501
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Discovery and engineered overproduction of antimicrobial nucleoside antibiotic A201A from the deep-sea marine actinomycete Marinactinospora thermotolerans SCSIO 00652. Antimicrob Agents Chemother 2011; 56:110-4. [PMID: 22064543 DOI: 10.1128/aac.05278-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marinactinospora thermotolerans SCSIO 00652, originating from a deep-sea marine sediment of the South China Sea, was discovered to produce antimicrobial nucleoside antibiotic A201A. Whole-genome scanning and annotation strategies enabled us to localize the genes responsible for A201A biosynthesis and to experimentally identify the gene cluster; inactivation of mtdF, an oxidoreductase gene within the suspected gene cluster, abolished A201A production. Bioinformatics analysis revealed that a gene designated mtdA furthest upstream within the A201A biosynthetic gene cluster encodes a GntR family transcriptional regulator. To determine the role of MtdA in regulating A201A production, the mtdA gene was inactivated in frame and the resulting ΔmtdA mutant was fermented alongside the wild-type strain as a control. High-performance liquid chromatography (HPLC) analyses of fermentation extracts revealed that the ΔmtdA mutant produced A201A in a yield ∼25-fold superior to that of the wild-type strain, thereby demonstrating that MtdA is a negative transcriptional regulator governing A201A biosynthesis. By virtue of its high production capacity, the ΔmtdA mutant constitutes an ideal host for the efficient large-scale production of A201A. These results validate M. thermotolerans as an emerging source of antibacterial agents and highlight the efficiency of metabolic engineering for antibiotic titer improvement.
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502
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Benson DR, Brooks JM, Huang Y, Bickhart DM, Mastronunzio JE. The biology of Frankia sp. strains in the post-genome era. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1310-1316. [PMID: 21848398 DOI: 10.1094/mpmi-06-11-0150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Progress in understanding symbiotic determinants involved in the N(2)-fixing actinorhizal plant symbioses has been slow but steady. Problems persist with studying the bacterial contributions to the symbiosis using traditional microbiological techniques. However, recent years have seen the emergence of several genomes from Frankia sp. strains and the development of techniques for manipulating plant gene expression. Approaches to understanding the bacterial side of the symbiosis have employed a range of techniques that reveal the proteomes and transcriptomes from both cultured and symbiotic frankiae. The picture beginning to emerge provides some perspective on the heterogeneity of frankial populations in both conditions. In general, frankial populations in root nodules seem to maintain a rather robust metabolism that includes nitrogen fixation and substantial biosynthesis and energy-generating pathways, along with a modified ammonium assimilation program. To date, particular bacterial genes have not been implicated in root nodule formation but some hypotheses are emerging with regard to how the plant and microorganism manage to coexist. In particular, frankiae seem to present a nonpathogenic presence to the plant that may have the effect of minimizing some plant defense responses. Future studies using high-throughput approaches will likely clarify the range of bacterial responses to symbiosis that will need to be understood in light of the more rapidly advancing work on the plant host.
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Affiliation(s)
- David R Benson
- Department of Molecular and Cell Biology, University of Connecticut, Stors, CT, USA.
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503
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Rokni-Zadeh H, Mangas-Losada A, De Mot R. PCR detection of novel non-ribosomal peptide synthetase genes in lipopeptide-producing Pseudomonas. MICROBIAL ECOLOGY 2011; 62:941-947. [PMID: 21647696 DOI: 10.1007/s00248-011-9885-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/24/2011] [Indexed: 05/30/2023]
Abstract
Bacterial lipopeptides (LPs) are a diverse group of secondary metabolites synthesized through one or more non-ribosomal peptide synthetases (NRPSs). In certain genera, such as Pseudomonas and Bacillus, these enzyme systems are often involved in synthesizing biosurfactants or antimicrobial compounds. Several different types of LPs have been reported for non-pathogenic plant-associated Pseudomonas. Focusing on this group of bacteria, we devised and validated a PCR method to detect novel LP-synthesizing NRPS genes by targeting their lipoinitiation and tandem thioesterase domains, thus avoiding amplification of genes for non-LP metabolites, such as the pyoverdine siderophores present in all fluorescent Pseudomonas. This approach enabled detection of as yet unknown NRPS genes in strains producing viscosin, viscosinamide, WLIP, or lokisin. Furthermore, it proved valuable to identify novel candidate LP producers among Pseudomonas rhizosphere isolates. By phylogenetic analysis of these amplicons, several of the corresponding NRPS genes can be tentatively assigned to the viscosin, amphisin, or entolysin biosynthetic groups, while some others may represent novel NRPS systems.
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Affiliation(s)
- Hassan Rokni-Zadeh
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
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504
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Nett M, Hertweck C. Farinamycin, a quinazoline from Streptomyces griseus. JOURNAL OF NATURAL PRODUCTS 2011; 74:2265-2268. [PMID: 21939253 DOI: 10.1021/np2002513] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The metabolic potential of a Streptomyces griseus strain was investigated under various cultivation conditions. After fermentation in a flour-based medium, a new quinazoline metabolite, farinamycin (1), could be isolated from the bacterium, which was previously known only for the production of phenoxazinone antibiotics. The structure of 1 illuminates the biosynthetic versatility of S. griseus, which assembles a defined set of building blocks into structurally diverse natural products.
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Affiliation(s)
- Markus Nett
- Junior Research Group Secondary Metabolism of Predatory Bacteria and Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany.
