1
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Rosenzweig A, Spotton K, Bhattacharjee A, Morales-Amador A, Brady SF. Identification of an Optimized Clinical Development Candidate from Cilagicin, an Antibiotic That Evades Resistance by Dual Polyprenyl Phosphate Binding. ACS Infect Dis 2024; 10:1536-1544. [PMID: 38626307 DOI: 10.1021/acsinfecdis.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Cilagicin is a dual polyprenyl phosphate binding lipodepsipeptide antibiotic with strong activity against clinically relevant Gram-positive pathogens while evading antibiotic resistance. Cilagicin showed high serum binding that reduced its in vivo efficacy. Cilagicin-BP, which contains a biphenyl moiety in place of the N-terminal myristic acid found on cilagicin, showed reduced serum binding and increased in vivo efficacy but decreased potency against some pathogens. Here, we manipulated the acyl tail and the peptide core of cilagicin to identify an optimized collection of structural features that maintain potent antibiotic activity against a wide range of pathogens in the presence of serum. This led to the identification of the optimized antibiotic dodecacilagicin, which contains an N-terminal dodecanoic acid. Dodecacilagicin exhibits low MICs against clinically relevant pathogens in the presence of serum, retains polyprenyl phosphate binding, and evades resistance development even after long-term antibiotic exposure, making dodecacilagicin an appealing candidate for further therapeutic development.
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Affiliation(s)
- Adam Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, New York 10065, United States
| | - Kaylyn Spotton
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, New York 10065, United States
| | - Abir Bhattacharjee
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Adrián Morales-Amador
- 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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2
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Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA. DNA glycosylases provide antiviral defence in prokaryotes. Nature 2024; 629:410-416. [PMID: 38632404 PMCID: PMC11078745 DOI: 10.1038/s41586-024-07329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Bacteria have adapted to phage predation by evolving a vast assortment of defence systems1. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data2. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library3 with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.
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Affiliation(s)
- Amer A Hossain
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Ying Z Pigli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexis Thomas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Vincent K Libis
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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3
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Wang Z, Kasper A, Takahashi M, Amador AM, Bhattacharjee A, Kan J, Hernandez Y, Ternei M, Brady SF. Tapcin, an In Vivo Active Dual Topoisomerase I/II Inhibitor Discovered by Synthetic Bioinformatic Natural Product (Syn-BNP)-Coupled Metagenomics. Angew Chem Int Ed Engl 2024; 63:e202317187. [PMID: 38231130 PMCID: PMC11018531 DOI: 10.1002/anie.202317187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
DNA topoisomerases are attractive targets for anticancer agents. Dual topoisomerase I/II inhibitors are particularly appealing due to their reduced rates of resistance. A number of therapeutically relevant topoisomerase inhibitors are bacterial natural products. Mining the untapped chemical diversity encoded by soil microbiomes presents an opportunity to identify additional natural topoisomerase inhibitors. Here we couple metagenome mining, bioinformatic structure prediction algorithms, and chemical synthesis to produce the dual topoisomerase inhibitor tapcin. Tapcin is a mixed p-aminobenzoic acid (PABA)-thiazole with a rare tri-thiazole substructure and picomolar antiproliferative activity. Tapcin reduced colorectal adenocarcinoma HT-29 cell proliferation and tumor volume in mouse hollow fiber and xenograft models, respectively. In both studies it showed similar activity to the clinically used topoisomerase I inhibitor irinotecan. The study suggests that the interrogation of soil microbiomes using synthetic bioinformatic natural product methods has the potential to be a rewarding strategy for identifying potent, biomedically relevant, antiproliferative agents.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Mai Takahashi
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Adrian Morales Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Abir Bhattacharjee
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Jingbo Kan
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
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4
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Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Author Correction: Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2024; 625:E3. [PMID: 38052939 PMCID: PMC10764284 DOI: 10.1038/s41586-023-06929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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5
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Rosenzweig AF, Wang Z, Morales-Amador A, Spotton K, Brady SF. A Family of Antibiotics That Evades Resistance by Binding Polyprenyl Phosphates. ACS Infect Dis 2023; 9:2394-2400. [PMID: 37937847 PMCID: PMC10904333 DOI: 10.1021/acsinfecdis.3c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Cilagicin is a Gram-positive active antibiotic that has a dual polyprenyl phosphate binding mechanism that impedes resistance development. Here we bioinformatically screened predicted non-ribosomal polypeptide synthetase encoded structures to search for antibiotics that might similarly avoid resistance development. Synthesis and bioactivity screening of the predicted structures that we identified led to three antibiotics that are active against multidrug-resistant Gram-positive pathogens, two of which, paenilagicin and virgilagicin, did not lead to resistance even after prolonged antibiotic exposure.
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Affiliation(s)
- Adam F Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Adrián Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Kaylyn Spotton
- 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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6
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Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2023; 623:1001-1008. [PMID: 37968393 PMCID: PMC10686824 DOI: 10.1038/s41586-023-06743-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.
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Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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7
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Rosenzweig AF, Burian J, Brady SF. Present and future outlooks on environmental DNA-based methods for antibiotic discovery. Curr Opin Microbiol 2023; 75:102335. [PMID: 37327680 PMCID: PMC11076179 DOI: 10.1016/j.mib.2023.102335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
Abstract
Novel antibiotics are in constant demand to combat a global increase in antibiotic-resistant infections. Bacterial natural products have been a long-standing source of antibiotic compounds, and metagenomic mining of environmental DNA (eDNA) has increasingly provided new antibiotic leads. The metagenomic small-molecule discovery pipeline can be divided into three main steps: surveying eDNA, retrieving a sequence of interest, and accessing the encoded natural product. Improvements in sequencing technology, bioinformatic algorithms, and methods for converting biosynthetic gene clusters into small molecules are steadily increasing our ability to discover metagenomically encoded antibiotics. We predict that, over the next decade, ongoing technological improvements will dramatically increase the rate at which antibiotics are discovered from metagenomes.
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Affiliation(s)
- Adam F Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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8
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Burian J, Libis VK, Hernandez YA, Guerrero-Porras L, Ternei MA, Brady SF. High-throughput retrieval of target sequences from complex clone libraries using CRISPRi. Nat Biotechnol 2023; 41:626-630. [PMID: 36411313 PMCID: PMC11042918 DOI: 10.1038/s41587-022-01531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022]
Abstract
The capture of metagenomic DNA in large clone libraries provides the opportunity to study microbial diversity that is inaccessible using culture-dependent methods. In this study, we harnessed nuclease-deficient Cas9 to establish a CRISPR counter-selection interruption circuit (CCIC) that can be used to retrieve target clones from complex libraries. Combining modern sequencing methods with CCIC cloning allows for rapid physical access to the genetic diversity present in natural ecosystems.
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Affiliation(s)
- Ján Burian
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Vincent K Libis
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Yozen A Hernandez
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Liliana Guerrero-Porras
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA.
