wirkstoffe, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
| | - Mark Brönstrup
- Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany.,Abteilung Chemische Biologie, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Andreas Kirschning
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
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62
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Kellogg JJ, Wallace ED, Graf TN, Oberlies NH, Cech NB. Conventional and accelerated-solvent extractions of green tea (camellia sinensis) for metabolomics-based chemometrics. J Pharm Biomed Anal 2017; 145:604-610. [PMID: 28787673 DOI: 10.1016/j.jpba.2017.07.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/21/2017] [Accepted: 07/23/2017] [Indexed: 01/05/2023]
Abstract
Metabolomics has emerged as an important analytical technique for multiple applications. The value of information obtained from metabolomics analysis depends on the degree to which the entire metabolome is present and the reliability of sample treatment to ensure reproducibility across the study. The purpose of this study was to compare methods of preparing complex botanical extract samples prior to metabolomics profiling. Two extraction methodologies, accelerated solvent extraction and a conventional solvent maceration, were compared using commercial green tea [Camellia sinensis (L.) Kuntze (Theaceae)] products as a test case. The accelerated solvent protocol was first evaluated to ascertain critical factors influencing extraction using a D-optimal experimental design study. The accelerated solvent and conventional extraction methods yielded similar metabolite profiles for the green tea samples studied. The accelerated solvent extraction yielded higher total amounts of extracted catechins, was more reproducible, and required less active bench time to prepare the samples. This study demonstrates the effectiveness of accelerated solvent as an efficient methodology for metabolomics studies.
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Affiliation(s)
- Joshua J Kellogg
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Emily D Wallace
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Tyler N Graf
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Nicholas H Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Nadja B Cech
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States.
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63
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Kellogg J, Graf TN, Paine MF, McCune JS, Kvalheim OM, Oberlies NH, Cech NB. Comparison of Metabolomics Approaches for Evaluating the Variability of Complex Botanical Preparations: Green Tea (Camellia sinensis) as a Case Study. JOURNAL OF NATURAL PRODUCTS 2017; 80:1457-1466. [PMID: 28453261 PMCID: PMC5469520 DOI: 10.1021/acs.jnatprod.6b01156] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 05/08/2023]
Abstract
A challenge that must be addressed when conducting studies with complex natural products is how to evaluate their complexity and variability. Traditional methods of quantifying a single or a small range of metabolites may not capture the full chemical complexity of multiple samples. Different metabolomics approaches were evaluated to discern how they facilitated comparison of the chemical composition of commercial green tea [Camellia sinensis (L.) Kuntze] products, with the goal of capturing the variability of commercially used products and selecting representative products for in vitro or clinical evaluation. Three metabolomic-related methods-untargeted ultraperformance liquid chromatography-mass spectrometry (UPLC-MS), targeted UPLC-MS, and untargeted, quantitative 1HNMR-were employed to characterize 34 commercially available green tea samples. Of these methods, untargeted UPLC-MS was most effective at discriminating between green tea, green tea supplement, and non-green-tea products. A method using reproduced correlation coefficients calculated from principal component analysis models was developed to quantitatively compare differences among samples. The obtained results demonstrated the utility of metabolomics employing UPLC-MS data for evaluating similarities and differences between complex botanical products.
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Affiliation(s)
- Joshua
J. Kellogg
- Department
of Chemistry & Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Tyler N. Graf
- Department
of Chemistry & Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Mary F. Paine
- College
of Pharmacy, Washington State University, Spokane, Washington 99202, United States
| | - Jeannine S. McCune
- Department
of Pharmaceutics, University of Washington, Seattle, Washington 99202, United States
| | - Olav M. Kvalheim
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
| | - Nicholas H. Oberlies
- Department
of Chemistry & Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Nadja B. Cech
- Department
of Chemistry & Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
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64
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Crüsemann M, O’Neill EC, Larson CB, Melnik AV, Floros DJ, da Silva RR, Jensen PR, Dorrestein PC, Moore BS. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. JOURNAL OF NATURAL PRODUCTS 2017; 80:588-597. [PMID: 28335604 PMCID: PMC5367486 DOI: 10.1021/acs.jnatprod.6b00722] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high-throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.