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505
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Chen Y, Ntai I, Ju KS, Unger M, Zamdborg L, Robinson SJ, Doroghazi JR, Labeda DP, Metcalf WW, Kelleher NL. A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria. J Proteome Res 2011; 11:85-94. [PMID: 21978092 DOI: 10.1021/pr2009115] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Actinobacteria such as streptomycetes are renowned for their ability to produce bioactive natural products including nonribosomal peptides (NRPs) and polyketides (PKs). The advent of genome sequencing has revealed an even larger genetic repertoire for secondary metabolism with most of the small molecule products of these gene clusters still unknown. Here, we employed a "protein-first" method called PrISM (Proteomic Investigation of Secondary Metabolism) to screen 26 unsequenced actinomycetes using mass spectrometry-based proteomics for the targeted detection of expressed nonribosomal peptide synthetases or polyketide synthases. Improvements to the original PrISM screening approach (Nat. Biotechnol. 2009, 27, 951-956), for example, improved de novo peptide sequencing, have enabled the discovery of 10 NRPS/PKS gene clusters from 6 strains. Taking advantage of the concurrence of biosynthetic enzymes and the secondary metabolites they generate, two natural products were associated with their previously "orphan" gene clusters. This work has demonstrated the feasibility of a proteomics-based strategy for use in screening for NRP/PK production in actinomycetes (often >8 Mbp, high GC genomes) versus the bacilli (2-4 Mbp genomes) used previously.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
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506
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Barona-Gómez F, Cruz-Morales P, Noda-García L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics? Antonie van Leeuwenhoek 2011; 101:35-43. [PMID: 22016333 DOI: 10.1007/s10482-011-9655-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 10/07/2011] [Indexed: 11/24/2022]
Abstract
It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1-5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.
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Affiliation(s)
- Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, Mexico.
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507
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A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 2011; 7:794-802. [PMID: 21983601 PMCID: PMC3258187 DOI: 10.1038/nchembio.684] [Citation(s) in RCA: 291] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 08/27/2011] [Indexed: 12/13/2022]
Abstract
Peptide natural products exhibit broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce Natural Product Peptidogenomics (NPP), a new mass spectrometry-guided genome mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo MSn structures to genomics-based structures following current biosynthetic logic. In this study we demonstrate that NPP enabled the rapid characterization of >10 chemically diverse ribosomal and nonribosomal peptide natural products of novel composition from streptomycete bacteria as a proof of concept to begin automating the genome mining process. We show the identification of lantipeptides, lasso peptides, linardins, formylated peptides and lipopeptides, many of which from well-characterized model streptomycetes, highlighting the power of NPP in the discovery of new peptide natural products from even intensely studied organisms.
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508
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Kersten RD, Yang YL, Xu Y, Cimermancic P, Nam SJ, Fenical W, Fischbach MA, Moore BS, Dorrestein PC. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 2011. [PMID: 21983601 DOI: 10.1038/nchem-bio.684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Peptide natural products show broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce here natural product peptidogenomics (NPP), a new MS-guided genome-mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo tandem MS (MS(n)) structures to genomics-based structures following biosynthetic logic. In this study, we show that NPP enabled the rapid characterization of over ten chemically diverse ribosomal and nonribosomal peptide natural products of previously unidentified composition from Streptomycete bacteria as a proof of concept to begin automating the genome-mining process. We show the identification of lantipeptides, lasso peptides, linardins, formylated peptides and lipopeptides, many of which are from well-characterized model Streptomycetes, highlighting the power of NPP in the discovery of new peptide natural products from even intensely studied organisms.
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Affiliation(s)
- Roland D Kersten
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA
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509
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Zhao LX, Huang SX, Tang SK, Jiang CL, Duan Y, Beutler JA, Henrich CJ, McMahon JB, Schmid T, Blees JS, Colburn NH, Rajski SR, Shen B. Actinopolysporins A-C and tubercidin as a Pdcd4 stabilizer from the halophilic actinomycete Actinopolyspora erythraea YIM 90600. JOURNAL OF NATURAL PRODUCTS 2011; 74:1990-5. [PMID: 21870828 PMCID: PMC3179765 DOI: 10.1021/np200603g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Our current natural product program utilizes new actinomycetes originating from unexplored and underexplored ecological niches, employing cytotoxicity against a selected panel of cancer cell lines as the preliminary screen to identify hit strains for natural product dereplication, followed by mechanism-based assays of the purified natural products to discover potential anticancer drug leads. Three new linear polyketides, actinopolysporins A (1), B (2), and C (3), along with the known antineoplastic antibiotic tubercidin (4), were isolated from the halophilic actinomycete Actinopolyspora erythraea YIM 90600, and the structures of the new compounds were elucidated on the basis of spectroscopic data interpretation. All four compounds were assayed for their ability to stabilize the tumor suppressor programmed cell death protein 4 (Pdcd4), which is known to antagonize critical events in oncogenic pathways. Only 4 significantly inhibited proteasomal degradation of a model Pdcd4-luciferase fusion protein, with an IC50 of 0.88±0.09 μM, unveiling a novel biological activity for this well-studied natural product.
