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García-Trevijano ER, Ortiz-Zapater E, Gimeno A, Viña JR, Zaragozá R. Calpains, the proteases of two faces controlling the epithelial homeostasis in mammary gland. Front Cell Dev Biol 2023; 11:1249317. [PMID: 37795261 PMCID: PMC10546029 DOI: 10.3389/fcell.2023.1249317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Abstract
Calpain-1 and calpain-2 are calcium-dependent Cys-proteases ubiquitously expressed in mammalian tissues with a processive, rather than degradative activity. They are crucial for physiological mammary gland homeostasis as well as for breast cancer progression. A growing number of evidences indicate that their pleiotropic functions depend on the cell type, tissue and biological context where they are expressed or dysregulated. This review considers these standpoints to cover the paradoxical role of calpain-1 and -2 in the mammary tissue either, under the physiological conditions of the postlactational mammary gland regression or the pathological context of breast cancer. The role of both calpains will be examined and discussed in both conditions, followed by a brief snapshot on the present and future challenges for calpains, the two-gateway proteases towards tissue homeostasis or tumor development.
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Affiliation(s)
- Elena R. García-Trevijano
- Department of Biochemistry and Molecular Biology, Universitat de Valencia, Valencia, Spain
- INLIVA Biomedical Research Institute, Valencia, Spain
| | - Elena Ortiz-Zapater
- Department of Biochemistry and Molecular Biology, Universitat de Valencia, Valencia, Spain
- INLIVA Biomedical Research Institute, Valencia, Spain
| | - Amparo Gimeno
- Department of Anatomy and Human Embryology, Universitat de Valencia, Valencia, Spain
| | - Juan R. Viña
- Department of Biochemistry and Molecular Biology, Universitat de Valencia, Valencia, Spain
- INLIVA Biomedical Research Institute, Valencia, Spain
| | - Rosa Zaragozá
- INLIVA Biomedical Research Institute, Valencia, Spain
- Department of Anatomy and Human Embryology, Universitat de Valencia, Valencia, Spain
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Herisse M, Ishida K, Staiger-Creed J, Judd L, Williams SJ, Howden BP, Stinear TP, Dahse HM, Voigt K, Hertweck C, Pidot SJ. Discovery and Biosynthesis of the Cytotoxic Polyene Terpenomycin in Human Pathogenic Nocardia. ACS Chem Biol 2023; 18:1872-1879. [PMID: 37498707 DOI: 10.1021/acschembio.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nocardia are opportunistic human pathogens that can cause a range of debilitating and difficult to treat infections of the lungs, brain, skin, and soft tissues. Despite their close relationship to the well-known secondary metabolite-producing genus, Streptomyces, comparatively few natural products are known from the Nocardia, and even less is known about their involvement in the pathogenesis. Here, we combine chemistry, genomics, and molecular microbiology to reveal the production of terpenomycin, a new cytotoxic and antifungal polyene from a human pathogenic Nocardia terpenica isolate. We unveil the polyketide synthase (PKS) responsible for terpenomycin biosynthesis and show that it combines several unusual features, including "split", skipped, and iteratively used modules, and the use of the unusual extender unit methoxymalonate as a starter unit. To link genes to molecules, we constructed a transposon mutant library in N. terpenica, identifying a terpenomycin-null mutant with an inactivated terpenomycin PKS. Our findings show that the neglected actinomycetes have an unappreciated capacity for the production of bioactive molecules with unique biosynthetic pathways waiting to be uncovered and highlights these organisms as producers of diverse natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Jordan Staiger-Creed
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Louise Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Melbourne, Victoria 3000, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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3
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Liu J, Zhang M, Huang Z, Fang J, Wang Z, Zhou C, Qiu X. Diversity, Biosynthesis and Bioactivity of Aeruginosins, a Family of Cyanobacteria-Derived Nonribosomal Linear Tetrapeptides. Mar Drugs 2023; 21:md21040217. [PMID: 37103356 PMCID: PMC10143770 DOI: 10.3390/md21040217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Aeruginosins, a family of nonribosomal linear tetrapeptides discovered from cyanobacteria and sponges, exhibit in vitro inhibitory activity on various types of serine proteases. This family is characterized by the existence of the 2-carboxy-6-hydroxy-octahydroindole (Choi) moiety occupied at the central position of the tetrapeptide. Aeruginosins have attracted much attention due to their special structures and unique bioactivities. Although many studies on aeruginosins have been published, there has not yet been a comprehensive review that summarizes the diverse research ranging from biogenesis, structural characterization and biosynthesis to bioactivity. In this review, we provide an overview of the source, chemical structure as well as spectrum of bioactivities of aeruginosins. Furthermore, possible opportunities for future research and development of aeruginosins were discussed.