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Affiliation(s)
- Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ellis C. O’Neill
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Charles B. Larson
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dimitrios J Floros
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R. da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Research Support Center in Natural and Synthetic Products, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Paul R. Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- 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, 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, University of California, San Diego, La Jolla, CA 92093, USA
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65
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Singh M, Chaudhary S, Sareen D. Non-ribosomal peptide synthetases: Identifying the cryptic gene clusters and decoding the natural product. J Biosci 2017; 42:175-187. [PMID: 28229977 DOI: 10.1007/s12038-017-9663-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) present in bacteria and fungi are the major multi-modular enzyme complexes which synthesize secondary metabolites like the pharmacologically important antibiotics and siderophores. Each of the multiple modules of an NRPS activates a different amino or aryl acid, followed by their condensation to synthesize a linear or cyclic natural product. The studies on NRPS domains, the knowledge of their gene cluster architecture and tailoring enzymes have helped in the in silico genetic screening of the ever-expanding sequenced microbial genomic data for the identification of novel NRPS/PKS clusters and thus deciphering novel non-ribosomal peptides (NRPs). Adenylation domain is an integral part of the NRPSs and is the substrate selecting unit for the final assembled NRP. In some cases, it also requires a small protein, the MbtH homolog, for its optimum activity. The presence of putative adenylation domain and MbtH homologs in a sequenced genome can help identify the novel secondary metabolite producers. The role of the adenylation domain in the NRPS gene clusters and its characterization as a tool for the discovery of novel cryptic NRPS gene clusters are discussed.
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Affiliation(s)
- Mangal Singh
- Department of Biochemistry, Panjab University, Chandigarh, India
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66
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Burgard C, Zaburannyi N, Nadmid S, Maier J, Jenke-Kodama H, Luxenburger E, Bernauer HS, Wenzel SC. Genomics-Guided Exploitation of Lipopeptide Diversity in Myxobacteria. ACS Chem Biol 2017; 12:779-786. [PMID: 28128551 DOI: 10.1021/acschembio.6b00953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of 122 myxobacterial genome sequences suggested 16 strains as producers of the myxochromide lipopeptide family. Detailed sequence comparison of the respective mch biosynthetic gene clusters informed a genome-mining approach, ultimately leading to the discovery and chemical characterization of four novel myxochromide core types. The myxochromide megasynthetase is subject to evolutionary diversification, resulting in considerable structural diversity of biosynthesis products. The observed differences are due to the number, type, sequence, and configuration of the incorporated amino acids. The analysis revealed molecular details on how point mutations and recombination events led to structural diversity. It also gave insights into the evolutionary scenarios that have led to the emergence of mch clusters in different strains and genera of myxobacteria.
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Affiliation(s)
- Christian Burgard
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research and Pharmaceutical Biotechnology at Saarland
University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Nestor Zaburannyi
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research and Pharmaceutical Biotechnology at Saarland
University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Suvd Nadmid
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research and Pharmaceutical Biotechnology at Saarland
University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Josef Maier
- IStLS − Information Services to Life Sciences, Härlestraße 24/1, 78727 Oberndorf am Neckar/Boll, Germany
| | - Holger Jenke-Kodama
- Microbiology
and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Eva Luxenburger
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research and Pharmaceutical Biotechnology at Saarland
University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | | | - Silke C. Wenzel
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research and Pharmaceutical Biotechnology at Saarland
University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
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67
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Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
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68
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Hiratsuka T, Suzuki H, Minami A, Oikawa H. Stepwise cyclopropanation on the polycyclopropanated polyketide formation in jawsamycin biosynthesis. Org Biomol Chem 2017; 15:1076-1079. [DOI: 10.1039/c6ob02675c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Cyclopropane deficient jawsamycin analogs were isolated from transformant harboring jaw genes, enabling us to propose an enzymatic cyclopropanation mechanism.