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Affiliation(s)
- Li-Xing Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic of China
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sheng-Xiong Huang
- Department of Chemistry, TSRI, Scripps Florida, Jupiter, FL 33458, USA
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic of China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic of China
| | - Yanwen Duan
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
| | | | - Curtis J. Henrich
- Molecular Targets Laboratory, NCI, Frederick, MD 21702, USA
- SAIC-Frederick, Inc., NCI, Frederick, MD 21702, USA
| | | | - Tobias Schmid
- Institute of Biochemistry I/ZAFES, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Johanna S. Blees
- Institute of Biochemistry I/ZAFES, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | | | - Scott R. Rajski
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ben Shen
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Chemistry, TSRI, Scripps Florida, Jupiter, FL 33458, USA
- Department of Molecular Therapeutics, TSRI, Scripps Florida, Jupiter, FL 33458, USA
- Natural Products Library Initiative, TSRI, Scripps Florida, Jupiter, FL 33458, USA
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510
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Qu X, Lei C, Liu W. Transcriptome mining of active biosynthetic pathways and their associated products in Streptomyces flaveolus. Angew Chem Int Ed Engl 2011; 50:9651-4. [PMID: 21948600 DOI: 10.1002/anie.201103085] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/30/2011] [Indexed: 01/08/2023]
Affiliation(s)
- Xudong Qu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd., Shanghai 200032, China
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511
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Qu X, Lei C, Liu W. Transcriptome Mining of Active Biosynthetic Pathways and Their Associated Products in Streptomyces flaveolus. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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512
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513
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Miyanaga A, Janso JE, McDonald L, He M, Liu H, Barbieri L, Eustáquio AS, Fielding EN, Carter GT, Jensen PR, Feng X, Leighton M, Koehn FE, Moore BS. Discovery and assembly-line biosynthesis of the lymphostin pyrroloquinoline alkaloid family of mTOR inhibitors in Salinispora bacteria. J Am Chem Soc 2011; 133:13311-3. [PMID: 21815669 PMCID: PMC3161154 DOI: 10.1021/ja205655w] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The pyrroloquinoline alkaloid family of natural products, which includes the immunosuppressant lymphostin, has long been postulated to arise from tryptophan. We now report the molecular basis of lymphostin biosynthesis in three marine Salinispora species that maintain conserved biosynthetic gene clusters harboring a hybrid nonribosomal peptide synthetase-polyketide synthase that is central to lymphostin assembly. Through a series of experiments involving gene mutations, stable isotope profiling, and natural product discovery, we report the assembly-line biosynthesis of lymphostin and nine new analogues that exhibit potent mTOR inhibitory activity.
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Affiliation(s)
- Akimasa Miyanaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Jeffrey E. Janso
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Leonard McDonald
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Min He
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Hongbo Liu
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Laurel Barbieri
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Alessandra S. Eustáquio
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Elisha N. Fielding
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Guy T. Carter
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Xidong Feng
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Margaret Leighton
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Frank E. Koehn
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
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514
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Genome-based studies of marine microorganisms to maximize the diversity of natural products discovery for medical treatments. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 2011:384572. [PMID: 21826184 PMCID: PMC3151524 DOI: 10.1155/2011/384572] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 04/15/2011] [Accepted: 06/03/2011] [Indexed: 01/22/2023]
Abstract
Marine microorganisms are rich source for natural products which play important roles in pharmaceutical industry. Over the past decade, genome-based studies of marine microorganisms have unveiled the tremendous diversity of the producers of natural products and also contributed to the efficiency of harness the strain diversity and chemical diversity, as well as the genetic diversity of marine microorganisms for the rapid discovery and generation of new natural products. In the meantime, genomic information retrieved from marine symbiotic microorganisms can also be employed for the discovery of new medical molecules from yet-unculturable microorganisms. In this paper, the recent progress in the genomic research of marine microorganisms is reviewed; new tools of genome mining as well as the advance in the activation of orphan pathways and metagenomic studies are summarized. Genome-based research of marine microorganisms will maximize the biodiscovery process and solve the problems of supply and sustainability of drug molecules for medical treatments.
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515
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Zhu F, Qin C, Tao L, Liu X, Shi Z, Ma X, Jia J, Tan Y, Cui C, Lin J, Tan C, Jiang Y, Chen Y. Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting. Proc Natl Acad Sci U S A 2011; 108:12943-8. [PMID: 21768386 PMCID: PMC3150889 DOI: 10.1073/pnas.1107336108] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Many drugs are nature derived. Low drug productivity has renewed interest in natural products as drug-discovery sources. Nature-derived drugs are composed of dozens of molecular scaffolds generated by specific secondary-metabolite gene clusters in selected species. It can be hypothesized that drug-like structures probably are distributed in selective groups of species. We compared the species origins of 939 approved and 369 clinical-trial drugs with those of 119 preclinical drugs and 19,721 bioactive natural products. In contrast to the scattered distribution of bioactive natural products, these drugs are clustered into 144 of the 6,763 known species families in nature, with 80% of the approved drugs and 67% of the clinical-trial drugs concentrated in 17 and 30 drug-prolific families, respectively. Four lines of evidence from historical drug data, 13,548 marine natural products, 767 medicinal plants, and 19,721 bioactive natural products suggest that drugs are derived mostly from preexisting drug-productive families. Drug-productive clusters expand slowly by conventional technologies. The lack of drugs outside drug-productive families is not necessarily the result of under-exploration or late exploration by conventional technologies. New technologies that explore cryptic gene clusters, pathways, interspecies crosstalk, and high-throughput fermentation enable the discovery of novel natural products. The potential impact of these technologies on drug productivity and on the distribution patterns of drug-productive families is yet to be revealed.