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Affiliation(s)
- Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Chengxu Zhou
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
- Correspondence:
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4
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Danaeifar M, Mazlomi MA. Combinatorial biosynthesis: playing chess with the metabolism. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:171-190. [PMID: 35435779 DOI: 10.1080/10286020.2022.2065265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Secondary metabolites are a group of natural products that produced by bacteria, fungi and plants. Many applications of these compounds from medicine to industry have been discovered. However, some changes in their structure and biosynthesis mechanism are necessary for their properties to be more suitable and also for their production to be profitable. The main and most useful method to achieve this goal is combinatorial biosynthesis. This technique uses the multi-unit essence of the secondary metabolites biosynthetic enzymes to make changes in their order, structure and also the organism that produces them.
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Affiliation(s)
- Mohsen Danaeifar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran
| | - Mohammad Ali Mazlomi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran
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5
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Stankey RJ, Johnson D, Duggan BM, Mead DA, La Clair JJ. A Survey of Didemnin Depsipeptide Production in Tistrella. Mar Drugs 2023; 21:md21020056. [PMID: 36827097 PMCID: PMC9964501 DOI: 10.3390/md21020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
As one of the first families of marine natural products to undergo clinical trials, the didemnin depsipeptides have played a significant role in inspiring the discovery of marine drugs. Originally developed as anticancer therapeutics, the recent re-evaluation of these compounds including synthetically derived dehydrodidemnin B or Aplidine, has led to their advancement towards antiviral applications. While conventionally associated with production in colonial tunicates of the family Didemnidae, recent studies have identified their biosynthetic gene clusters from the marine-derived bacteria Tistrella mobilis. While these studies confirm the production of didemnin X/Y, the low titer and general lack of understanding of their biosynthesis in Tistrella currently prevents the development of effective microbial or synthetic biological approaches for their production. To this end, we conducted a survey of known species of Tistrella and report on their ability to produce the didemnin depsipeptides. These data were used to develop conditions to produce didemnin B at titers over 15 mg/L.
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Affiliation(s)
| | - Don Johnson
- Terra Bioworks Inc., Middleton, WI 53562, USA
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive, San Diego, CA 92093-0657, USA
| | - David A. Mead
- Terra Bioworks Inc., Middleton, WI 53562, USA
- Correspondence: (D.A.M.); (J.J.L.C.)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0358, USA
- Xenobe Research Institute, P.O. Box 3052, San Diego, CA 92163-1052, USA
- Correspondence: (D.A.M.); (J.J.L.C.)
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Tang JW, Liu X, Ye W, Li ZR, Qian PY. Biosynthesis and bioactivities of microbial genotoxin colibactins. Nat Prod Rep 2022; 39:991-1014. [PMID: 35288725 DOI: 10.1039/d1np00050k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to 2021Colibactin(s), a group of secondary metabolites produced by the pks island (clb cluster) of Escherichia coli, shows genotoxicity relevant to colorectal cancer and thus significantly affects human health. Over the last 15 years, substantial efforts have been exerted to reveal the molecular structure of colibactin, but progress is slow owing to its instability, low titer, and elusive and complex biosynthesis logic. Fortunately, benefiting from the discovery of the prodrug mechanism, over 40 precursors of colibactin have been reported. Some key biosynthesis genes located on the pks island have also been characterised. Using an integrated bioinformatics, metabolomics, and chemical synthesis approach, researchers have recently characterised the structure and possible biosynthesis processes of colibactin, thereby providing new insights into the unique biosynthesis logic and the underlying mechanism of the biological activity of colibactin. Early developments in the study of colibactin have been summarised in several previous reviews covering various study periods, whereas the two most recent reviews have focused primarily on the chemical synthesis of colibactin. The present review aims to provide an update on the biosynthesis and bioactivities of colibactin.