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Affiliation(s)
- Tomoshige Hiratsuka
- Division of chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Hideaki Suzuki
- Division of chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Atsushi Minami
- Division of chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Hideaki Oikawa
- Division of chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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69
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Pluskal T, Yanagida M. Metabolomic Analysis of Schizosaccharomyces pombe: Sample Preparation, Detection, and Data Interpretation. Cold Spring Harb Protoc 2016; 2016:2016/12/pdb.top079921. [PMID: 27934694 DOI: 10.1101/pdb.top079921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Metabolomics is a modern field of chemical biology that strives to simultaneously quantify hundreds of cellular metabolites. Techniques for metabolomic analysis in Schizosaccharomyces pombe have only recently been developed. Here we introduce methods that provide a complete workflow for metabolomic analysis in S. pombe Based on available literature, we estimate the yeast metabolome to comprise on the order of several thousand different metabolites. We discuss the feasibility of extraction and detection of such a large number of metabolites, and the influences of various parameters on the results. Among the parameters addressed are cell cultivation conditions, metabolite extraction techniques, and detection and quantification methods. Further, we provide recommendations on data management and data processing for metabolomic experiments, and describe possible pitfalls regarding the interpretation of metabolomic data. Finally, we briefly discuss potential future developments of this technique.
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Affiliation(s)
- Tomáš Pluskal
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Kunigami, Okinawa 904-0495, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Kunigami, Okinawa 904-0495, Japan
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70
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Rakshith D, Santosh P, Pradeep TP, Gurudatt DM, Baker S, Yashavantha Rao HC, Pasha A, Satish S. Application of Bioassay-Guided Fractionation Coupled with a Molecular Approach for the Dereplication of Antimicrobial Metabolites. Chromatographia 2016. [DOI: 10.1007/s10337-016-3188-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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71
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Sugiyama R, Nishimura S, Ozaki T, Asamizu S, Onaka H, Kakeya H. Discovery and Total Synthesis of Streptoaminals: Antimicrobial [5,5]-Spirohemiaminals from the Combined-Culture of Streptomyces nigrescens
and Tsukamurella pulmonis. Angew Chem Int Ed Engl 2016; 55:10278-82. [DOI: 10.1002/anie.201604126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
- Present address; RIKEN Center for Sustainable Resource Science; 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taro Ozaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shumpei Asamizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
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72
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Sugiyama R, Nishimura S, Ozaki T, Asamizu S, Onaka H, Kakeya H. Discovery and Total Synthesis of Streptoaminals: Antimicrobial [5,5]-Spirohemiaminals from the Combined-Culture of Streptomyces nigrescens
and Tsukamurella pulmonis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
- Present address; RIKEN Center for Sustainable Resource Science; 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taro Ozaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shumpei Asamizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
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73
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Lu S, Nishimura S, Ito M, Tsuchida T, Kakeya H. Isolation and Structure Elucidation of Cytotoxic Saccharothriolides D to F from a Rare Actinomycete Saccharothrix sp. and Their Structure-Activity Relationship. JOURNAL OF NATURAL PRODUCTS 2016; 79:1891-1895. [PMID: 27332142 DOI: 10.1021/acs.jnatprod.6b00372] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Three new 10-membered macrolides, saccharothriolides D-F (1-3), were isolated from a rare actinomycete, Saccharothrix sp. A1506. The planar structures were determined from analysis of extensive NMR and HR-ESI-MS data, and the absolute configurations were established by ECD spectroscopy analysis. Saccharothriolides D (1) and E (2) were determined to be C-2 epimers of saccharothriolides A (4) and B (5), respectively. Saccharothriolide F (3) was identified to be a demethylated congener of saccharothriolides D (1) and A (4) at the C-2 position. The availability of compounds 1-6 enabled a structure-activity relationship study that revealed the importance of the phenolic hydroxy group at C-2″ and the stereochemistry of C-2 for the inhibition of human fibrosarcoma HT1080 cell growth.