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Affiliation(s)
- Feng Zhu
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Chu Qin
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
- Department of Pharmacy, National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 117456; and
| | - Lin Tao
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
- Department of Pharmacy, National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 117456; and
| | - Xin Liu
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Zhe Shi
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Xiaohua Ma
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Jia Jia
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Ying Tan
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
| | - Cheng Cui
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
| | - Jinshun Lin
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
| | - Chunyan Tan
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
| | - Yuyang Jiang
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
- School of Medicine and Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yuzong Chen
- Key Laboratory of Chemical Biology, Guangdong Province Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055, People's Republic of China
- Bioinformatics and Drug Design Group, Department of Pharmacy, and
- Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
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516
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Schmitt EK, Moore CM, Krastel P, Petersen F. Natural products as catalysts for innovation: a pharmaceutical industry perspective. Curr Opin Chem Biol 2011; 15:497-504. [DOI: 10.1016/j.cbpa.2011.05.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 05/11/2011] [Accepted: 05/23/2011] [Indexed: 12/21/2022]
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517
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van Wezel GP, McDowall KJ. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 2011; 28:1311-33. [PMID: 21611665 DOI: 10.1039/c1np00003a] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Streptomycetes and other actinobacteria are renowned as a rich source of natural products of clinical, agricultural and biotechnological value. They are being mined with renewed vigour, supported by genome sequencing efforts, which have revealed a coding capacity for secondary metabolites in vast excess of expectations that were based on the detection of antibiotic activities under standard laboratory conditions. Here we review what is known about the control of production of so-called secondary metabolites in streptomycetes, with an emphasis on examples where details of the underlying regulatory mechanisms are known. Intriguing links between nutritional regulators, primary and secondary metabolism and morphological development are discussed, and new data are included on the carbon control of development and antibiotic production, and on aspects of the regulation of the biosynthesis of microbial hormones. Given the tide of antibiotic resistance emerging in pathogens, this review is peppered with approaches that may expand the screening of streptomycetes for new antibiotics by awakening expression of cryptic antibiotic biosynthetic genes. New technologies are also described that have potential to greatly further our understanding of gene regulation in what is an area fertile for discovery and exploitation
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518
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Draft genome sequence of the marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea. J Bacteriol 2011; 193:3691-2. [PMID: 21571991 DOI: 10.1128/jb.05097-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces, a branch of aerobic Gram-positive bacteria, represents the largest genus of actinobacteria. The streptomycetes are characterized by a complex secondary metabolism and produce over two-thirds of the clinically used natural antibiotics today. Here we report the draft genome sequence of a Streptomyces strain, PP-C42, isolated from the marine environment. A subset of unique genes and gene clusters for diverse secondary metabolites as well as antimicrobial peptides could be identified from the genome, showing great promise as a source for novel bioactive compounds.
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519
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Significant natural product biosynthetic potential of actinorhizal symbionts of the genus frankia, as revealed by comparative genomic and proteomic analyses. Appl Environ Microbiol 2011; 77:3617-25. [PMID: 21498757 DOI: 10.1128/aem.00038-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteria of the genus Frankia are mycelium-forming actinomycetes that are found as nitrogen-fixing facultative symbionts of actinorhizal plants. Although soil-dwelling actinomycetes are well-known producers of bioactive compounds, the genus Frankia has largely gone uninvestigated for this potential. Bioinformatic analysis of the genome sequences of Frankia strains ACN14a, CcI3, and EAN1pec revealed an unexpected number of secondary metabolic biosynthesis gene clusters. Our analysis led to the identification of at least 65 biosynthetic gene clusters, the vast majority of which appear to be unique and for which products have not been observed or characterized. More than 25 secondary metabolite structures or structure fragments were predicted, and these are expected to include cyclic peptides, siderophores, pigments, signaling molecules, and specialized lipids. Outside the hopanoid gene locus, no cluster could be convincingly demonstrated to be responsible for the few secondary metabolites previously isolated from other Frankia strains. Few clusters were shared among the three species, demonstrating species-specific biosynthetic diversity. Proteomic analysis of Frankia sp. strains CcI3 and EAN1pec showed that significant and diverse secondary metabolic activity was expressed in laboratory cultures. In addition, several prominent signals in the mass range of peptide natural products were observed in Frankia sp. CcI3 by intact-cell matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). This work supports the value of bioinformatic investigation in natural products biosynthesis using genomic information and presents a clear roadmap for natural products discovery in the Frankia genus.
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520
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Donia MS, Fricke WF, Ravel J, Schmidt EW. Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PLoS One 2011; 6:e17897. [PMID: 21445351 PMCID: PMC3062557 DOI: 10.1371/journal.pone.0017897] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 02/14/2011] [Indexed: 11/19/2022] Open
Abstract
The complex evolution of secondary metabolism is important in biology, drug development, and synthetic biology. To examine this problem at a fine scale, we compared the genomes and chemistry of 24 strains of uncultivated cyanobacteria, Prochloron didemni, that live symbiotically with tropical ascidians and that produce natural products isolated from the animals. Although several animal species were obtained along a >5500 km transect of the Pacific Ocean, P. didemni strains are >97% identical across much of their genomes, with only a few exceptions concentrated in secondary metabolism. Secondary metabolic gene clusters were sporadically present or absent in identical genomic locations with no consistent pattern of co-occurrence. Discrete mutations were observed, leading to new chemicals that we isolated from animals. Functional cassettes encoding diverse chemicals are exchanged among a single population of symbiotic P. didemni that spans the tropical Pacific, providing the host animals with a varying arsenal of secondary metabolites.
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Affiliation(s)
- Mohamed S. Donia
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - W. Florian Fricke
- Institute for Genome Sciences, Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
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521
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Bosello M, Robbel L, Linne U, Xie X, Marahiel MA. Biosynthesis of the siderophore rhodochelin requires the coordinated expression of three independent gene clusters in Rhodococcus jostii RHA1. J Am Chem Soc 2011; 133:4587-95. [PMID: 21381663 DOI: 10.1021/ja1109453] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work we report the isolation, structural characterization, and the genetic analysis of the biosynthetic origin of rhodochelin, a unique mixed-type catecholate-hydroxamate siderophore isolated from Rhodococcus jostii RHA1. Rhodochelin structural elucidation was accomplished via MS(n)- and NMR-analysis and revealed the tetrapeptide to contain an unusual ester bond between an L-δ-N-formyl-δ-N-hydroxyornithine moiety and the side chain of a threonine residue. Gene deletions within three putative biosynthetic gene clusters abolish rhodochelin production, proving that the ORFs responsible for rhodochelin biosynthesis are located in different chromosomal loci. These results demonstrate the efficient cross-talk between distantly located secondary metabolite gene clusters and outline new insights into the comprehension of natural product biosynthesis.
