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Hou P, Woolner VH, Bracegirdle J, Hunt P, Keyzers RA, Owen JG. Stictamycin, an Aromatic Polyketide Antibiotic Isolated from a New Zealand Lichen-Sourced Streptomyces Species. JOURNAL OF NATURAL PRODUCTS 2023; 86:526-532. [PMID: 36795480 DOI: 10.1021/acs.jnatprod.2c00801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Here we describe the isolation and characterization of stictamycin, a new aromatic polyketide with activity against Staphylococcus aureus. Stictamycin was identified following metabolic profiling and bioactivity guided fractionation of organic extracts from Streptomyces sp. 438-3, an isolate from the New Zealand lichen Sticta felix. Comprehensive 1D and 2D NMR analyses were performed to determine the planar structure of stictamycin and relative configurations of stereo centers, with subsequent comparison of experimental and theoretical ECD spectra allowing elucidation of the absolute configuration. Whole-genome sequencing and biosynthetic gene cluster (BGC) analysis revealed that the Streptomyces sp. 438-3 strain contains an atypical type II polyketide (T2PKS) BGC capable of assembling polycyclic-aromatic ring skeletons. Cloning and knockout studies of this T2PKS BGC were used to confirm that it is responsible for the biosynthesis of stictamycin and elucidate a plausible biosynthetic scheme.
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Affiliation(s)
- Peng Hou
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - V Helen Woolner
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Joe Bracegirdle
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Patricia Hunt
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Robert A Keyzers
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
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2
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Santana-Pereira ALR. Identification of PKS Gene Clusters from Metagenomic Libraries Using a Next-Generation Sequencing Approach. Methods Mol Biol 2023; 2555:73-90. [PMID: 36306079 DOI: 10.1007/978-1-0716-2795-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbial secondary metabolites have been an important source of bioactive compounds with diverse applications from medicine to agriculture, noticeably those encoded by polyketide synthase (PKS) clusters due to their astounding chemical diversity. While most discovered compounds originate from culturable microorganisms, yet-to-be cultured microbes represent a reservoir of previously inaccessible compounds. The advent and development of metagenomics have allowed not only the characterization of these microorganisms but also their metabolic potential, making viable the prospection of environmental PKS for natural product discovery.Study of environmental PKSs often relies on the construction of metagenomic libraries and their mining, with clones containing PKS clusters identified via amplification of conserved domains and then screened for an activity of interest. Compounds produced by clones exhibiting the desired bioactivity can be isolated and characterized. However, these approaches can be less sensitive and biased against more divergent clusters, in addition to precluding the use of bioinformatics for cluster characterization prior to expression. While direct shotgun sequencing of metagenomes has identified and profiled a great number of PKSs from different environments and yet-to-be cultured microorganisms, it does not lend itself well to heterologous expression, the cruxes of natural product discovery.Here, we describe a strategy for sequencing entire metagenomic libraries while maintaining correspondence between sequence and clone, allowing the full characterization and annotation of all clusters present in a library using bioinformatic tools and then seamlessly passing clones of interest for activity screening through heterologous expression. Once a library is sequenced, the methods herein can be adapted for the mining of any biosynthetic gene cluster of interest within a metagenomic library.
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3
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Stevenson LJ, Bracegirdle J, Liu L, Sharrock AV, Ackerley DF, Keyzers RA, Owen JG. Metathramycin, a new bioactive aureolic acid discovered by heterologous expression of a metagenome derived biosynthetic pathway. RSC Chem Biol 2021; 2:556-567. [PMID: 34458799 PMCID: PMC8341913 DOI: 10.1039/d0cb00228c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/21/2021] [Indexed: 12/14/2022] Open
Abstract
Bacterial natural products have been a rich source of bioactive compounds for drug development, and advances in DNA sequencing, informatics and molecular biology have opened new avenues for their discovery. Here, we describe the isolation of an aureolic acid biosynthetic gene cluster from a metagenome library derived from a New Zealand soil sample. Heterologous expression of this pathway in Streptomyces albus resulted in the production and isolation of two new aureolic acid compounds, one of which (metathramycin, 6) possesses potent bioactivity against a human colon carcinoma cell line (HCT-116, IC50 = 14.6 nM). As metathramycin was a minor constituent of the fermentation extract, its discovery relied on a combination of approaches including bioactivity guided fractionation, MS/MS characterisation and pathway engineering. This study not only demonstrates the presence of previously uncharacterised aureolic acids in the environment, but also the value of an integrated natural product discovery approach which may be generally applicable to low abundance bioactive metabolites.