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9
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Wang Z, Koirala B, Hernandez Y, Brady SF. Discovery of Paenibacillaceae Family Gram-Negative-Active Cationic Lipopeptide Antibiotics Using Evolution-Guided Chemical Synthesis. Org Lett 2022; 24:4943-4948. [PMID: 35776528 DOI: 10.1021/acs.orglett.2c01879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cationic nonribosomal lipopeptides (CNRLPs) from Paenibacillus spp. have been a rewarding source of Gram-negative-active antibiotics. Here we systematically screened sequenced bacterial genomes for CNRLP biosynthetic gene clusters (BGCs) that we predicted might encode additional Gram-negative-active antibiotics. Total chemical synthesis of the bioinformatically predicted products of seven such BGCs led to our identification of new laterocidine, tridecaptin, and paenibacterin-like antibiotics with potent activity against both multiple-drug-resistant Gram-negative and Gram-positive pathogens.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Yozen Hernandez
- 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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10
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Cohen LJ, Han SM, Lau P, Guisado D, Liang Y, Nakashige TG, Ali T, Chiang D, Rahman A, Brady SF. Unraveling function and diversity of bacterial lectins in the human microbiome. Nat Commun 2022; 13:3101. [PMID: 35661736 PMCID: PMC9166713 DOI: 10.1038/s41467-022-29949-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/07/2022] [Indexed: 11/08/2022] Open
Abstract
The mechanisms by which commensal organisms affect human physiology remain poorly understood. Lectins are non-enzymatic carbohydrate binding proteins that all organisms employ as part of establishing a niche, evading host-defenses and protecting against pathogens. Although lectins have been extensively studied in plants, bacterial pathogens and human immune cells for their role in disease pathophysiology and as therapeutics, the role of bacterial lectins in the human microbiome is largely unexplored. Here we report on the characterization of a lectin produced by a common human associated bacterium that interacts with myeloid cells in the blood and intestine. In mouse and cell-based models, we demonstrate that this lectin induces distinct immunologic responses in peripheral and intestinal leukocytes and that these responses are specific to monocytes, macrophages and dendritic cells. Our analysis of human microbiota sequencing data reveal thousands of unique sequences that are predicted to encode lectins, many of which are highly prevalent in the human microbiome yet completely uncharacterized. Based on the varied domain architectures of these lectins we predict they will have diverse effects on the human host. The systematic investigation of lectins in the human microbiome should improve our understanding of human health and provide new therapeutic opportunities.
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Affiliation(s)
- Louis J Cohen
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Sun M Han
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pearson Lau
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Guisado
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yupu Liang
- Rockefeller University, New York, NY, USA
| | - Toshiki G Nakashige
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Thamina Ali
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - David Chiang
- Division of Internal Medicine-Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Adeeb Rahman
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA.
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11
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Wang Z, Koirala B, Hernandez Y, Zimmerman M, Brady SF. Bioinformatic prospecting and synthesis of a bifunctional lipopeptide antibiotic that evades resistance. Science 2022; 376:991-996. [PMID: 35617397 PMCID: PMC10904332 DOI: 10.1126/science.abn4213] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Emerging resistance to currently used antibiotics is a global public health crisis. Because most of the biosynthetic capacity within the bacterial kingdom has remained silent in previous antibiotic discovery efforts, uncharacterized biosynthetic gene clusters found in bacterial genome-sequencing studies remain an appealing source of antibiotics with distinctive modes of action. Here, we report the discovery of a naturally inspired lipopeptide antibiotic called cilagicin, which we chemically synthesized on the basis of a detailed bioinformatic analysis of the cil biosynthetic gene cluster. Cilagicin's ability to sequester two distinct, indispensable undecaprenyl phosphates used in cell wall biosynthesis, together with the absence of detectable resistance in laboratory tests and among multidrug-resistant clinical isolates, makes it an appealing candidate for combating antibiotic-resistant pathogens.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Matthew Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
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12
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Wang Z, Forelli N, Hernandez Y, Ternei M, Brady SF. Lapcin, a potent dual topoisomerase I/II inhibitor discovered by soil metagenome guided total chemical synthesis. Nat Commun 2022; 13:842. [PMID: 35149673 PMCID: PMC8837603 DOI: 10.1038/s41467-022-28292-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/21/2023] Open
Abstract
In natural product discovery programs, the power of synthetic chemistry is often leveraged for the total synthesis and diversification of characterized metabolites. The synthesis of structures that are bioinformatically predicted to arise from uncharacterized biosynthetic gene clusters (BGCs) provides a means for synthetic chemistry to enter this process at an early stage. The recent identification of non-ribosomal peptides (NRPs) containing multiple ρ-aminobenzoic acids (PABAs) led us to search soil metagenomes for BGCs that polymerize PABA. Here, we use PABA-specific adenylation-domain sequences to guide the cloning of the lap BGC directly from soil. This BGC was predicted to encode a unique N-acylated PABA and thiazole containing structure. Chemical synthesis of this structure gave lapcin, a dual topoisomerase I/II inhibitor with nM to pM IC50s against diverse cancer cell lines. The discovery of lapcin highlights the power of coupling metagenomics, bioinformatics and total chemical synthesis to unlock the biosynthetic potential contained in even complex uncharacterized BGCs. Chemical synthesis of secondary metabolites isolated from nature, and derivatives thereof, is still a paradigm of significance to drug development. Here the authors instead use bioinformatics to analyze a biosynthetic gene cluster found in the soil metagenome, and chemical synthesis of its predict product to produce lapcin, a dual topoisomerase I/II inhibitor with promising activity against cancer cell lines.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA.
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13
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Peek J, Koirala B, Brady SF. Synthesis and evaluation of dual-action kanglemycin-fluoroquinolone hybrid antibiotics. Bioorg Med Chem Lett 2022; 57:128484. [PMID: 34861348 PMCID: PMC8779240 DOI: 10.1016/j.bmcl.2021.128484] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/12/2021] [Accepted: 11/25/2021] [Indexed: 02/03/2023]
Abstract
Bacterial resistance threatens the utility of currently available antibiotics. Rifampicin, a cornerstone in the treatment of persistent Gram-positive infections, is prone to the development of resistance resulting from single point mutations in the antibiotic's target, RNA polymerase. One strategy to circumvent resistance is the use of 'hybrid' antibiotics consisting of two covalently linked antibiotic entities. These compounds generally have two distinct cellular targets, reducing the probability of resistance development and potentially providing simplified pharmacological properties compared to combination therapies using the individual antibiotics. Here we evaluate a series of semi-synthetic hybrid antibiotics formed by linking kanglemycin A (Kang A), a rifampicin analog, and a collection of fluoroquinolones. Kang A is a natural product antibiotic which contains a novel dimethyl succinic acid moiety that offers a new attachment point for the synthesis of hybrid antibiotics. We compare the activity of the Kang A hybrids generated via the acid attachment point to a series of hybrids linked at the compound's naphthoquinone ring system. Several hybrids exhibit activity against bacteria resistant to Kang A via the action of the partnered antibiotic, suggesting that the Kang scaffold may provide new avenues for generating antibiotics effective against drug-resistant infections.
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Affiliation(s)
| | | | - Sean F. Brady
- Corresponding Author: Sean F. Brady, Contact: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, Phone: 212-327-8280, Fax: 212-327-8281,
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14
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Li L, Koirala B, Hernandez Y, MacIntyre LW, Ternei MA, Russo R, Brady SF. Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens. Nat Microbiol 2022; 7:120-131. [PMID: 34949828 PMCID: PMC8732328 DOI: 10.1038/s41564-021-01013-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
The emergence of multidrug-resistant bacteria poses a threat to global health and necessitates the development of additional in vivo active antibiotics with diverse modes of action. Directly targeting menaquinone (MK), which plays an important role in bacterial electron transport, is an appealing, yet underexplored, mode of action due to a dearth of MK-binding molecules. Here we combine sequence-based metagenomic mining with a motif search of bioinformatically predicted natural product structures to identify six biosynthetic gene clusters that we predicted encode MK-binding antibiotics (MBAs). Their predicted products (MBA1-6) were rapidly accessed using a synthetic bioinformatic natural product approach, which relies on bioinformatic structure prediction followed by chemical synthesis. Among these six structurally diverse MBAs, four make up two new MBA structural families. The most potent member of each new family (MBA3, MBA6) proved effective at treating methicillin-resistant Staphylococcus aureus infection in a murine peritonitis-sepsis model. The only conserved feature present in all MBAs is the sequence 'GXLXXXW', which we propose represents a minimum MK-binding motif. Notably, we found that a subset of MBAs were active against Mycobacterium tuberculosis both in vitro and in macrophages. Our findings suggest that naturally occurring MBAs are a structurally diverse and untapped class of mechanistically interesting, in vivo active antibiotics.