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Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse D-35043 Marburg, Germany
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522
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Tierrafría VH, Ramos‐Aboites HE, Gosset G, Barona‐Gómez F. Disruption of the siderophore-binding desE receptor gene in Streptomyces coelicolor A3(2) results in impaired growth in spite of multiple iron-siderophore transport systems. Microb Biotechnol 2011; 4:275-85. [PMID: 21342472 PMCID: PMC3818867 DOI: 10.1111/j.1751-7915.2010.00240.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Accepted: 11/16/2010] [Indexed: 11/30/2022] Open
Abstract
Ferrioxamines-mediated iron acquisition by Streptomyces coelicolor A3(2) has recently received increased attention. In addition to the biological role of desferrioxamines (dFOs) as hydroxamate siderophores, and the pharmaceutical application of dFO-B as an iron-chelator, the ferrioxamines have been shown to mediate microbial interactions. In S. coelicolor the siderophore-binding receptors DesE (Sco2780) and CdtB (Sco7399) have been postulated to specifically recognize and uptake FO-E (cyclic) and FO-B (linear) respectively. Here, disruption of the desE gene in S. coelicolor, and subsequent phenotypic analysis, is used to demonstrate a link between iron metabolism and physiological and morphological development. Streptomyces coelicolor desE mutants, isolated in both wild-type (M145) and a coelichelin biosynthesis and transport minus background (mutant W3), a second hydroxamate siderophore system only found in S. coelicolor and related species, resulted in impaired growth and lack of sporulation. This phenotype could only be partially rescued by expression in trans of either desE and cdtB genes, which contrasted with the ability of FO-E, and to a lesser extent of FO-B, to fully restore growth at µM concentrations, with a concomitant induction of a marked phenotypic response involving precocious synthesis of actinorhodin and sporulation. Moreover, growth restoration of the desE mutant by complementation with desE and cdtB showed that DesE, which is universally conserved in Streptomyces, and CdtB, only present in certain streptomycetes, have partial equivalent functional roles under laboratory conditions, implying overlapping ferrioxamine specificities. The biotechnological and ecological implications of these observations are discussed.
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Affiliation(s)
- Víctor H. Tierrafría
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV‐IPN, Km 9.6 Libramiento Norte, Carretera Irapuato – León, Irapuato, C.P. 36822, México
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, C.P. 62210, México
| | - Hilda E. Ramos‐Aboites
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV‐IPN, Km 9.6 Libramiento Norte, Carretera Irapuato – León, Irapuato, C.P. 36822, México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, C.P. 62210, México
| | - Francisco Barona‐Gómez
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV‐IPN, Km 9.6 Libramiento Norte, Carretera Irapuato – León, Irapuato, C.P. 36822, México
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523
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Ostash B, Rebets Y, Myronovskyy M, Tsypik O, Ostash I, Kulachkovskyy O, Datsyuk Y, Nakamura T, Walker S, Fedorenko V. Identification and characterization of the Streptomyces globisporus 1912 regulatory gene lndYR that affects sporulation and antibiotic production. MICROBIOLOGY-SGM 2011; 157:1240-1249. [PMID: 21292750 DOI: 10.1099/mic.0.045088-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Here, we report the identification and functional characterization of the Streptomyces globisporus 1912 gene lndYR, which encodes a GntR-like regulator of the YtrA subfamily. Disruption of lndYR arrested sporulation and antibiotic production in S. globisporus. The results of in vivo and in vitro studies revealed that the ABC transporter genes lndW-lndW2 are targets of LndYR repressive action. In Streptomyces coelicolor M145, lndYR overexpression caused a significant increase in the amount of extracellular actinorhodin. We suggest that lndYR controls the transcription of transport system genes in response to an as-yet-unidentified signal. Features that distinguish lndYR-based regulation from other known regulators are discussed.
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Affiliation(s)
- Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Yuriy Rebets
- Department of Microbiology, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, 956-8603 Niigata, Japan.,Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA.,Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Maksym Myronovskyy
- Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Olga Tsypik
- Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Oleksandr Kulachkovskyy
- Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Yuriy Datsyuk
- Department of Physics of the Earth, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
| | - Tatsunosuke Nakamura
- Department of Microbiology, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, 956-8603 Niigata, Japan
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of L'viv, Grushevskogo St 4, L'viv 79005, Ukraine
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524
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Abstract
The years 2000 through mid-2010 marked a transformational period in understanding of the biosynthesis of marine natural products. During this decade the field emerged from one largely dominated by chemical approaches to understanding biosynthetic pathways to one incorporating the full force of modern molecular biology and bioinformatics. Fusion of chemical and biological approaches yielded great advances in understanding the genetic and enzymatic basis for marine natural product biosynthesis. Progress was particularly pronounced for marine microbes, especially actinomycetes and cyanobacteria. During this single decade, both the first complete marine microbial natural product biosynthetic gene cluster sequence was released as well as the first entire genome sequence for a secondary metabolite-rich marine microbe. The decade also saw tremendous progress in recognizing the key role of marine microbial symbionts of invertebrates in natural product biosynthesis. Application of genetic and enzymatic knowledge led to genetic engineering of novel “unnatural” natural products during this time, as well as opportunities for discovery of novel natural products through genome mining. The current review highlights selected seminal studies from 2000 through to June 2010 that illustrate breakthroughs in understanding of marine natural product biosynthesis at the genetic, enzymatic, and small-molecule natural product levels. A total of 154 references are cited.