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Affiliation(s)
- Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington Wellington New Zealand .,Maurice Wilkins Centre for Molecular Biodiscovery New Zealand.,Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington Wellington New Zealand
| | - Joe Bracegirdle
- Maurice Wilkins Centre for Molecular Biodiscovery New Zealand.,Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington Wellington New Zealand.,School of Chemical and Physical Sciences, Victoria University of Wellington Wellington New Zealand
| | - Liwei Liu
- School of Biological Sciences, Victoria University of Wellington Wellington New Zealand
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington Wellington New Zealand .,Maurice Wilkins Centre for Molecular Biodiscovery New Zealand.,Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington Wellington New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington Wellington New Zealand .,Maurice Wilkins Centre for Molecular Biodiscovery New Zealand.,Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington Wellington New Zealand
| | - Robert A Keyzers
- Maurice Wilkins Centre for Molecular Biodiscovery New Zealand.,Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington Wellington New Zealand.,School of Chemical and Physical Sciences, Victoria University of Wellington Wellington New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington Wellington New Zealand .,Maurice Wilkins Centre for Molecular Biodiscovery New Zealand.,Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington Wellington New Zealand
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4
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Santana-Pereira ALR, Sandoval-Powers M, Monsma S, Zhou J, Santos SR, Mead DA, Liles MR. Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library. Front Microbiol 2020; 11:585398. [PMID: 33365020 PMCID: PMC7750434 DOI: 10.3389/fmicb.2020.585398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.
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Affiliation(s)
| | | | - Scott Monsma
- Lucigen Corporation, Middleton, WI, United States
| | - Jinglie Zhou
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Scott R. Santos
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - David A. Mead
- Varigen Biosciences Corporation, Madison, WI, United States
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Varigen Biosciences Corporation, Madison, WI, United States
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5
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Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences. Nat Commun 2019; 10:3848. [PMID: 31451725 PMCID: PMC6710260 DOI: 10.1038/s41467-019-11658-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/24/2019] [Indexed: 11/09/2022] Open
Abstract
Sequencing of DNA extracted from environmental samples can provide key insights into the biosynthetic potential of uncultured bacteria. However, the high complexity of soil metagenomes, which can contain thousands of bacterial species per gram of soil, imposes significant challenges to explore secondary metabolites potentially produced by rare members of the soil microbiome. Here, we develop a targeted sequencing workflow termed CONKAT-seq (co-occurrence network analysis of targeted sequences) that detects physically clustered biosynthetic domains, a hallmark of bacterial secondary metabolism. Following targeted amplification of conserved biosynthetic domains in a highly partitioned metagenomic library, CONKAT-seq evaluates amplicon co-occurrence patterns across library subpools to identify chromosomally clustered domains. We show that a single soil sample can contain more than a thousand uncharacterized biosynthetic gene clusters, most of which originate from low frequency genomes which are practically inaccessible through untargeted sequencing. CONKAT-seq allows scalable exploration of largely untapped biosynthetic diversity across multiple soils, and can guide the discovery of novel secondary metabolites from rare members of the soil microbiome.