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Affiliation(s)
- Lei Li
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Logan W MacIntyre
- 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
| | - Riccardo Russo
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, 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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15
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Wang Z, Kasper A, Mehmood R, Ternei M, Li S, Freundlich JS, Brady SF. Metagenome-Guided Analogue Synthesis Yields Improved Gram-Negative-Active Albicidin- and Cystobactamid-Type Antibiotics. Angew Chem Int Ed Engl 2021; 60:22172-22177. [PMID: 34355488 DOI: 10.1002/anie.202104874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/05/2021] [Indexed: 11/11/2022]
Abstract
Natural products are a major source of new antibiotics. Here we utilize biosynthetic instructions contained within metagenome-derived congener biosynthetic gene clusters (BGCs) to guide the synthesis of improved antibiotic analogues. Albicidin and cystobactamid are the first members of a new class of broad-spectrum ρ-aminobenzoic acid (PABA)-based antibiotics. Our search for PABA-specific adenylation domain sequences in soil metagenomes revealed that BGCs in this family are common in nature. Twelve BGCs that were bio-informatically predicted to encode six new congeners were recovered from soil metagenomic libraries. Synthesis of these six predicted structures led to the identification of potent antibiotics with changes in their spectrum of activity and the ability to circumvent resistance conferred by endopeptidase cleavage enzymes.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Rabia Mehmood
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Shaogang Li
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ, 07103, USA
| | - Joel S Freundlich
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ, 07103, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
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16
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Piscotta FJ, Whitfield ST, Nakashige TG, Estrela AB, Ali T, Brady SF. Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state. Cell Rep 2021; 36:109746. [PMID: 34551287 PMCID: PMC8480279 DOI: 10.1016/j.celrep.2021.109746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/19/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
The human microbiota plays a critical role in host health. Proper development of the infant microbiome is particularly important. Its dysbiosis leads to both short-term health issues and long-term disorders lasting into adulthood. A central way in which the microbiome interacts with the host is through the production of effector molecules, such as proteins and small molecules. Here, a metagenomic library constructed from 14 infant stool microbiomes is analyzed for the production of effectors that modulate three distinct host pathways: immune response (nuclear factor κB [NF-κB] activation), autophagy (LC3-B puncta formation), and redox potential (NADH:NAD ratio). We identify microbiome-encoded bioactive metabolites, including commendamide and hydrogen sulfide and their associated biosynthetic genes, as well as a previously uncharacterized autophagy-inducing operon from Klebsiella spp. This work extends our understanding of microbial effector molecules that are known to influence host pathways. Parallel functional screening of metagenomic libraries can be easily expanded to investigate additional host processes. Construction of a metagenomic library from stool of infants A multiplexed screen for bacterial effectors of host cellular processes Identification of microbiome-encoded effectors hydrogen sulfide and commendamide The products of a Klebsiella pneumoniae operon induce autophagy
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Affiliation(s)
- Frank J Piscotta
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Shawn T Whitfield
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Toshiki G Nakashige
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Andreia B Estrela
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Thahmina Ali
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
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17
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Wang Z, Kasper A, Mehmood R, Ternei M, Li S, Freundlich JS, Brady SF. Metagenome‐Guided Analogue Synthesis Yields Improved Gram‐Negative‐Active Albicidin‐ and Cystobactamid‐Type Antibiotics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Rabia Mehmood
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Shaogang Li
- Department of Medicine, Center for Emerging and Re-emerging Pathogens Rutgers University—New Jersey Medical School Newark NJ 07103 USA
| | - Joel S. Freundlich
- Department of Medicine, Center for Emerging and Re-emerging Pathogens Rutgers University—New Jersey Medical School Newark NJ 07103 USA
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
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18
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Li L, Maclntyre LW, Brady SF. Refactoring biosynthetic gene clusters for heterologous production of microbial natural products. Curr Opin Biotechnol 2021; 69:145-152. [PMID: 33476936 PMCID: PMC8238852 DOI: 10.1016/j.copbio.2020.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/03/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023]
Abstract
Microbial natural products (NPs) are of paramount importance in human medicine, animal health and plant crop protection. Large-scale microbial genome and metagenomic mining has revealed tremendous biosynthetic potential to produce new NPs. However a majority of NP biosynthetic gene clusters (BGCs) are functionally inaccessible under standard laboratory conditions. BGC refactoring and heterologous expression provide a promising synthetic biology approach to NP discovery, yield optimization and combinatorial biosynthesis studies. In this review, we summarize the recent advances pertaining to the heterologous production of bacterial and fungal NPs, with an emphasis on next-generation transcriptional regulatory modules, novel BGC refactoring techniques and optimized heterologous hosts.
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Affiliation(s)
- Lei Li
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Logan W Maclntyre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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19
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Li L, MacIntyre LW, Ali T, Russo R, Koirala B, Hernandez Y, Brady SF. Biosynthetic Interrogation of Soil Metagenomes Reveals Metamarin, an Uncommon Cyclomarin Congener with Activity against Mycobacterium tuberculosis. J Nat Prod 2021; 84:1056-1066. [PMID: 33621083 PMCID: PMC8068612 DOI: 10.1021/acs.jnatprod.0c01104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Indexed: 05/21/2023]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases. Unfortunately, the development of antibiotic resistance threatens our current therapeutic arsenal, which has necessitated the discovery and development of novel antibiotics against drug-resistant Mycobacterium tuberculosis (Mtb). Cyclomarin A and rufomycin I are structurally related cyclic heptapeptides assembled by nonribosomal peptide synthetases (NRPSs), which show potent anti-Mtb activity with a new cellular target, the caseinolytic protein ClpC1. An NRPS adenylation domain survey using DNA extracted from ∼2000 ecologically diverse soils found low cyclomarin/rufomycin biosynthetic diversity. In this survey, a family of cyclomarin/rufomycin-like biosynthetic gene clusters (BGC) that encode metamarin, an uncommon cyclomarin congener with potent activity against both Mtb H37Rv and multidrug-resistant Mtb clinical isolates was identified. Metamarin effectively inhibits Mtb growth in murine macrophages and increases the activities of ClpC1 ATPase and the associated ClpC1/P1/P2 protease complex, thus causing cell death by uncontrolled protein degradation.