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Affiliation(s)
- Amy L. Lane
- Department of Chemistry, University of North Florida, Jacksonville, FL, 32224, USA.
| | - Bradley S. Moore
- Scripps Institution of Oceanography and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
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525
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Baltz RH. Strain improvement in actinomycetes in the postgenomic era. J Ind Microbiol Biotechnol 2011; 38:657-66. [PMID: 21253811 DOI: 10.1007/s10295-010-0934-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 12/20/2010] [Indexed: 01/08/2023]
Abstract
With the recent advances in DNA sequencing technologies, it is now feasible to sequence multiple actinomycete genomes rapidly and inexpensively. An important observation that emerged from early Streptomyces genome sequencing projects was that each strain contains genes that encode 20 or more potential secondary metabolites, only a fraction of which are expressed during fermentation. More recently, this observation has been extended to many other actinomycetes with large genomes. The discovery of a wealth of orphan or cryptic secondary metabolite biosynthetic gene clusters has suggested that sequencing large numbers of actinomycete genomes may provide the starting materials for a productive new approach to discover novel secondary metabolites. The key issue for this approach to be successful is to find ways to turn on or turn up the expression of cryptic or poorly expressed pathways to provide material for structure elucidation and biological testing. In this review, I discuss several genetic approaches that are potentially applicable to many actinomycetes for this application.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 6438 North Olney Street, Indianapolis, IN 46220, USA.
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526
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Zhang H, Boghigian BA, Armando J, Pfeifer BA. Methods and options for the heterologous production of complex natural products. Nat Prod Rep 2011; 28:125-51. [PMID: 21060956 PMCID: PMC9896020 DOI: 10.1039/c0np00037j] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, Medford, MA 02155, USA.
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527
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Natural and synthetic small boron-containing molecules as potential inhibitors of bacterial and fungal quorum sensing. Chem Rev 2010; 111:209-37. [PMID: 21171664 DOI: 10.1021/cr100093b] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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528
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Winter JM, Behnken S, Hertweck C. Genomics-inspired discovery of natural products. Curr Opin Chem Biol 2010; 15:22-31. [PMID: 21111667 DOI: 10.1016/j.cbpa.2010.10.020] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 10/15/2010] [Indexed: 12/30/2022]
Abstract
The massive surge in genome sequencing projects has opened our eyes to the overlooked biosynthetic potential and metabolic diversity of microorganisms. While traditional approaches have been successful at identifying many useful therapeutic agents from these organisms, new tactics are needed in order to exploit their true biosynthetic potential. Several genomics-inspired strategies have been successful in unveiling new metabolites that were overlooked under standard fermentation and detection conditions. In addition, genome sequences have given us valuable insight for genetically engineering biosynthesis gene clusters that remain silent or are poorly expressed in the absence of a specific trigger. As more genome sequences are becoming available, we are noticing the emergence of underexplored or neglected organisms as alternative resources for new therapeutic agents.
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Affiliation(s)
- Jaclyn M Winter
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena D-07745, Germany
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529
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Pentalenic acid is a shunt metabolite in the biosynthesis of the pentalenolactone family of metabolites: hydroxylation of 1-deoxypentalenic acid mediated by CYP105D7 (SAV_7469) of Streptomyces avermitilis. J Antibiot (Tokyo) 2010; 64:65-71. [PMID: 21081950 DOI: 10.1038/ja.2010.135] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pentalenic acid (1) has been isolated from many Streptomyces sp. as a co-metabolite of the sesquiterpenoid antibiotic pentalenolactone and related natural products. We have previously reported the identification of a 13.4-kb gene cluster in the genome of Streptomyces avermitilis implicated in the biosynthesis of the pentalenolactone family of metabolites consisting of 13 open reading frames. Detailed molecular genetic and biochemical studies have revealed that at least seven genes are involved in the biosynthesis of the newly discovered metabolites, neopentalenoketolactone, but no gene specifically dedicated to the formation of pentalenic acid (1) was evident in the same gene cluster. The wild-type strain of S. avermitilis, as well as its derivatives, mainly produce pentalenic acid (1), together with neopentalenoketolactone (9). Disruption of the sav7469 gene encoding a cytochrome P450 (CYP105D7), members of which class are associated with the hydroxylation of many structurally different compounds, abolished the production of pentalenic acid (1). The sav7469-deletion mutant derived from SUKA11 carrying pKU462∷ptl-clusterΔptlH accumulated 1-deoxypentalenic acid (5), but not pentalenic acid (1). Reintroduction of an extra-copy of the sav7469 gene to SUKA11 Δsav7469 carrying pKU462∷ptl-clusterΔptlH restored the production of pentalenic acid (1). Recombinant CYP105D7 prepared from Escherichia coli catalyzed the oxidative conversion of 1-deoxypentalenic acid (5) to pentalenic acid (1) in the presence of the electron-transport partners, ferredoxin (Fdx) and Fdx reductase, both in vivo and in vitro. These results unambiguously demonstrate that CYP105D7 is responsible for the conversion of 1-deoxypentalenic acid (5) to pentalenic acid (1), a shunt product in the biosynthesis of the pentalenolactone family of metabolites.
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530
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Ichikawa N, Oguchi A, Ikeda H, Ishikawa J, Kitani S, Watanabe Y, Nakamura S, Katano Y, Kishi E, Sasagawa M, Ankai A, Fukui S, Hashimoto Y, Kamata S, Otoguro M, Tanikawa S, Nihira T, Horinouchi S, Ohnishi Y, Hayakawa M, Kuzuyama T, Arisawa A, Nomoto F, Miura H, Takahashi Y, Fujita N. Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae. DNA Res 2010; 17:393-406. [PMID: 21059706 PMCID: PMC2993542 DOI: 10.1093/dnares/dsq026] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Kitasatospora setae NBRC 14216T (=KM-6054T) is known to produce setamycin (bafilomycin B1) possessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the genus Streptomyces, although they are distinguishable from each other on the basis of cell wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of K. setae NBRC 14216T as the first Streptomycetaceae genome other than Streptomyces. The genome is a single linear chromosome of 8 783 278 bp with terminal inverted repeats of 127 148 bp, predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes. Although these features resemble those of Streptomyces, genome-wide comparison of orthologous genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the Streptomyces genus. Although many of the genes related to morphological differentiation identified in Streptomyces were highly conserved in K. setae, there were some differences such as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the copy number and variation of paralogous components involved in cell wall synthesis.