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Affiliation(s)
- Jian-Wei Tang
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Xin Liu
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Wei Ye
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhong-Rui Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
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7
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Donkor IO. An update on the therapeutic potential of calpain inhibitors: a patent review. Expert Opin Ther Pat 2020; 30:659-675. [PMID: 32700591 DOI: 10.1080/13543776.2020.1797678] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Calpain is a cytosolic proteinase that regulates of a wide range of physiological functions. The enzyme has been implicated in various pathological conditions including neurodegenerative disorders, cardiovascular disorders, cancer, and several other diseases. Therefore, calpain inhibitors are of interest as therapeutic agents and have been studied in preclinical models of several diseases in which the enzyme has been implicated. AREAS COVERED Calpain inhibitors that were disclosed over the last 5 years (2015-2019) include calpastatin-based peptidomimetics; thalassospiramide lipopeptides; disulfide analogs of alpha-mercaptoacrylic acids; allosteric modulators; azoloimidazolidenones; and macrocyclic/non-macrocyclic carboxamides. The effectiveness of some of the inhibitors in preclinical animal models is discussed. EXPERT OPINION Significant milestones that were made over this time frame include: a) disclosure of novel blood-brain barrier (BBB) permeable calpastatin analogs as calpain inhibitors; b) disclosure that potent calpain inhibitors can be obtained by targeting the hydrophobic pockets on chain A of PEF(S) of the small subunit of calpain; c) use of PEF(S) (PDB ID: 4WQ2) in virtual screening to identify novel structurally diverse calpain inhibitors; and d) mitigation of the metabolic instability of the alpha-ketoamide warhead of calpain inhibitors.
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Affiliation(s)
- Isaac O Donkor
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, College of Pharmacy , Memphis, Tennessee, United States
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8
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Lundy TA, Mori S, Garneau-Tsodikova S. A thorough analysis and categorization of bacterial interrupted adenylation domains, including previously unidentified families. RSC Chem Biol 2020; 1:233-250. [PMID: 34458763 PMCID: PMC8341866 DOI: 10.1039/d0cb00092b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022] Open
Abstract
Interrupted adenylation (A) domains are key to the immense structural diversity seen in the nonribosomal peptide (NRP) class of natural products (NPs). Interrupted A domains are A domains that contain within them the catalytic portion of another domain, most commonly a methylation (M) domain. It has been well documented that methylation events occur with extreme specificity on either the backbone (N-) or side chain (O- or S-) of the amino acid (or amino acid-like) building blocks of NRPs. Here, through taxonomic and phylogenetic analyses as well as multiple sequence alignments, we evaluated the similarities and differences between interrupted A domains. We probed their taxonomic distribution amongst bacterial organisms, their evolutionary relatedness, and described conserved motifs of each type of M domain found to be embedded in interrupted A domains. Additionally, we categorized interrupted A domains and the M domains within them into a total of seven distinct families and six different types, respectively. The families of interrupted A domains include two new families, 6 and 7, that possess new architectures. Rather than being interrupted between the previously described a2–a3 or a8–a9 of the ten conserved A domain sequence motifs (a1–a10), family 6 contains an M domain between a6–a7, a previously unknown interruption site. Family 7 demonstrates that di-interrupted A domains exist in Nature, containing an M domain between a2–a3 as well as one between a6–a7, displaying a novel arrangement. These in-depth investigations of amino acid sequences deposited in the NCBI database highlighted the prevalence of interrupted A domains in bacterial organisms, with each family of interrupted A domains having a different taxonomic distribution. They also emphasized the importance of utilizing a broad range of bacteria for NP discovery. Categorization of the families of interrupted A domains and types of M domains allowed for a better understanding of the trends of naturally occurring interrupted A domains, which illuminated patterns and insights on how to harness them for future engineering studies. In-depth study of intriguing bacterial interrupted adenylation domains from seven distinct families and six different types.![]()
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Affiliation(s)
- Taylor A Lundy
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| | - Shogo Mori
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
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9
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Marine microbial natural products: the evolution of a new field of science. J Antibiot (Tokyo) 2020; 73:481-487. [PMID: 32713942 DOI: 10.1038/s41429-020-0331-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 12/29/2022]
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10