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Affiliation(s)
- Lei Li
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Logan W. MacIntyre
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thahmina Ali
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Riccardo Russo
- Rutgers,
The State University of New Jersey, International Center for Public Health, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Bimal Koirala
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Yozen Hernandez
- 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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20
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Sun Z, Shang Z, Forelli N, Po KHL, Chen S, Brady SF, Li X. Total Synthesis of Malacidin A by β‐Hydroxyaspartic Acid Ligation‐Mediated Cyclization and Absolute Structure Establishment. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhenquan Sun
- Department of Chemistry State Key Laboratory of Synthetic Chemistry The University of Hong Kong Hong Kong SAR 999077 P. R. China
| | - Zhuo Shang
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University New York NY 10065 USA
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University New York NY 10065 USA
| | - Kathy Hiu Laam Po
- Department of Infectious Diseases and Public Health The City University of Hong Kong Hong Kong SAR 999077 P. R. China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health The City University of Hong Kong Hong Kong SAR 999077 P. R. China
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University New York NY 10065 USA
| | - Xuechen Li
- Department of Chemistry State Key Laboratory of Synthetic Chemistry The University of Hong Kong Hong Kong SAR 999077 P. R. China
- Laboratory for Marine Drugs and Bioproducts Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 P. R. China
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21
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Peek J, Xu J, Wang H, Suryavanshi S, Zimmerman M, Russo R, Park S, Perlin DS, Brady SF. A Semisynthetic Kanglemycin Shows In Vivo Efficacy against High-Burden Rifampicin Resistant Pathogens. ACS Infect Dis 2020; 6:2431-2440. [PMID: 32786275 PMCID: PMC7497472 DOI: 10.1021/acsinfecdis.0c00223] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Semisynthetic rifamycin
derivatives such as rifampicin (Rif) are first line treatments for
tuberculosis and other bacterial infections. Historically, synthetic
modifications made to the C-3/C-4 region of the rifamycin naphthalene
core, like those seen in Rif, have yielded the biggest improvements
in pharmacological properties. However, modifications found in natural
product rifamycin congeners occur at other positions in the structure.
The kanglemycins (Kangs) are a family of rifamycin congeners with
a unique collection of natural modifications including a dimethylsuccinic
acid appended to their polyketide backbone. These modifications confer
activity against the single most common clinically relevant Rif resistance
(RifR) mutation in the antibiotic’s target, the
bacterial RNA polymerase (RNAP). Here we evaluate the in vivo efficacy
of Kang A, the parent compound in the Kang family, in a murine model
of bacterial peritonitis/sepsis. We then set out to improve its potency
by combining its natural tailoring modifications with semisynthetic
derivatizations at either its acid moiety or in the C-3/C-4 region.
A collection of C-3/C-4 benzoxazino Kang derivatives exhibit improved
activity against wild-type bacteria, and acquire activity against
the second most common clinically relevant RifR mutation.
The semisynthetic analogue 3′-hydroxy-5′-[4-isobutyl-1-piperazinyl]
benzoxazino Kang A (Kang KZ) protected mice against infection with
either Rif sensitive MRSA or a highly virulent RifRStaphylococcus aureus strain in a neutropenic peritonitis/sepsis
model and led to reduced bacterial burdens. The compounds generated
in this study may represent promising candidates for treating RifR infections.
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Affiliation(s)
- James Peek
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Jiayi Xu
- Tri-Institutional Therapeutics Discovery Institute, Belfer Research Building, 413 E 69th Street, New York, New York 10021, United States
| | - Han Wang
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Shraddha Suryavanshi
- Rutgers, The State University of New Jersey, International Center for Public Health, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Matthew Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Riccardo Russo
- Rutgers, The State University of New Jersey, International Center for Public Health, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, United States
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, 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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22
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Sun Z, Shang Z, Forelli N, Po KHL, Chen S, Brady SF, Li X. Total Synthesis of Malacidin A by β-Hydroxyaspartic Acid Ligation-Mediated Cyclization and Absolute Structure Establishment. Angew Chem Int Ed Engl 2020; 59:19868-19872. [PMID: 32725837 DOI: 10.1002/anie.202009092] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 11/08/2022]
Abstract
The development of novel antibiotics is critical to combating the growing emergence of drug-resistant pathogens. Malacidin A is a new member of the calcium-dependent antibiotic (CDAs) family with activity against antibiotic-resistant pathogens. Its mode of action is distinct from classical CDAs. However, the absolute structure of malacidin A has not been established. Herein, the total syntheses of malacidin A and its analogues are reported by a combination of Fmoc-based solid-phase peptide synthesis (SPPS) and β-hydroxyaspartic acid ligation-mediated peptide cyclization. The total synthesis enabled us to establish the absolute configuration of malacidin A, which is in agreement with those for natural malacidin A confirmed by advanced Marfey's analysis in our study.
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Affiliation(s)
- Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, 999077, P. R. China
| | - Zhuo Shang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, 10065, USA
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, 10065, USA
| | - Kathy Hiu Laam Po
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, SAR, 999077, P. R. China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, SAR, 999077, P. R. China
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, 10065, USA
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, 999077, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
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23
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Chu J, Koirala B, Forelli N, Vila-Farres X, Ternei MA, Ali T, Colosimo DA, Brady SF. Synthetic-Bioinformatic Natural Product Antibiotics with Diverse Modes of Action. J Am Chem Soc 2020; 142:14158-14168. [PMID: 32697091 DOI: 10.1021/jacs.0c04376] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have inspired the development of numerous antibiotics in use today. As resistance to existing antibiotics has become more prevalent, new antibiotic lead structures and activities are desperately needed. An increasing number of natural product biosynthetic gene clusters, to which no known molecules can be assigned, are found in genome and metagenome sequencing data. Here we access structural information encoded in this underexploited resource using a synthetic-bioinformatic natural product (syn-BNP) approach, which relies on bioinformatic algorithms followed by chemical synthesis to predict and then produce small molecules inspired by biosynthetic gene clusters. In total, 157 syn-BNP cyclic peptides inspired by 96 nonribosomal peptide synthetase gene clusters were synthesized and screened for antibacterial activity. This yielded nine antibiotics with activities against ESKAPE pathogens as well as Mycobacterium tuberculosis. Not only are antibiotic-resistant pathogens susceptible to many of these syn-BNP antibiotics, but they were also unable to develop resistance to these antibiotics in laboratory experiments. Characterized modes of action for these antibiotics include cell lysis, membrane depolarization, inhibition of cell wall biosynthesis, and ClpP protease dysregulation. Increasingly refined syn-BNP-based explorations of biosynthetic gene clusters should allow for more rapid identification of evolutionarily inspired bioactive small molecules, in particular antibiotics with diverse mechanism of actions that could help confront the imminent crisis of antimicrobial resistance.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Xavier Vila-Farres
- 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
| | - Thahmina Ali
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Dominic A Colosimo
- 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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24
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Estrela AB, Nakashige TG, Lemetre C, Woodworth ID, Weisman JL, Cohen LJ, Brady SF. Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors. mBio 2019; 10:e02587-19. [PMID: 31744921 PMCID: PMC6867899 DOI: 10.1128/mbio.02587-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/29/2022] Open
Abstract
The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes.IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.