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Affiliation(s)
- Shan Lu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University , Kyoto 606-8501, Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University , Kyoto 606-8501, Japan
| | - Masashi Ito
- Bioresource Laboratories, MicroBioPharm Japan Co., Ltd. (MBJ) , Iwata, Shizuoka 438-0078, Japan
| | - Toshio Tsuchida
- Bioresource Laboratories, MicroBioPharm Japan Co., Ltd. (MBJ) , Iwata, Shizuoka 438-0078, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University , Kyoto 606-8501, Japan
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74
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Fukuhara K, Takada K, Okada S, Matsunaga S. Nazumazoles D-F, Cyclic Pentapeptides That Inhibit Chymotrypsin, from the Marine Sponge Theonella swinhoei. JOURNAL OF NATURAL PRODUCTS 2016; 79:1694-1697. [PMID: 27213234 DOI: 10.1021/acs.jnatprod.6b00261] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nazumazoles D-F (1-3) were isolated from the marine sponge Theonella swinhoei. The compounds gave extremely broad peaks by reversed-phase HPLC using an ODS column. HPLC using a gel permeation column was instrumental for the separation of the three compounds. Their planar structures were determined by interpretation of NMR data to be cyclic pentapeptides. Nazumazoles D-F contained one residue each of α-keto-l-norvaline (l-Knv) {or α-keto-d-leucine (l-Kle)}, l-alanyloxazole (l-Aox), d-Abu (or d-Ser), N-α-CHO-β-l-Dpr, and cis-4-methyl-l-proline. The absolute configuration of each amino acid residue was determined by Marfey's method in combination with conversion of the α-keto-β-amino acid to the α-amino acid by oxidation. Nazumazoles D-F are not cytotoxic against P388 cells at 50 μM, but inhibit chymotrypsin.
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Affiliation(s)
- Kazuya Fukuhara
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
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75
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Saleh H, Petras D, Mainz A, Kerwat D, Nalbantsoy A, Erzurumlu Y, Süssmuth RD. Deuterium-Labeled Precursor Feeding Reveals a New pABA-Containing Meroterpenoid from the Mango Pathogen Xanthomonas citri pv. mangiferaeindicae. JOURNAL OF NATURAL PRODUCTS 2016; 79:1532-1537. [PMID: 27232656 DOI: 10.1021/acs.jnatprod.5b01049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new para-aminobenzoic-acid-containing natural product from the mango pathogenic organism Xanthomonas citri pv. mangiferaeindicae is described. By means of stable isotope precursor feeding combined with nontargeted LC-MS/MS, the generated spectra were clustered and visualized in a molecular network. This led to the identification of a new member of the meroterpenoids, termed xanthomonic acid, which is composed of an isoprenylated para-aminobenzoic acid. In vitro cytotoxicity assays demonstrated activity of xanthomonic acid against several human cancer cell lines by induction of autophagy.