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6
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Wu C, Shang Z, Lemetre C, Ternei MA, Brady SF. Cadasides, Calcium-Dependent Acidic Lipopeptides from the Soil Metagenome That Are Active against Multidrug-Resistant Bacteria. J Am Chem Soc 2019; 141:3910-3919. [PMID: 30735616 PMCID: PMC6592427 DOI: 10.1021/jacs.8b12087] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The growing threat of antibiotic resistance necessitates the discovery of antibiotics that are active against resistant pathogens. Calcium-dependent antibiotics are a small family of structurally diverse acidic lipopeptides assembled by nonribosomal peptide synthetases (NRPSs) that are known to display various modes of action against antibiotic-resistant pathogens. Here we use NRPS adenylation (AD) domain sequencing to guide the identification, recovery, and cloning of the cde biosynthetic gene cluster from a soil metagenome. Heterologous expression of the cde biosynthetic gene cluster led to the production of cadasides A (1) and B (2), a subfamily of acidic lipopeptides that is distinct from previously characterized calcium-dependent antibiotics in terms of both overall structure and acidic residue rich peptide core. The cadasides inhibit the growth of multidrug-resistant Gram-positive pathogens by disrupting cell wall biosynthesis in the presence of high concentrations of calcium. Interestingly, sequencing of AD domains from diverse soils revealed that sequences predicted to arise from cadaside-like gene clusters are predominantly found in soils containing high levels of calcium carbonate.
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Affiliation(s)
| | | | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065
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7
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Kim SH, Lu W, Ahmadi MK, Montiel D, Ternei MA, Brady SF. Atolypenes, Tricyclic Bacterial Sesterterpenes Discovered Using a Multiplexed In Vitro Cas9-TAR Gene Cluster Refactoring Approach. ACS Synth Biol 2019; 8:109-118. [PMID: 30575381 DOI: 10.1021/acssynbio.8b00361] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Most natural product biosynthetic gene clusters identified in bacterial genomic and metagenomic sequencing efforts are silent under laboratory growth conditions. Here, we describe a scalable biosynthetic gene cluster activation method wherein the gene clusters are disassembled at interoperonic regions in vitro using CRISPR/Cas9 and then reassembled with PCR-amplified, short DNAs, carrying synthetic promoters, using transformation assisted recombination (TAR) in yeast. This simple, cost-effective, and scalable method allows for the simultaneous generation of combinatorial libraries of refactored gene clusters, eliminating the need to understand the transcriptional hierarchy of the silent genes. In two test cases, this in vitro disassembly-TAR reassembly method was used to create collections of promoter-replaced gene clusters that were tested in parallel to identify versions that enabled secondary metabolite production. Activation of the atolypene ( ato) gene cluster led to the characterization of two unprecedented bacterial cyclic sesterterpenes, atolypene A (1) and B (2), which are moderately cytotoxic to human cancer cell lines. This streamlined in vitro disassembly- in vivo reassembly method offers a simplified approach for silent gene cluster refactoring that should facilitate the discovery of natural products from silent gene clusters cloned from either metagenomes or cultured bacteria.
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Affiliation(s)
- Seong-Hwan Kim
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Wanli Lu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Mahmoud Kamal Ahmadi
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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8
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High-Yield Production of Herbicidal Thaxtomins and Thaxtomin Analogs in a Nonpathogenic Streptomyces Strain. Appl Environ Microbiol 2018; 84:AEM.00164-18. [PMID: 29602787 DOI: 10.1128/aem.00164-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Thaxtomins are virulence factors of most plant-pathogenic Streptomyces strains. Due to their potent herbicidal activity, attractive environmental compatibility, and inherent biodegradability, thaxtomins are key active ingredients of bioherbicides approved by the U.S. Environmental Protection Agency. However, the low yield of thaxtomins in native Streptomyces producers limits their wide agricultural applications. Here, we describe the high-yield production of thaxtomins in a heterologous host. The thaxtomin gene cluster from S. scabiei 87.22 was cloned and expressed in S. albus J1074 after chromosomal integration. The production of thaxtomins and nitrotryptophan analogs was observed using liquid chromatography-mass spectrometry (LC-MS) analysis. When the engineered S. albus J1074 was cultured in the minimal medium Thx defined medium supplemented with 1% cellobiose (TDMc), the yield of the most abundant and herbicidal analog, thaxtomin A, was 10 times higher than that in S. scabiei 87.22, and optimization of the medium resulted in the highest yield of thaxtomin analogs