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Affiliation(s)
- Andreia B Estrela
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Toshiki G Nakashige
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Ian D Woodworth
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Jazz L Weisman
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Louis J Cohen
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
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25
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Chu J, Vila-Farres X, Brady SF. Bioactive Synthetic-Bioinformatic Natural Product Cyclic Peptides Inspired by Nonribosomal Peptide Synthetase Gene Clusters from the Human Microbiome. J Am Chem Soc 2019; 141:15737-15741. [PMID: 31545899 DOI: 10.1021/jacs.9b07317] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioinformatic analysis of sequenced bacterial genomes has uncovered an increasing number of natural product biosynthetic gene clusters (BGCs) to which no known bacterial metabolite can be ascribed. One emerging method we have investigated for studying these BGCs is the synthetic-Bioinformatic Natural Product (syn-BNP) approach. The syn-BNP approach replaces transcription, translation, and in vivo enzymatic biosynthesis of natural products with bioinformatic algorithms to predict the output of a BGC and in vitro chemical synthesis to produce the predicted structure. Here we report on expanding the syn-BNP approach to the design and synthesis of cyclic peptides inspired by nonribosomal peptide synthetase BGCs associated with the human microbiota. While no syn-BNPs we tested inhibited the growth of bacteria or yeast, five were found to be active in the human cell-based MTT metabolic activity assay. Interestingly, active peptides were mostly inspired by BGCs found in the genomes of opportunistic pathogens that are often more commonly associated with environments outside the human microbiome. The cyclic syn-BNP studies presented here provide further evidence of its potential for identifying bioactive small molecules directly from the instructions encoded in the primary sequences of natural product BGCs.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
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26
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Colosimo DA, Kohn JA, Luo PM, Piscotta FJ, Han SM, Pickard AJ, Rao A, Cross JR, Cohen LJ, Brady SF. Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors. Cell Host Microbe 2019; 26:273-282.e7. [PMID: 31378678 PMCID: PMC6706627 DOI: 10.1016/j.chom.2019.07.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/09/2019] [Accepted: 07/11/2019] [Indexed: 02/07/2023]
Abstract
Despite evidence linking the human microbiome to health and disease, how the microbiota affects human physiology remains largely unknown. Microbiota-encoded metabolites are expected to play an integral role in human health. Therefore, assigning function to these metabolites is critical to understanding these complex interactions and developing microbiota-inspired therapies. Here, we use large-scale functional screening of molecules produced by individual members of a simplified human microbiota to identify bacterial metabolites that agonize G-protein-coupled receptors (GPCRs). Multiple metabolites, including phenylpropanoic acid, cadaverine, 9-10-methylenehexadecanoic acid, and 12-methyltetradecanoic acid, were found to interact with GPCRs associated with diverse functions within the nervous and immune systems, among others. Collectively, these metabolite-receptor pairs indicate that diverse aspects of human health are potentially modulated by structurally simple metabolites arising from primary bacterial metabolism. Metabolite library from human microbiota screened for direct agonism of 241 GPCRs Taxa-specific primary metabolites agonize individual GPCRs or broad GPCR families Bacteria agonize receptors linked to metabolism, neurotransmission, and immunity Simple bacterial metabolites may play a role in modulating host pathways
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Affiliation(s)
- Dominic A Colosimo
- Laboratory of Genetically Encoded Small Molecules, the Rockefeller University, 1230 York Avenue, New York City, NY 10065, USA
| | - Jeffrey A Kohn
- Laboratory of Genetically Encoded Small Molecules, the Rockefeller University, 1230 York Avenue, New York City, NY 10065, USA
| | - Peter M Luo
- Laboratory of Genetically Encoded Small Molecules, the Rockefeller University, 1230 York Avenue, New York City, NY 10065, USA
| | - Frank J Piscotta
- Laboratory of Genetically Encoded Small Molecules, the Rockefeller University, 1230 York Avenue, New York City, NY 10065, USA
| | - Sun M Han
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Amanda J Pickard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York City, NY 10065, USA
| | - Arka Rao
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York City, NY 10065, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York City, NY 10065, USA
| | - Louis J Cohen
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, the Rockefeller University, 1230 York Avenue, New York City, NY 10065, USA.
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27
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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 DOI: 10.1021/jacs.8b12087] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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)
- Changsheng Wu
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Zhuo Shang
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF. Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun 2018; 9:4147. [PMID: 30297823 PMCID: PMC6175910 DOI: 10.1038/s41467-018-06587-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/25/2022] Open
Abstract
Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
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Affiliation(s)
- James Peek
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Ian Woodworth
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Danziger
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Thulasi Warrier
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kohta Saito
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathaniel Braffman
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | | | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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30
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Cohen LJ, Esterhazy D, Kim SH, Lemetre C, Aguilar RR, Gordon EA, Pickard AJ, Cross JR, Emiliano AB, Han SM, Chu J, Vila-Farres X, Kaplitt J, Rogoz A, Calle PY, Hunter C, Bitok JK, Brady SF. Erratum: Corrigendum: Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 2018; 556:135. [DOI: 10.1038/nature25997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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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: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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Bitok JK, Lemetre C, Ternei MA, Brady SF. Identification of biosynthetic gene clusters from metagenomic libraries using PPTase complementation in a Streptomyces host. FEMS Microbiol Lett 2018; 364:3983257. [PMID: 28817927 DOI: 10.1093/femsle/fnx155] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/19/2017] [Indexed: 01/08/2023] Open
Abstract
The majority of environmental bacteria are not readily cultured in the lab, leaving the natural products they make inaccessible using culture-dependent discovery methods. Cloning and heterologous expression of DNA extracted from environmental samples (environmental DNA, eDNA) provides a means of circumventing this discovery bottleneck. To facilitate the identification of clones containing biosynthetic gene clusters, we developed a model heterologous expression reporter strain Streptomyces albus::bpsA ΔPPTase. This strain carries a 4΄-phosphopantetheinyl transferase (PPTase)-dependent blue pigment synthase A gene, bpsA, in a PPTase deletion background. eDNA clones that express a functional PPTase restore production of the blue pigment, indigoidine. As PPTase genes often occur in biosynthetic gene clusters (BGCs), indigoidine production can be used to identify eDNA clones containing BGCs. We screened a soil eDNA library hosted in S. albus::bpsA ΔPPTase and identified clones containing non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS) and mixed NRPS/PKS biosynthetic gene clusters. One NRPS gene cluster was shown to confer the production of myxochelin A to S. albus::bpsA ΔPPTase.
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Affiliation(s)
- J Kipchirchir Bitok
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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33
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Chu J, Vila-Farres X, Inoyama D, Gallardo-Macias R, Jaskowski M, Satish S, Freundlich JS, Brady SF. Human Microbiome Inspired Antibiotics with Improved β-Lactam Synergy against MDR Staphylococcus aureus. ACS Infect Dis 2018; 4:33-38. [PMID: 28845973 DOI: 10.1021/acsinfecdis.7b00056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The flippase MurJ is responsible for transporting the cell wall intermediate lipid II from the cytoplasm to the outside of the cell. While essential for the survival of bacteria, it remains an underexploited target for antibacterial therapy. The humimycin antibiotics are lipid II flippase (MurJ) inhibitors that were synthesized on the basis of bioinformatic predictions derived from secondary metabolite gene clusters found in the human microbiome. Here, we describe an SAR campaign around humimycin A that produced humimycin 17S. Compared to humimycin A, 17S is a more potent β-lactam potentiator, has a broader spectrum of activity, which now includes both methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus faecalis (VRE), and did not lead to any detectable resistance when used in combination with a β-lactam. Combinations of β-lactam and humimycin 17S provide a potentially useful long-term MRSA regimen.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Daigo Inoyama
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University−New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Ricardo Gallardo-Macias
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University−New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Mark Jaskowski
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University−New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Shruthi Satish
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University−New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Joel S. Freundlich
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University−New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, 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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34
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Cohen LJ, Han S, Huang YH, Brady SF. Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library. ACS Infect Dis 2018; 4:27-32. [PMID: 28810737 DOI: 10.1021/acsinfecdis.7b00081] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The forces that shape human microbial ecology are complex. It is likely that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli. Characterization of the metagenomic DNA sequence identified a colicin V biosynthetic cluster as being responsible for the observed antibiotic effect of the metagenomic clone against E. coli. This study presents a scalable method to recover antibiotic gene clusters from humans using functional metagenomics and highlights a strategy to study bacteriocins in the human microbiome which can provide a resource for therapeutic discovery.