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Affiliation(s)
- Hesham Saleh
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Dennis Kerwat
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University , 35100 Bornova Izmir, Turkey
| | - Yalcin Erzurumlu
- Department of Biochemistry, Faculty of Pharmacy, Ege University , 35100 Bornova Izmir, Turkey
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 124, 10623 Berlin, Germany
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76
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Wang M, Bi W, Huang X, Chen DDY. Ball mill assisted rapid mechanochemical extraction method for natural products from plants. J Chromatogr A 2016; 1449:8-16. [DOI: 10.1016/j.chroma.2016.04.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
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77
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Tautz T, Hoffmann J, Hoffmann T, Steinmetz H, Washausen P, Kunze B, Huch V, Kitsche A, Reichenbach H, Höfle G, Müller R, Kalesse M. Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species. Org Lett 2016; 18:2560-3. [DOI: 10.1021/acs.orglett.6b00810] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas Tautz
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
| | - Judith Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Heinrich Steinmetz
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Peter Washausen
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Brigitte Kunze
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Volker Huch
- Institute
for Inorganic Chemistry, Saarland University, Building B2.2, D-66123 Saarbrücken, Germany
| | - Andreas Kitsche
- Institute
for Biostatistics, Leibniz Universität Hannover, Herrenhäuser
Straße 2, D-30419 Hannover, Germany
| | - Hans Reichenbach
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Gerhard Höfle
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Markus Kalesse
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
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79
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Zhang G, Li J, Zhu T, Gu Q, Li D. Advanced tools in marine natural drug discovery. Curr Opin Biotechnol 2016; 42:13-23. [PMID: 26954946 DOI: 10.1016/j.copbio.2016.02.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/10/2023]
Abstract
Marine natural products (MNPs) remain promising drug sources with several marine-derived drugs having been successfully approved. Nevertheless, it is never a smooth sailing to seek bioactive compounds from marine environments, during which many challenges are need to be faced to, for example, discovering unique marine resources, reviving unculturable organisms outside the marine environment, distinguishing novel compounds from the known ones, and disclosing the function of MNPs and optimizing their pharmacological use. Herein we review some advanced techniques and methodologies that can be employed to deal with above challenges with the intent of inspiring the forthcoming efforts in MNPs discovery pipelines.
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Affiliation(s)
- Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
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80
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Karwehl S, Jansen R, Huch V, Stadler M. Sorazolons, Carbazole Alkaloids from Sorangium cellulosum Strain Soce375. JOURNAL OF NATURAL PRODUCTS 2016; 79:369-375. [PMID: 26866461 DOI: 10.1021/acs.jnatprod.5b00997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sorazolons A (1) to E2 (9) were isolated from Sorangium cellulosum strain Soce375. Their molecular structures were elucidated using extensive HRESIMS and NMR analysis. The absolute configuration of sorazolon A (1) was determined by comparison of the experimental CD spectrum with quantum chemical calculated spectra for both enantiomers. Sorazolons D2 (7), E (8), and E2 (9) exhibit a moderate cytotoxic activity against mouse fibroblast cell line L929 with IC50 values between 5.0 μM and 0.09 mM.
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Affiliation(s)
- Sabrina Karwehl
- Department of Microbial Drugs, Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, Germany
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, Germany
| | - Volker Huch
- Department of Inorganic Chemistry, Saarland University , Building C 4.1, 66123 Saarbrücken, Germany
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, Germany
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81
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Genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via Red/ET recombineering. Sci Rep 2016; 6:21066. [PMID: 26875499 PMCID: PMC4753468 DOI: 10.1038/srep21066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/18/2016] [Indexed: 11/08/2022] Open
Abstract
Disorazol, a macrocyclic polykitide produced by the myxobacterium Sorangium cellulosum So ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. The disorazol biosynthetic gene cluster (dis) from Sorangium cellulosum (So ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (BAC) library. The 58-kb dis core gene cluster was reconstituted from BACs via Red/ET recombineering and expressed in Myxococcus xanthus DK1622. For the first time ever, a myxobacterial trans-AT polyketide synthase has been expressed heterologously in this study. Expression in M. xanthus allowed us to optimize the yield of several biosynthetic products using promoter engineering. The insertion of an artificial synthetic promoter upstream of the disD gene encoding a discrete acyl transferase (AT), together with an oxidoreductase (Or), resulted in 7-fold increase in disorazol production. The successful reconstitution and expression of the genetic sequences encoding for these promising cytotoxic compounds will allow combinatorial biosynthesis to generate novel disorazol derivatives for further bioactivity evaluation.