at about 222 mg/liter. Further engineering of the thaxtomin biosynthetic gene cluster through gene deletion led to the production of multiple biosynthetic intermediates important to the chemical synthesis of new analogs. Additionally, the versatility of the thaxtomin biosynthetic system in S. albus J1074 was capitalized on to produce one unnatural fluorinated analog, 5-fluoro-thaxtomin A (5-F-thaxtomin A), whose structure was elucidated by a combination of MS and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) analyses. Natural and unnatural thaxtomins demonstrated potent herbicidal activity in radish seedling assays. These results indicated that S. albus J1074 has the potential to produce thaxtomins and analogs thereof with high yield, fostering their agricultural applications.IMPORTANCE Thaxtomins are agriculturally valuable herbicidal natural products, but the productivity of native producers is limiting. Heterologous expression of the thaxtomin gene cluster in S. albus J1074 resulted in the highest yield of thaxtomins ever reported, representing a significant leap forward in its wide agricultural use. Furthermore, current synthetic routes to thaxtomins and analogs are lengthy, and two thaxtomin biosynthetic intermediates produced at high yields in this work can provide precursors and building blocks to advanced synthetic routes. Importantly, the production of 5-F-thaxtomin A in engineered S. albus J1074 demonstrated a viable alternative to chemical methods in the synthesis of new thaxtomin analogs. Moreover, our work presents an attractive synthetic biology strategy to improve the supply of herbicidal thaxtomins, likely finding general applications in the discovery and production of many other bioactive natural products.
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9
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Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, Maniko J, Estrela AB, Molina H, Park S, Perlin DS, Brady SF. Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. Nat Microbiol 2018; 3:415-422. [PMID: 29434326 PMCID: PMC5874163 DOI: 10.1038/s41564-018-0110-1] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022]
Abstract
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide 1 . In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates2,3. As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome. In an effort to access these hidden NPs, we have developed a culture-independent NP discovery platform that involves sequencing, bioinformatic analysis and heterologous expression of biosynthetic gene clusters captured on DNA extracted from environmental samples. Here, we describe the application of this platform to the discovery of the malacidins, a distinctive class of antibiotics that are commonly encoded in soil microbiomes but have never been reported in culture-based NP discovery efforts. The malacidins are active against multidrug-resistant pathogens, sterilize methicillin-resistant Staphylococcus aureus skin infections in an animal wound model and did not select for resistance under our laboratory conditions.
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Affiliation(s)
- Bradley M Hover
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Seong-Hwan Kim
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Micah Katz
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Jeremy G Owen
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Jeffrey Maniko
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Andreia B Estrela
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Steven Park
- Public Health Research Institute, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - David S Perlin
- Public Health Research Institute, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA.
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10
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Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale. Proc Natl Acad Sci U S A 2017; 114:11615-11620. [PMID: 29078342 DOI: 10.1073/pnas.1710262114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts.
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11
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Zou X, Wang L, Li Z, Luo J, Wang Y, Deng Z, Du S, Chen S. Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics. Med Res Rev 2017; 38:229-260. [PMID: 28295439 DOI: 10.1002/med.21439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/06/2017] [Accepted: 01/14/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Xuan Zou
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Lianrong Wang
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Zhiqiang Li
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Jie Luo
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Yunfu Wang
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Zixin Deng
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Shiming Du
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Shi Chen
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
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12
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Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 2015; 43:129-41. [PMID: 26586404 DOI: 10.1007/s10295-015-1706-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.