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Affiliation(s)
- Louis J. Cohen
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, 1 Gustave Levy Place, Box 1069, New York, New York 10029, United States
| | - Sun Han
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, 1 Gustave Levy Place, Box 1069, New York, New York 10029, United States
| | - Yun-Han Huang
- 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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35
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Cohen LJ, Esterhazy D, Kim SH, Lemetre C, Aguilar RR, Gordon EA, Pickard AJ, Cross JR, Emiliano AB, Han SM, Chu J, Vila-Farres X, Kaplitt J, Rogoz A, Calle PY, Hunter C, Bitok JK, Brady SF. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 2017; 549:48-53. [PMID: 28854168 PMCID: PMC5777231 DOI: 10.1038/nature23874] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 08/01/2017] [Indexed: 02/08/2023]
Abstract
Commensal bacteria are believed to have important roles in human health. The mechanisms by which they affect mammalian physiology remain poorly understood, but bacterial metabolites are likely to be key components of host interactions. Here we use bioinformatics and synthetic biology to mine the human microbiota for N-acyl amides that interact with G-protein-coupled receptors (GPCRs). We found that N-acyl amide synthase genes are enriched in gastrointestinal bacteria and the lipids that they encode interact with GPCRs that regulate gastrointestinal tract physiology. Mouse and cell-based models demonstrate that commensal GPR119 agonists regulate metabolic hormones and glucose homeostasis as efficiently as human ligands, although future studies are needed to define their potential physiological role in humans. Our results suggest that chemical mimicry of eukaryotic signalling molecules may be common among commensal bacteria and that manipulation of microbiota genes encoding metabolites that elicit host cellular responses represents a possible small-molecule therapeutic modality (microbiome-biosynthetic gene therapy).
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Affiliation(s)
- Louis J Cohen
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Daria Esterhazy
- Laboratory of Mucosal Immunology, Rockefeller University, New York, New York 10065, USA
| | - Seong-Hwan Kim
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Rhiannon R Aguilar
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Emma A Gordon
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Amanda J Pickard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ana B Emiliano
- Laboratory of Molecular Genetics, Rockefeller University, New York, New York 10065, USA
| | - Sun M Han
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - John Chu
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Jeremy Kaplitt
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Aneta Rogoz
- Laboratory of Mucosal Immunology, Rockefeller University, New York, New York 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Craig Hunter
- Comparative Biosciences Center, Rockefeller University, New York, New York 10065, USA
| | - J Kipchirchir Bitok
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
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36
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Vila-Farres X, Chu J, Inoyama D, Ternei MA, Lemetre C, Cohen LJ, Cho W, Reddy BVB, Zebroski HA, Freundlich JS, Perlin DS, Brady SF. Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters. J Am Chem Soc 2017; 139:1404-1407. [PMID: 28055186 DOI: 10.1021/jacs.6b11861] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial culture broth extracts have been the starting point for the development of numerous therapeutics. However, only a small fraction of bacterial biosynthetic diversity is accessible using this strategy. Here, we apply a discovery approach that bypasses the culturing step entirely by bioinformatically predicting small molecule structures from the primary sequences of the biosynthetic gene clusters. These structures are then chemically synthesized to give synthetic-bioinformatic natural products (syn-BNPs). Using this approach, we screened syn-BNPs inspired by nonribosomal peptide synthetases against microbial pathogens, and discovered an antibiotic for which no resistance could be identified and an antifungal agent with activity against diverse fungal pathogens.
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Affiliation(s)
- Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - John Chu
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Daigo Inoyama
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Louis J Cohen
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Wooyoung Cho
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Boojala Vijay B Reddy
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Henry A Zebroski
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Joel S Freundlich
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - David S Perlin
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
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37
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Abstract
Arixanthomycins are pentangular polyphenols (PP) with potent antiproliferative activities that were discovered through the heterologous expression of environmental DNA-derived gene clusters. The biosynthesis of arixanthomycin and other PPs is unusual because it requires several novel type II polyketide synthase (PKS) enzymes for its complete maturation. Most type II PKSs contain a ketoreductase (KR) that mediates the C7-C12 first ring cyclization and C-9 reduction. In contrast, based on previous studies of product analysis and genome mining, the arixanthomycin (ARX) gene cluster harbors a C-11 reducing KR (ARX 27), a C9-C14 first-ring aromatase/cyclase (ARX 19), and an unprecedented C-17 and C-19 reducing KR (ARX 21). While bioinformatics is useful for predicting novel enzymes, the functions of ARX 19, ARX 21, and ARX 27 have yet to be confirmed. Further, the structural features that predispose the ARX biosynthetic enzymes to process atypical poly-β-ketone scaffolds remain unknown. We report the crystal structure of ARX 21, the first structure of an enzyme involved in PP biosynthesis and likely a C-17 and C-19 reducing-KR, which is structurally similar to C-15 reducing KRs. Structural comparison of ARX 21 and other C-9 reducing KRs revealed a difference in the enzyme active site that may enlighten the molecular basis of KR substrate specificity. In addition, we report the successful in vitro reconstitution of ARX 19. The structural characterization of ARX 21 in conjunction with the in vitro results of ARX 19 lays the groundwork toward a complete in vitro and structural characterization of type II PKS enzymes involved in PP biogenesis.
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Affiliation(s)
- Timothy R. Valentic
- Department
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - David R. Jackson
- Department
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Shiou-Chuan Tsai
- Department
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, Irvine, California 92697, United States
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38
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Chu J, Vila-Farres X, Inoyama D, Ternei M, Cohen LJ, Gordon EA, Reddy BVB, Charlop-Powers Z, Zebroski HA, Gallardo-Macias R, Jaskowski M, Satish S, Park S, Perlin DS, Freundlich JS, Brady SF. Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nat Chem Biol 2016; 12:1004-1006. [PMID: 27748750 PMCID: PMC5117632 DOI: 10.1038/nchembio.2207] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/11/2016] [Indexed: 01/21/2023]
Abstract
Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonribosomal peptide synthetase gene clusters from human-associated bacteria, we identified the humimycins. These antibiotics inhibit lipid II flippase and potentiate β-lactam activity against methicillin-resistant Staphylococcus aureus in mice, potentially providing a new treatment regimen.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Daigo Inoyama
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Louis J. Cohen
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Emma A. Gordon
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Boojala Vijay B. Reddy
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Henry A. Zebroski
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Ricardo Gallardo-Macias
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Mark Jaskowski
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Shruthi Satish
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Steven Park
- Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - David S. Perlin
- Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
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39
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Kang HS, Charlop-Powers Z, Brady SF. Multiplexed CRISPR/Cas9- and TAR-Mediated Promoter Engineering of Natural Product Biosynthetic Gene Clusters in Yeast. ACS Synth Biol 2016; 5:1002-10. [PMID: 27197732 DOI: 10.1021/acssynbio.6b00080] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The use of DNA sequencing to guide the discovery of natural products has emerged as a new paradigm for revealing chemistries encoded in bacterial genomes. A major obstacle to implementing this approach to natural product discovery is the transcriptional silence of biosynthetic gene clusters under laboratory growth conditions. Here we describe an improved yeast-based promoter engineering platform (mCRISTAR) that combines CRISPR/Cas9 and TAR to enable single-marker multiplexed promoter engineering of large gene clusters. mCRISTAR highlights the first application of the CRISPR/Cas9 system to multiplexed promoter engineering of natural product biosynthetic gene clusters. In this method, CRISPR/Cas9 is used to induce DNA double-strand breaks in promoter regions of biosynthetic gene clusters, and the resulting operon fragments are reassembled by TAR using synthetic gene-cluster-specific promoter cassettes. mCRISTAR uses a CRISPR array to simplify the construction of a CRISPR plasmid for multiplex CRISPR and a single auxotrophic selection to improve the inefficiency of using a CRISPR array for multiplex gene cluster refactoring. mCRISTAR is a simple and generic method for multiplexed replacement of promoters in biosynthetic gene clusters that will facilitate the discovery of natural products from the rapidly growing collection of gene clusters found in microbial genome and metagenome sequencing projects.