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82
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Zhou T, Wang M, Cheng H, Cui C, Su S, Xu P, Xue M. UPLC-HRMS based metabolomics reveals the sphingolipids with long fatty chains and olefinic bonds up-regulated in metabolic pathway for hypoxia preconditioning. Chem Biol Interact 2015; 242:145-52. [DOI: 10.1016/j.cbi.2015.09.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/02/2015] [Accepted: 09/28/2015] [Indexed: 10/23/2022]
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83
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Wu C, Du C, Gubbens J, Choi YH, van Wezel GP. Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced by Streptomyces Species MBT28. JOURNAL OF NATURAL PRODUCTS 2015; 78:2355-2363. [PMID: 26438963 DOI: 10.1021/acs.jnatprod.5b00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Actinomycetes are a major source of antimicrobials, anticancer compounds, and other medically important products, and their genomes harbor extensive biosynthetic potential. Major challenges in the screening of these microorganisms are to activate the expression of cryptic biosynthetic gene clusters and the development of technologies for efficient dereplication of known molecules. Here we report the identification of a previously unidentified isatin-type antibiotic produced by Streptomyces sp. MBT28, following a strategy based on NMR-based metabolomics combined with the introduction of streptomycin resistance in the producer strain. NMR-guided isolation by tracking the target proton signal resulted in the characterization of 7-prenylisatin (1) with antimicrobial activity against Bacillus subtilis. The metabolite-guided genome mining of Streptomyces sp. MBT28 combined with proteomics identified a gene cluster with an indole prenyltransferase that catalyzes the conversion of tryptophan into 7-prenylisatin. This study underlines the applicability of NMR-based metabolomics in facilitating the discovery of novel antibiotics.
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Affiliation(s)
| | | | - Jacob Gubbens
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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84
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Abstract
Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.
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Affiliation(s)
- Constanze Kuhlisch
- Friedrich Schiller University, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743 Jena, Germany.
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85
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Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries. Proc Natl Acad Sci U S A 2015; 112:11999-2004. [PMID: 26371303 DOI: 10.1073/pnas.1507743112] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Traditional natural products discovery using a combination of live/dead screening followed by iterative bioassay-guided fractionation affords no information about compound structure or mode of action until late in the discovery process. This leads to high rates of rediscovery and low probabilities of finding compounds with unique biological and/or chemical properties. By integrating image-based phenotypic screening in HeLa cells with high-resolution untargeted metabolomics analysis, we have developed a new platform, termed Compound Activity Mapping, that is capable of directly predicting the identities and modes of action of bioactive constituents for any complex natural product extract library. This new tool can be used to rapidly identify novel bioactive constituents and provide predictions of compound modes of action directly from primary screening data. This approach inverts the natural products discovery process from the existing "grind and find" model to a targeted, hypothesis-driven discovery model where the chemical features and biological function of bioactive metabolites are known early in the screening workflow, and lead compounds can be rationally selected based on biological and/or chemical novelty. We demonstrate the utility of the Compound Activity Mapping platform by combining 10,977 mass spectral features and 58,032 biological measurements from a library of 234 natural products extracts and integrating these two datasets to identify 13 clusters of fractions containing 11 known compound families and four new compounds. Using Compound Activity Mapping we discovered the quinocinnolinomycins, a new family of natural products with a unique carbon skeleton that cause endoplasmic reticulum stress.
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86
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Metabolic profiling as a tool for prioritizing antimicrobial compounds. J Ind Microbiol Biotechnol 2015; 43:299-312. [PMID: 26335567 PMCID: PMC4752588 DOI: 10.1007/s10295-015-1666-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/25/2015] [Indexed: 11/29/2022]
Abstract
Metabolomics is an analytical technique that allows scientists to globally profile low molecular weight metabolites between samples in a medium- or high-throughput environment. Different biological samples are statistically analyzed and correlated to a bioactivity of interest, highlighting differentially produced compounds as potential biomarkers. Here, we review NMR- and MS-based metabolomics as technologies to facilitate the identification of novel antimicrobial natural products from microbial sources. Approaches to elicit the production of poorly expressed (cryptic) molecules are thereby a key to allow statistical analysis of samples to identify bioactive markers, while connection of compounds to their biosynthetic gene cluster is a determining step in elucidating the biosynthetic pathway and allows downstream process optimization and upscaling. The review focuses on approaches built around NMR-based metabolomics, which enables efficient dereplication and guided fractionation of (antimicrobial) compounds.