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Affiliation(s)
- Natsuko Ichikawa
- NITE Bioresource Information Center, Department of Biotechnology, National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan
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Ostash B, Walker S. Moenomycin family antibiotics: chemical synthesis, biosynthesis, and biological activity. Nat Prod Rep 2010; 27:1594-617. [PMID: 20730219 PMCID: PMC2987538 DOI: 10.1039/c001461n] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The review (with 214 references cited) is devoted to moenomycins, the only known group of antibiotics that directly inhibit bacterial peptidoglycan glycosytransferases. Naturally occurring moenomycins and chemical and biological approaches to their derivatives are described. The biological properties of moenomycins and plausible mechanisms of bacterial resistance to them are also covered here, portraying a complete picture of the chemistry and biology of these fascinating natural products
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Affiliation(s)
- Bohdan Ostash
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Armenise Bldg. 2, Rm 630, Boston, MA 02115, USA
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532
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Actinobacteria: the good, the bad, and the ugly. Antonie Van Leeuwenhoek 2010; 98:143-50. [PMID: 20390355 DOI: 10.1007/s10482-010-9440-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 03/30/2010] [Indexed: 10/19/2022]
Abstract
The actinobacteria are arguably the richest source of small molecule diversity on the planet. These compounds have an incredible variety of chemical structures and biological activities (in nature and in the laboratory). Their potential for the development of therapeutic applications cannot be underestimated. It is suggested that an improved understanding of the biological roles of low molecular weight compounds in nature will lead to the discovery an inexhaustible supply of novel therapeutic agents in the next decade. To support this objective, a functional marriage of biochemistry, genomics, genetics, microbiology, and modern natural product chemistry will be essential.
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533
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Gallagher KA, Fenical W, Jensen PR. Hybrid isoprenoid secondary metabolite production in terrestrial and marine actinomycetes. Curr Opin Biotechnol 2010; 21:794-800. [PMID: 20951024 DOI: 10.1016/j.copbio.2010.09.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 09/16/2010] [Indexed: 01/06/2023]
Abstract
Terpenoids are among the most ubiquitous and diverse secondary metabolites observed in nature. Although actinomycete bacteria are one of the primary sources of microbially derived secondary metabolites, they rarely produce compounds in this biosynthetic class. The terpenoid secondary metabolites that have been discovered from actinomycetes are often in the form of biosynthetic hybrids called hybrid isoprenoids (HIs). HIs include significant structural diversity and biological activity and thus are important targets for natural product discovery. Recent screening of marine actinomycetes has led to the discovery of a new lineage that is enriched in the production of biologically active HI secondary metabolites. These strains represent a promising resource for natural product discovery and provide unique opportunities to study the evolutionary history and ecological functions of an unusual group of secondary metabolites.
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Affiliation(s)
- Kelley A Gallagher
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0204, USA
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534
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Genilloud O, González I, Salazar O, Martín J, Tormo JR, Vicente F. Current approaches to exploit actinomycetes as a source of novel natural products. J Ind Microbiol Biotechnol 2010; 38:375-89. [DOI: 10.1007/s10295-010-0882-7] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 09/16/2010] [Indexed: 11/28/2022]
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535
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Takamatsu S, Lin X, Nara A, Komatsu M, Cane DE, Ikeda H. Characterization of a silent sesquiterpenoid biosynthetic pathway in Streptomyces avermitilis controlling epi-isozizaene albaflavenone biosynthesis and isolation of a new oxidized epi-isozizaene metabolite. Microb Biotechnol 2010; 4:184-91. [PMID: 21342464 PMCID: PMC3711710 DOI: 10.1111/j.1751-7915.2010.00209.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The genome-sequenced, Gram-positive bacterium Streptomyces avermitilis harbours an orthologue (SAV_3032) of the previously identified epi-isozizaene synthase (SCO5222) in Streptomyces coelicolor A3(2). The sav3032 is translationally coupled with the downstream sav3031 gene encoding the cytochrome P450 CYP170A2 analogous to SCO5223 (CYP170A1) of S. coelicolor A3(2), which exhibits a similar translation coupling. Streptomyces avermitilis did not produce epi-isozizaene or any of its oxidized derivatives, albaflavenols and albaflavenone, under in any culture conditions examined. Nonetheless, recombinant SAV_3032 protein expressed in Escherichia coli catalysed the Mg²+-dependent cyclization of farnesyl diphosphate to epi-isozizaene. To effect the production of epi-isozizaene in S. avermitilis, the sav3032 gene was cloned and placed under control of a copy of the native S. avermitilis promoter rpsJp (sav4925). The derived expression construct was introduced by transformation into a large-deletion mutant of S. avermitilis SUKA16 and the resulting transformants accumulated epi-isozizaene. The previously characterized oxidized epi-isozizaene metabolites (4R)- and (4S)-albaflavenols and albaflavenone, as well as a previously undescribed doubly oxidized epi-isozizaene derivative were isolated from cultures of S. avermitilis SUKA16 transformants in which sav3032 was coexpressed with the P450-encoding sav3031. This new metabolite was identified as 4β,5β-epoxy-2-epi-zizaan-6β-ol which is most likely formed by oxidation of (4S)-albaflavenol.