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13
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Derewacz DK, Covington BC, McLean JA, Bachmann BO. Mapping Microbial Response Metabolomes for Induced Natural Product Discovery. ACS Chem Biol 2015; 10:1998-2006. [PMID: 26039241 DOI: 10.1021/acschembio.5b00001] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Intergeneric microbial interactions may originate a significant fraction of secondary metabolic gene regulation in nature. Herein, we expose a genomically characterized Nocardiopsis strain, with untapped polyketide biosynthetic potential, to intergeneric interactions via coculture with low inoculum exposure to Escherichia, Bacillus, Tsukamurella, and Rhodococcus. The challenge-induced responses of extracted metabolites were characterized via multivariate statistical and self-organizing map (SOM) analyses, revealing the magnitude and selectivity engendered by the limiting case of low inoculum exposure. The collected inventory of cocultures revealed substantial metabolomic expansion in comparison to monocultures with nearly 14% of metabolomic features in cocultures undetectable in monoculture conditions and many features unique to coculture genera. One set of SOM-identified responding features was isolated, structurally characterized by multidimensional NMR, and revealed to comprise previously unreported polyketides containing an unusual pyrrolidinol substructure and moderate and selective cytotoxicity. Designated ciromicin A and B, they are detected across mixed cultures with intergeneric preferences under coculture conditions. The structural novelty of ciromicin A is highlighted by its ability to undergo a diastereoselective photochemical 12-π electron rearrangement to ciromicin B at visible wavelengths. This study shows how organizing trends in metabolomic responses under coculture conditions can be harnessed to characterize multipartite cultures and identify previously silent secondary metabolism.
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Affiliation(s)
- Dagmara K. Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brett C. Covington
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O. Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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14
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Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters. Proc Natl Acad Sci U S A 2015; 112:8953-8. [PMID: 26150486 DOI: 10.1073/pnas.1507606112] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Large-scale sequencing of prokaryotic (meta)genomic DNA suggests that most bacterial natural product gene clusters are not expressed under common laboratory culture conditions. Silent gene clusters represent a promising resource for natural product discovery and the development of a new generation of therapeutics. Unfortunately, the characterization of molecules encoded by these clusters is hampered owing to our inability to express these gene clusters in the laboratory. To address this bottleneck, we have developed a promoter-engineering platform to transcriptionally activate silent gene clusters in a model heterologous host. Our approach uses yeast homologous recombination, an auxotrophy complementation-based yeast selection system and sequence orthogonal promoter cassettes to exchange all native promoters in silent gene clusters with constitutively active promoters. As part of this platform, we constructed and validated a set of bidirectional promoter cassettes consisting of orthogonal promoter sequences, Streptomyces ribosome binding sites, and yeast selectable marker genes. Using these tools we demonstrate the ability to simultaneously insert multiple promoter cassettes into a gene cluster, thereby expediting the reengineering process. We apply this method to model active and silent gene clusters (rebeccamycin and tetarimycin) and to the silent, cryptic pseudogene-containing, environmental DNA-derived Lzr gene cluster. Complete promoter refactoring and targeted gene exchange in this "dead" cluster led to the discovery of potent indolotryptoline antiproliferative agents, lazarimides A and B. This potentially scalable and cost-effective promoter reengineering platform should streamline the discovery of natural products from silent natural product biosynthetic gene clusters.
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Li Y, Li Z, Yamanaka K, Xu Y, Zhang W, Vlamakis H, Kolter R, Moore BS, Qian PY. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. Sci Rep 2015; 5:9383. [PMID: 25807046 PMCID: PMC4894447 DOI: 10.1038/srep09383] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/03/2015] [Indexed: 11/21/2022] Open
Abstract
Bacilli are ubiquitous low G+C environmental Gram-positive bacteria that produce a wide assortment of specialized small molecules. Although their natural product biosynthetic potential is high, robust molecular tools to support the heterologous expression of large biosynthetic gene clusters in Bacillus hosts are rare. Herein we adapt transformation-associated recombination (TAR) in yeast to design a single genomic capture and expression vector for antibiotic production in Bacillus subtilis. After validating this direct cloning “plug-and-play” approach with surfactin, we genetically interrogated amicoumacin biosynthetic gene cluster from the marine isolate Bacillus subtilis 1779. Its heterologous expression allowed us to explore an unusual maturation process involving the N-acyl-asparagine pro-drug intermediates preamicoumacins, which are hydrolyzed by the asparagine-specific peptidase into the active component amicoumacin A. This work represents the first direct cloning based heterologous expression of natural products in the model organism B. subtilis and paves the way to the development of future genome mining efforts in this genus.