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87
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Medema MH, Fischbach MA. Computational approaches to natural product discovery. Nat Chem Biol 2015; 11:639-48. [PMID: 26284671 PMCID: PMC5024737 DOI: 10.1038/nchembio.1884] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/07/2015] [Indexed: 01/13/2023]
Abstract
Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.
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Affiliation(s)
- Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Michael A. Fischbach
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158
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88
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Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes. Proc Natl Acad Sci U S A 2015; 112:12175-80. [PMID: 26324907 DOI: 10.1073/pnas.1500873112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N(5)-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.
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89
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Son S, Ko SK, Jang M, Lee JK, Ryoo IJ, Lee JS, Lee KH, Soung NK, Oh H, Hong YS, Kim BY, Jang JH, Ahn JS. Ulleungamides A and B, Modified α,β-Dehydropipecolic Acid Containing Cyclic Depsipeptides from Streptomyces sp. KCB13F003. Org Lett 2015; 17:4046-9. [DOI: 10.1021/acs.orglett.5b01969] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sangkeun Son
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | - Sung-Kyun Ko
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | - Mina Jang
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | | | | | - Jung-Sook Lee
- Microbial
Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 306-809, Korea
| | | | - Nak-Kyun Soung
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | - Hyuncheol Oh
- College
of Pharmacy, Wonkwang University, Iksan 570-749, Korea
| | - Young-Soo Hong
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | - Bo Yeon Kim
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | - Jae-Hyuk Jang
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
| | - Jong Seog Ahn
- Department
of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea
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90
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass spectrometry tools and workflows for revealing microbial chemistry. Analyst 2015; 140:4949-66. [PMID: 25996313 PMCID: PMC5444374 DOI: 10.1039/c5an00171d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.
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91
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Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
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Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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92
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Functional metabolomics: from biomarker discovery to metabolome reprogramming. Protein Cell 2015; 6:628-37. [PMID: 26135925 PMCID: PMC4537470 DOI: 10.1007/s13238-015-0185-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.
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93
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Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 2015; 13:509-23. [PMID: 26119570 DOI: 10.1038/nrmicro3496] [Citation(s) in RCA: 610] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
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94
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Abdelmohsen UR, Grkovic T, Balasubramanian S, Kamel MS, Quinn RJ, Hentschel U. Elicitation of secondary metabolism in actinomycetes. Biotechnol Adv 2015; 33:798-811. [PMID: 26087412 DOI: 10.1016/j.biotechadv.2015.06.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/29/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Genomic sequence data have revealed the presence of a large fraction of putatively silent biosynthetic gene clusters in the genomes of actinomycetes that encode for secondary metabolites, which are not detected under standard fermentation conditions. This review focuses on the effects of biological (co-cultivation), chemical, as well as molecular elicitation on secondary metabolism in actinomycetes. Our review covers the literature until June 2014 and exemplifies the diversity of natural products that have been recovered by such approaches from the phylum Actinobacteria.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt.
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Srikkanth Balasubramanian
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
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95
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Wu C, Kim HK, van Wezel GP, Choi YH. Metabolomics in the natural products field--a gateway to novel antibiotics. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 13:11-17. [PMID: 26190678 DOI: 10.1016/j.ddtec.2015.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/09/2015] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
Metabolomics is a high throughput analytical technique used to globally measure low molecular weight metabolites, allowing simultaneous metabolic comparison of different biological samples and thus highlighting differentially produced compounds as potential biomarkers. Although microbes are renowned as prolific sources of antibiotics, the traditional approach for new anti-infectives discovery is time-consuming and labor-intensive. In this review, the use of NMR- or MS-based metabolomics is proposed as an efficient approach to find antimicrobials in microbial single- or co-cultures.