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Affiliation(s)
- Satoshi Takamatsu
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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536
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Molinski TF. Microscale methodology for structure elucidation of natural products. Curr Opin Biotechnol 2010; 21:819-26. [PMID: 20880694 DOI: 10.1016/j.copbio.2010.09.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 09/01/2010] [Accepted: 09/02/2010] [Indexed: 11/15/2022]
Abstract
Advances in microscale spectroscopic techniques, particularly microcryoprobe NMR, allow discovery and structure elucidation of new molecules down to only a few nanomole. Newer methods for utilizing circular dichroism (CD) have pushed the limits of detection to picomole levels. NMR and CD methods are complementary to the task of elucidation of complete stereostructures of complex natural products. Together, integrated microprobe NMR spectroscopy, microscale degradation and synthesis, are synergistic tools for the discovery of bioactive natural products and have opened new realms for discovery among extreme sources including compounds from uncultured microbes, rare invertebrates and environmental samples.
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Affiliation(s)
- Tadeusz F Molinski
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive MC0358, CA 92093, USA.
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537
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Baltz RH. Genomics and the ancient origins of the daptomycin biosynthetic gene cluster. J Antibiot (Tokyo) 2010; 63:506-11. [DOI: 10.1038/ja.2010.82] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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538
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Abstract
Natural products have evolved to encompass a broad spectrum of chemical and functional diversity. It is this diversity, along with their structural complexity, that enables nature's small molecules to target a nearly limitless number of biological macromolecules and to often do so in a highly selective fashion. Because of these characteristics, natural products have seen great success as therapeutic agents. However, this vast pool of compounds holds much promise beyond the development of future drugs. These features also make them ideal tools for the study of biological systems. Recent examples of the use of natural products and their derivatives as chemical probes to explore biological phenomena and assemble biochemical pathways are presented here.
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Affiliation(s)
- Erin E. Carlson
- Departments of Chemistry and Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, Indiana 47405
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539
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Flinspach K, Westrich L, Kaysser L, Siebenberg S, Gomez-Escribano JP, Bibb M, Gust B, Heide L. Heterologous expression of the biosynthetic gene clusters of coumermycin A1, clorobiocin and caprazamycins in genetically modified Streptomyces coelicolor strains. Biopolymers 2010; 93:823-32. [DOI: 10.1002/bip.21493] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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540
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Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 2010; 37:759-72. [DOI: 10.1007/s10295-010-0730-9] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
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541
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Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci U S A 2010; 107:2646-51. [PMID: 20133795 DOI: 10.1073/pnas.0914833107] [Citation(s) in RCA: 380] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To construct a versatile model host for heterologous expression of genes encoding secondary metabolite biosynthesis, the genome of the industrial microorganism Streptomyces avermitilis was systematically deleted to remove nonessential genes. A region of more than 1.4 Mb was deleted stepwise from the 9.02-Mb S. avermitilis linear chromosome to generate a series of defined deletion mutants, corresponding to 83.12-81.46% of the wild-type chromosome, that did not produce any of the major endogenous secondary metabolites found in the parent strain. The suitability of the mutants as hosts for efficient production of foreign metabolites was shown by heterologous expression of three different exogenous biosynthetic gene clusters encoding the biosynthesis of streptomycin (from S. griseus Institute for Fermentation, Osaka [IFO] 13350), cephamycin C (from S. clavuligerus American type culture collection (ATCC) 27064), and pladienolide (from S. platensis Mer-11107). Both streptomycin and cephamycin C were efficiently produced by individual transformants at levels higher than those of the native-producing species. Although pladienolide was not produced by a deletion mutant transformed with the corresponding intact biosynthetic gene cluster, production of the macrolide was enabled by introduction of an extra copy of the regulatory gene pldR expressed under control of an alternative promoter. Another mutant optimized for terpenoid production efficiently produced the plant terpenoid intermediate, amorpha-4,11-diene, by introduction of a synthetic gene optimized for Streptomyces codon usage. These findings highlight the strength and flexibility of engineered S. avermitilis as a model host for heterologous gene expression, resulting in the production of exogenous natural and unnatural metabolites.
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542
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543
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Liang ZX. Complexity and simplicity in the biosynthesis of enediyne natural products. Nat Prod Rep 2010; 27:499-528. [DOI: 10.1039/b908165h] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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544
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Linking species concepts to natural product discovery in the post-genomic era. J Ind Microbiol Biotechnol 2009; 37:219-24. [PMID: 20033830 PMCID: PMC2820216 DOI: 10.1007/s10295-009-0683-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 12/10/2009] [Indexed: 11/24/2022]
Abstract
A widely accepted species concept for bacteria has yet to be established. As a result, species designations are inconsistently applied and tied to what can be considered arbitrary metrics. Increasing access to DNA sequence data and clear evidence that bacterial genomes are dynamic entities that include large numbers of horizontally acquired genes have added a new level of insight to the ongoing species concept debate. Despite uncertainties over how to apply species concepts to bacteria, there is clear evidence that sequence-based approaches can be used to resolve cohesive groups that maintain the properties of species. This cohesion is clearly evidenced in the genus Salinispora, where three species have been discerned despite very close relationships based on 16S rRNA sequence analysis. The major phenotypic differences among the three species are associated with secondary metabolite production, which occurs in species-specific patterns. These patterns are maintained on a global basis and provide evidence that secondary metabolites have important ecological functions. These patterns also suggest that an effective strategy for natural product discovery is to target the cultivation of new Salinispora taxa. Alternatively, bioinformatic analyses of biosynthetic genes provide opportunities to predict secondary metabolite novelty and reduce the redundant isolation of well-known metabolites. Although much remains to be learned about the evolutionary relationships among bacteria and how fundamental units of diversity can be resolved, genus and species descriptions remain the most effective method of scientific communication.
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