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Al-Awadhi FH, Luesch H. Targeting eukaryotic proteases for natural products-based drug development. Nat Prod Rep 2020; 37:827-860. [PMID: 32519686 PMCID: PMC7406119 DOI: 10.1039/c9np00060g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to April 2020 Proteases are involved in the regulation of many physiological processes. Their overexpression and dysregulated activity are linked to diseases such as hypertension, diabetes, viral infections, blood clotting disorders, respiratory diseases, and cancer. Therefore, they represent an important class of therapeutic targets. Several protease inhibitors have reached the market and >60% of them are directly related to natural products, even when excluding synthetic natural product mimics. Historically, natural products have been a valuable and validated source of therapeutic agents, as over half of the marketed drugs across targets and diseases are inspired by natural product structures. In the past two decades the number of new protease inhibitors discovered from nature has sharply increased. Additionally, the availability of 3D structural information for proteases has permitted structure-based design and accelerated the synthesis of optimized lead structures with improved potency and selectivity profiles, resulting in some of the most-potent-in-class inhibitors. These discoveries were oftentimes maximized by in-depth biological assessments of lead inhibitors, linking them to a relevant disease state. This review will discuss some of the current and emerging drug targets and their involvement in various disease processes, highlighting selected success stories behind several FDA-approved protease inhibitors that have natural products scaffolds as well as recent selected pharmacologically well-characterized inhibitors derived from marine or terrestrial sources.
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Affiliation(s)
- Fatma H Al-Awadhi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait.
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, USA.
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11
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Reimer JM, Eivaskhani M, Harb I, Guarné A, Weigt M, Schmeing TM. Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility. Science 2020; 366:366/6466/eaaw4388. [PMID: 31699907 DOI: 10.1126/science.aaw4388] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/04/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes that synthesize natural product therapeutics using a modular synthetic logic, whereby each module adds one aminoacyl substrate to the nascent peptide. We have determined five x-ray crystal structures of large constructs of the NRPS linear gramicidin synthetase, including a structure of a full core dimodule in conformations organized for the condensation reaction and intermodular peptidyl substrate delivery. The structures reveal differences in the relative positions of adjacent modules, which are not strictly coupled to the catalytic cycle and are consistent with small-angle x-ray scattering data. The structures and covariation analysis of homologs allowed us to create mutants that improve the yield of a peptide from a module-swapped dimodular NRPS.
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Affiliation(s)
- Janice M Reimer
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Maximilian Eivaskhani
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Ingrid Harb
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Alba Guarné
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France
| | - T Martin Schmeing
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada.
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12
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Promiscuous Enzymes Cause Biosynthesis of Diverse Siderophores in Shewanella oneidensis. Appl Environ Microbiol 2020; 86:AEM.00030-20. [PMID: 32005730 DOI: 10.1128/aem.00030-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/23/2020] [Indexed: 02/05/2023] Open
Abstract
The siderophore synthetic system in Shewanella species is able to synthesize dozens of macrocyclic siderophores in vitro with synthetic precursors. In vivo, however, although three siderophores are produced naturally in Shewanella algae B516, which carries a lysine decarboxylase (AvbA) specific for siderophore synthesis, only one siderophore can be detected from many other Shewanella species. In this study, we examined a siderophore-overproducing mutant of Shewanella oneidensis which lacks an AvbA counterpart, and we found that it can also produce these three siderophores. We identified both SpeC and SpeF as promiscuous decarboxylases for both lysine and ornithine to synthesize the siderophore precursors cadaverine and putrescine, respectively. Intriguingly, putrescine is mainly synthesized from arginine through an arginine decarboxylation pathway in a constitutive manner, not liable to the concentrations of iron and siderophores. Our results provide further evidence that the substrate availability plays a determining role in siderophore production. Furthermore, we provide evidence to suggest that under iron starvation conditions, cells allocate more putrescine for siderophore biosynthesis by downregulating the expression of the enzyme that transforms putrescine into spermidine. Overall, this study provides another example of the great flexibility of bacterial metabolism that is honed by evolution to better fit living environments of these bacteria.IMPORTANCE The simultaneous production of multiple siderophores is considered a general strategy for microorganisms to rapidly adapt to their ever-changing environments. In this study, we show that some Shewanella spp. may downscale their capability for siderophore synthesis to facilitate adaptation. Although S. oneidensis lacks an enzyme specifically synthesizing cadaverine, it can produce it by using promiscuous ornithine decarboxylases. Despite this ability, this bacterium predominately produces the primary siderophore while restraining the production of secondary siderophores by regulating substrate availability. In addition to using the arginine decarboxylase (ADC) pathway for putrescine synthesis, cells optimize the putrescine pool for siderophore production. Our work provides an insight into the coordinated synthesis of multiple siderophores by harnessing promiscuous enzymes in bacteria and underscores the importance of substrate pools for the biosynthesis of natural products.