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Affiliation(s)
- Hahk-Soo Kang
- Laboratory of Genetically
Encoded Small Molecules, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Zachary Charlop-Powers
- 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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40
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Abstract
Because the majority of environmental bacteria are not easily culturable, access to many bacterially encoded secondary metabolites will be dependent on the development of improved functional metagenomic screening methods. In this study, we examined a collection of diverse Streptomyces species for the best innate ability to heterologously express biosynthetic gene clusters. We then optimized methods for constructing high quality metagenomic cosmid libraries in the best Streptomyces host. An initial screen of a 1.5 million-membered metagenomic library constructed in Streptomyces albus, the species that exhibited the highest propensity for heterologous expression of gene clusters, led to the identification of the novel natural product metatricycloene (1). Metatricycloene is a tricyclic polyene encoded by a reductive, iterative polyketide-like gene cluster. Related gene clusters found in sequenced genomes appear to encode a largely unexplored collection of structurally diverse, polyene-based metabolites.
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Affiliation(s)
- Hala A. Iqbal
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Lila Low-Beinart
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Joseph U. Obiajulu
- 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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41
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Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJN, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJM, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O’Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 2015; 11:625-31. [PMID: 26284661 PMCID: PMC5714517 DOI: 10.1038/nchembio.1890] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marnix H Medema
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Matthew Cummings
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Irene de Bruijn
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands
| | - Yit Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, USA,Departmentof Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA,School of Chemistry and Biochemistry, University of Western Australia, Perth, Western Australia, Australia
| | - Jan Claesen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - R Cameron Coates
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Srikanth Duddela
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Stephanie Düsterhus
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Daniel J Edwards
- Department of Chemistry and Biochemistry, California State University, Chico, California, USA
| | - David P Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Christoph Geiger
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | - Anja Greule
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Michalis Hadjithomas
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | | | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthew L Hillwig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, USA
| | - Carla S Jones
- Sustainable Studies Program, Roosevelt University Chicago, Illinois, USA
| | - Katrin Jungmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Carsten Kegler
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany
| | - Hyun Uk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark,BioInformatics Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Joleen Masschelein
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium,Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Simone M Mantovani
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Emily A Monroe
- Department of Biology, William Paterson University, Wayne, New Jersey, USA
| | - Marcus Moore
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Nathan Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork–National University of Ireland, Cork, Ireland
| | - Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, IBCE, Montevideo, Uruguay
| | - Zhe Rui
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California, USA,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, USA
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Nicholas J Tobias
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany
| | - Yuta Tsunematsu
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Elizabeth Wyckoff
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA,Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Grace Yim
- Department of Biochemistry and Biomedical Sciences, The M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yunchang Xie
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, Université de Lorraine and Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1128, Vandoeuvre-lès-Nancy, France
| | - Alexander K Apel
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Carl J Balibar
- Infectious Disease Research, Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt, Germany
| | - Rainer Borriss
- Fachbereich Phytomedizin, Albrecht Thaer Institut, Humboldt Universität Berlin, Berlin, Germany
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Axel A Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Patrick Caffrey
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Russell J Cox
- Institut für Organische Chemie, Leibniz Universität Hannover, Hannover, Germany,School of Chemistry, University of Bristol, Bristol, UK
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, University of Leuven, Heverlee, Belgium
| | | | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA,Howard Hughes Medical Institute, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA,Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, California, USA
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Bertolt Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,Friedrich Schiller University, Jena, Germany
| | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Susan E Jensen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jianhua Ju
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Leonard Katz
- Synthetic Biology Engineering Research Center (SynBERC), University of California Emeryville, Emeryville, California, USA
| | - Leonard Kaysser
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, USA,Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Nikos C Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hyung-Jin Kwon
- Division of Bioscience and Bioinformatics, Myongji University, Yongin-si, Gyeonggi-Do, South Korea
| | - Sylvie Lautru
- Institute of Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Orsay, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium
| | - Chia Y Lee
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Bai Linquan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China,School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Yvonne Mast
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Carmen Méndez
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain,Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
| | | | | | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leonilde M Moreira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark,Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fergal O’Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork–National University of Ireland, Cork, Ireland,Curtin University, School of Biomedical Sciences, Perth, Western Australia, Australia
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Shelley M Payne
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA,Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas, USA
| | - Jean-Luc Pernodet
- Institute of Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Orsay, France
| | - Miroslav Petricek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czech Republic
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Olivier Ploux
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236 CNRS, Université Paris Diderot, Paris, France
| | - Jos M Raaijmakers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands
| | - José A Salas
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Esther K Schmitt
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA,Molecular Therapeutics and Natural Products Library Initiative, The Scripps Research Institute, Jupiter, Florida, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota–Twin Cities, Saint Paul, Minnesota, USA,BioTechnology Institute, University of Minnesota–Twin Cities, Saint Paul, Minnesota, USA
| | | | - Evi Stegmann
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | | | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | | | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, USA,Departmentof Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Muriel Viaud
- Unité BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA), Grignon, France
| | - Jonathan D Walton
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Christopher T Walsh
- Chemistry, Engineering & Medicine for Human Health (ChEM-H) Institute, Stanford University, Stanford, California, USA
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Joanne M Willey
- Hofstra North Shore–Long Island Jewish School of Medicine, Hempstead, New York, USA
| | - Wolfgang Wohlleben
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, The M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Sergey B Zotchev
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Eriko Takano
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany,Jacobs University Bremen gGmbH, Bremen, Germany
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42
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Abstract
Natural product discovery from environmental genomes (metagenomics) has largely been limited to the screening of existing environmental DNA (eDNA) libraries. Here, we have coupled a chemical-biogeographic survey of chromopyrrolic acid synthase (CPAS) gene diversity with targeted eDNA library production to more efficiently access rare tryptophan dimer (TD) biosynthetic gene clusters. A combination of traditional and synthetic biology-based heterologous expression efforts using eDNA-derived gene clusters led to the production of hydroxysporine (1) and reductasporine (2), two bioactive TDs. As suggested by our phylogenetic analysis of CPAS genes, identified in our survey of crude eDNA extracts, reductasporine (2) contains an unprecedented TD core structure: a pyrrolinium indolocarbazole core that is likely key to its unusual bioactivity profile. This work demonstrates the potential for the discovery of structurally rare and biologically interesting natural products using targeted metagenomics, where environmental samples are prescreened to identify the most phylogenetically unique gene sequences and molecules associated with these genes are accessed through targeted metagenomic library construction and heterologous expression.
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Affiliation(s)
- Fang-Yuan Chang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Paula Y. Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
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43
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Charlop-Powers Z, Brady SF. phylogeo: an R package for geographic analysis and visualization of microbiome data. Bioinformatics 2015; 31:2909-11. [PMID: 25913208 DOI: 10.1093/bioinformatics/btv269] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/23/2015] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language. AVAILABILITY AND IMPLEMENTATION phylogeo is documented and freely available http://zachcp.github.io/phylogeo CONTACT : zcharlop@rockefeller.edu.