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Affiliation(s)
- Yongxin Li
- 1] KAUST Global Collaborative Research, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong [2] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States
| | - Zhongrui Li
- KAUST Global Collaborative Research, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Kazuya Yamanaka
- 1] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States [2] JNC Corporation, Yokohama Research Center, 5-1 Okawa, Kanazawa-ku, Yokohama, Kanagawa 2368605, Japan
| | - Ying Xu
- KAUST Global Collaborative Research, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Weipeng Zhang
- KAUST Global Collaborative Research, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Hera Vlamakis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, United States
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, United States
| | - Bradley S Moore
- 1] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States [2] Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, United States
| | - Pei-Yuan Qian
- KAUST Global Collaborative Research, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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Kang HS, Brady SF. Mining soil metagenomes to better understand the evolution of natural product structural diversity: pentangular polyphenols as a case study. J Am Chem Soc 2014; 136:18111-9. [PMID: 25521786 PMCID: PMC4291760 DOI: 10.1021/ja510606j] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
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Sequence-guided
mining of metagenomic libraries provides a means
of recovering specific natural product gene clusters of interest from
the environment. In this study, we use ketosynthase gene (KS) PCR
amplicon sequences (sequence tags) to explore the structural and biosynthetic
diversities of pentangular polyphenols (PP). In phylogenetic analyses,
eDNA-derived sequence tags often fall between closely related clades
that are associated with gene clusters known to encode distinct chemotypes.
We show that these common “intermediate” sequence tags
are useful for guiding the discovery of not only novel bioactive metabolites
but also collections of closely related gene clusters that can provide
new insights into the evolution of natural product structural diversity.
Gene clusters corresponding to two eDNA-derived KSβ sequence tags that reside between well-defined KSβ clades associated with the biosynthesis of (C24)-pradimicin and
(C26)-xantholipin type metabolites were recovered from archived soil
eDNA libraries. Heterologous expression of these gene clusters in Streptomyces albus led to
the isolation of three new PPs (compounds 1–3). Calixanthomycin A (1) shows potent antiproliferative
activity against HCT-116 cells, whereas arenimycins C (2) and D (3) display potent antibacterial activity. By
comparing genotypes and chemotypes across all known PP gene clusters,
we define four PP subfamilies, and also observe that the horizontal
transfer of PP tailoring genes has likely been restricted to gene
clusters that encode closely related chemical structures, suggesting
that only a fraction of the “natural product-like” chemical
space that can theoretically be encoded by these secondary metabolite
tailoring genes has likely been sampled naturally.
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Affiliation(s)
- Hahk-Soo Kang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, Howard Hughes Medical Institute , 1230 York Avenue, New York, New York 10065, United States
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Kang HS, Brady SF. Arixanthomycins A-C: Phylogeny-guided discovery of biologically active eDNA-derived pentangular polyphenols. ACS Chem Biol 2014; 9:1267-72. [PMID: 24730509 PMCID: PMC4076013 DOI: 10.1021/cb500141b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Soil
microbiomes are a rich source of uncharacterized natural product biosynthetic
gene clusters. Here we use short conserved biosynthetic gene sequences
(natural product sequence tags) amplified from soil microbiomes as
phylogenetic markers to correlate genotype to chemotype and target
the discovery of novel bioactive pentangular polyphenols from the
environment. The heterologous expression of an environmental DNA-derived
gene cluster (the ARX cluster), whose ketosynthase beta (KSβ) sequence tag was phylogenetically distinct from any known KSβ sequence, led to the discovery of the arixanthomycins.
Arixanthomycin A (1) exhibits potent antiproliferative
activity against human cancer cell lines.
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Affiliation(s)
- Hahk-Soo Kang
- Howard
Hughes Medical Institute, Laboratory of Genetically Encoded Small
Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F. Brady
- Howard
Hughes Medical Institute, Laboratory of Genetically Encoded Small
Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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