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Affiliation(s)
- Changsheng Wu
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Hye Kyong Kim
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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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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97
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Moon K, Chung B, Shin Y, Rheingold AL, Moore CE, Park SJ, Park S, Lee SK, Oh KB, Shin J, Oh DC. Pentacyclic antibiotics from a tidal mud flat-derived actinomycete. JOURNAL OF NATURAL PRODUCTS 2015; 78:524-529. [PMID: 25495422 DOI: 10.1021/np500736b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The combination of investigating a unique source of chemically prolific bacterium with an LC/MS-based bacterial strain selection approach resulted in the discovery of two new secondary metabolites, buanmycin (1) and buanquinone (2), from the culture of a marine Streptomyces strain, which was isolated from a tidal mudflat in Buan, Republic of Korea. The carbon backbone of buanmycin (1), comprising 20 quaternary carbons out of 30 total carbons, was determined via (13)C-(13)C COSY NMR analysis after labeling 1 with (13)C by culturing the bacterium with (13)C-glucose. The complete structure of 1 was confidently elucidated, primarily based on 1D and 2D NMR spectroscopic and X-ray crystallographic analysis, as that of a new pentacyclic xanthone. The absolute configuration of the α-methyl serine unit in 1 was established by applying the advanced Marfey's method. The structure of buanquinone (2) was determined to be a new pentacyclic quinone based on NMR and MS spectroscopic data. Buanmycin exhibited potent cytotoxicity against colorectal carcinoma cells (HCT-116) and gastric carcinoma cells (SNU-638) with submicromolar IC50 values and strongly inhibited the pathogenic Gram-negative bacterium Salmonella enterica (MIC = 0.7 μM). In particular, buanmycin demonstrated inhibition of sortase A, which is a promising target for antibiotic discovery.
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Affiliation(s)
- Kyuho Moon
- †Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Beomkoo Chung
- ‡Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Yoonho Shin
- †Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Arnold L Rheingold
- §Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Curtis E Moore
- §Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Sung Jean Park
- ⊥College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon 406-799, Republic of Korea
| | - Sunghyouk Park
- †Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Sang Kook Lee
- †Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Ki-Bong Oh
- ‡Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Jongheon Shin
- †Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Dong-Chan Oh
- †Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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Wolfender JL, Marti G, Thomas A, Bertrand S. Current approaches and challenges for the metabolite profiling of complex natural extracts. J Chromatogr A 2015; 1382:136-64. [DOI: 10.1016/j.chroma.2014.10.091] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/11/2022]
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99
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Yang Z, Wu Y, Zhou H, Cao X, Jiang X, Wang K, Wu S. A novel strategy for screening new natural products by a combination of reversed-phase liquid chromatography fractionation and 13C NMR pattern recognition: the discovery of new anti-cancer flavone dimers from Dysosma versipellis (Hance). RSC Adv 2015. [DOI: 10.1039/c5ra13756j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A new screening strategy for the discovery of new natural products by a combination of reversed-phase liquid chromatography (RPLC) and 13C NMR pattern recognition.
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Affiliation(s)
- Zhi Yang
- Research Center of Siyuan Natural Pharmacy and Biotoxicology
- College of Life Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Youqian Wu
- Research Center of Siyuan Natural Pharmacy and Biotoxicology
- College of Life Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Hui Zhou
- Department of Pharmaceutical Analysis and Drug Metabolism
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Xiaoji Cao
- Research Center of Analysis and Measurement
- Zhejiang University of Technology
- Hangzhou
- China
| | - Xinhang Jiang
- Equipment & Technology Service Platform
- College of Life Sciences
- Zhejiang University
- Hangzhou 310058
- P. R. China
| | - Kuiwu Wang
- School of Food Science and Biotechnology
- Zhejiang Gongshang University
- Hangzhou 310018
- China
| | - Shihua Wu
- Research Center of Siyuan Natural Pharmacy and Biotoxicology
- College of Life Sciences
- Zhejiang University
- Hangzhou 310058
- China
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