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Affiliation(s)
- Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
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44
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Charlop-Powers Z, Owen JG, Reddy BVB, Ternei MA, Guimarães DO, de Frias UA, Pupo MT, Seepe P, Feng Z, Brady SF. Global biogeographic sampling of bacterial secondary metabolism. eLife 2015; 4:e05048. [PMID: 25599565 PMCID: PMC4383359 DOI: 10.7554/elife.05048] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 01/07/2015] [Indexed: 12/27/2022] Open
Abstract
Recent bacterial (meta)genome sequencing efforts suggest the existence of an enormous
untapped reservoir of natural-product-encoding biosynthetic gene clusters in the
environment. Here we use the pyro-sequencing of PCR amplicons derived from both
nonribosomal peptide adenylation domains and polyketide ketosynthase domains to
compare biosynthetic diversity in soil microbiomes from around the globe. We see
large differences in domain populations from all except the most proximal and
biome-similar samples, suggesting that most microbiomes will encode largely distinct
collections of bacterial secondary metabolites. Our data indicate a correlation
between two factors, geographic distance and biome-type, and the biosynthetic
diversity found in soil environments. By assigning reads to known gene clusters we
identify hotspots of biomedically relevant biosynthetic diversity. These observations
not only provide new insights into the natural world, they also provide a road map
for guiding future natural products discovery efforts. DOI:http://dx.doi.org/10.7554/eLife.05048.001 Many of the most useful medicinal drugs—including antibiotics and cancer
drugs—are derived from bacteria living in the soil that produce these
chemicals as part of their natural life cycle. Many of these chemicals have been
found by culturing bacteria in the laboratory, but this approach is limited because
it only provides access to the chemicals produced by the small fraction of bacteria
species that we can culture in this way. Also, many bacteria do not produce as many
different chemicals when they are grown under these artificial conditions, instead of
their natural environment. This suggests that bacteria living in the environment are
likely to provide an additional source of new chemicals that could have medicinal
benefits. Here, Charlop-Powers et al. tackle this issue by employing a high-throughput genetic
method for assessing the potential of soil-dwelling bacteria to make compounds with
biological activity. They extracted DNA directly from soil samples collected from
five continents, in part through the efforts of a citizen-science project called
‘Drugs from Dirt’ (drugsfromdirt.org). These samples came from many different
environments, including rainforests, deserts, and coastal sediments. After extracting the DNA from the soil samples, Charlop-Powers et al. focused on
sequencing the genes that encode enzymes called NRPS and PKS. These enzymes are
involved in the production of a range of diverse compounds, including many clinically
useful antibiotics. By comparing the sequences of the genes found in the different
soils, it was possible to estimate how common the genes were in each sample, and also
to compare the collections of genes found in different soil types. This comparison
revealed that the DNA sequences of the genes encoding NRPS and PKS vary widely among
the soil samples, except for samples that came from similar environments in close
proximity to each other. These findings show that populations of soil-dwelling bacteria living in different
locations are likely to produce related, but different and largely unexplored,
natural compounds that could have the potential to be used in drug therapies or in
other industries. DOI:http://dx.doi.org/10.7554/eLife.05048.002
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Affiliation(s)
- Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Jeremy G Owen
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Boojala Vijay B Reddy
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Denise O Guimarães
- Laboratório de Produtos Naturais, Curso de Farmácia, Universidade Federal do Rio de Janeiro-Campus Macaé, Rio de Janeiro, Brazil
| | - Ulysses A de Frias
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Monica T Pupo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Prudy Seepe
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, Durban, South Africa
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
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45
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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: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
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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46
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Chang FY, Kawashima SA, Brady SF. Mutations in the proteolipid subunits of the vacuolar H+-ATPase provide resistance to indolotryptoline natural products. Biochemistry 2014; 53:7123-31. [PMID: 25319670 PMCID: PMC4238801 DOI: 10.1021/bi501078j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Indolotryptoline natural products
represent a small family of structurally
unique chromopyrrolic acid-derived antiproliferative agents. Like
many prospective anticancer agents before them, the exploration of
their potential clinical utility has been hindered by the limited
information known about their mechanism of action. To study the mode
of action of two closely related indolotryptolines (BE-54017, cladoniamide
A), we selected for drug resistant mutants using a multidrug resistance-suppressed
(MDR-sup) Schizosaccharomyces pombe strain. As fission
yeast maintains many of the basic cancer-relevant cellular processes
present in human cells, it represents an appealing model to use in
determining the potential molecular target of antiproliferative natural
products through resistant mutant screening. Full genome sequencing
of resistant mutants identified mutations in the c and c′ subunits
of the proteolipid substructure of the vacuolar H+-ATPase
complex (V-ATPase). This collection of resistance-conferring mutations
maps to a site that is distant from the nucleotide-binding sites of
V-ATPase and distinct from sites found to confer resistance to known
V-ATPase inhibitors. Acid vacuole staining, cross-resistance studies,
and direct c/c′ subunit mutagenesis all suggest that indolotryptolines
are likely a structurally novel class of V-ATPase inhibitors. This
work demonstrates the general utility of resistant mutant selection
using MDR-sup S. pombe as a rapid and potentially
systematic approach for studying the modes of action of cytotoxic
natural products.
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Affiliation(s)
- Fang-Yuan Chang
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
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47
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Milshteyn A, Schneider JS, Brady SF. Mining the metabiome: identifying novel natural products from microbial communities. Chem Biol 2014; 21:1211-23. [PMID: 25237864 PMCID: PMC4171686 DOI: 10.1016/j.chembiol.2014.08.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022]
Abstract
Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.
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Affiliation(s)
- Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jessica S Schneider
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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48
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Charlop-Powers Z, Milshteyn A, Brady SF. Metagenomic small molecule discovery methods. Curr Opin Microbiol 2014; 19:70-75. [PMID: 25000402 DOI: 10.1016/j.mib.2014.05.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/10/2014] [Accepted: 05/28/2014] [Indexed: 12/18/2022]
Abstract
Metagenomic approaches to natural product discovery provide the means to harvest bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence-based and functional-based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes.
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Affiliation(s)
- Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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49
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Abstract
![]()
Increasing evidence has shown that
small-molecule chemistry in
microbes (i.e., secondary metabolism) can modulate the microbe–host
response in infection and pathogenicity. The bacterial disease melioidosis
is conferred by the highly virulent, antibiotic-resistant pathogen Burkholderia pseudomallei (BP). Whereas
some macromolecular structures have been shown to influence BP virulence (e.g., secretion systems, cellular capsule,
pili), the role of the large cryptic secondary metabolome encoded
within its genome has been largely unexplored for its importance to
virulence. Herein we demonstrate that BP-encoded
small-molecule biosynthesis is indispensible for in vivo BP pathogenicity. Promoter exchange experiments were used to induce
high-level molecule production from two gene clusters (MPN and SYR)
found to be essential for in vivo virulence. NMR
structural characterization of these metabolites identified a new
class of lipopeptide biosurfactants/biofilm modulators (the
malleipeptins) and syrbactin-type proteasome inhibitors, both
of which represent overlooked small-molecule virulence factors for BP. Disruption of Burkholderia virulence by inhibiting the
biosynthesis of these small-molecule biosynthetic pathways may prove
to be an effective strategy for developing novel melioidosis-specific
therapeutics.
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Affiliation(s)
- John B Biggins
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute , The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
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Abstract
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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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