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13
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Futaki E, Takeda N, Yasui M, Shinada T, Miyata O, Ueda M. γ-C (sp 3)-H bond functionalisation of α,β-unsaturated amides through an umpolung strategy. Org Biomol Chem 2020; 18:1563-1566. [PMID: 32030394 DOI: 10.1039/d0ob00125b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nucleophilic γ-phenylation and γ-alkylation of α,β-unsaturated amides have been developed. This umpolung reaction allows the regioselective introduction of phenyl and alkyl groups to a vinylketene N,O-acetal, which is generated in situ from an α,β-unsaturated N-alkoxyamide, followed by N-O bond cleavage in a two-step, one-pot process.
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Affiliation(s)
- Erika Futaki
- Kobe Pharmaceutical University, Motoyamakita, Higashinada, Kobe 658-8558, Japan.
| | - Norihiko Takeda
- Kobe Pharmaceutical University, Motoyamakita, Higashinada, Kobe 658-8558, Japan.
| | - Motohiro Yasui
- Kobe Pharmaceutical University, Motoyamakita, Higashinada, Kobe 658-8558, Japan.
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Okiko Miyata
- Kobe Pharmaceutical University, Motoyamakita, Higashinada, Kobe 658-8558, Japan. and Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Masafumi Ueda
- Kobe Pharmaceutical University, Motoyamakita, Higashinada, Kobe 658-8558, Japan.
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14
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Pass-back chain extension expands multimodular assembly line biosynthesis. Nat Chem Biol 2019; 16:42-49. [PMID: 31636431 PMCID: PMC6917876 DOI: 10.1038/s41589-019-0385-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 11/26/2022]
Abstract
Modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymatic assembly lines are large and dynamic protein machines that generally effect a linear sequence of catalytic cycles. Here we report the heterologous reconstitution and comprehensive characterization of two hybrid NRPS-PKS assembly lines that defy many standard rules of assembly line biosynthesis to generate a large combinatorial library of cyclic lipodepsipeptide protease inhibitors called thalassospiramides. We generate a series of precise domain-inactivating mutations in thalassospiramide assembly lines and present evidence for an unprecedented biosynthetic model that invokes inter-module substrate activation and tailoring, module skipping, and pass-back chain extension, whereby the ability to pass the growing chain back to a preceding module is flexible and substrate-driven. Expanding bidirectional inter-module domain interactions could represent a viable mechanism for generating chemical diversity without increasing the size of biosynthetic assembly lines and challenges our understanding of the potential elasticity of multi-modular megaenzymes.
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15
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Hao L, Zheng X, Wang Y, Li S, Shang C, Xu Y. Inhibition of Tomato Early Blight Disease by Culture Extracts of a Streptomyces puniceus Isolate from Mangrove Soil. PHYTOPATHOLOGY 2019; 109:1149-1156. [PMID: 30794487 DOI: 10.1094/phyto-12-18-0444-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study investigates the potential of natural products derived from a mangrove rhizosphere bacterium in tomato early blight management. A Streptomyces puniceus strain L75 was isolated from the rhizosphere of Acanthus ilicifolius Linn in the Mai Po Reserve, Hong Kong. The crude ethyl acetate (EA) extract of L75 fermentation cultures has broad-spectrum antifungal bioactivities. L75 EA extract was significantly more effective in Alternaria solani growth inhibition at 25 μg/ml or lower compared with Mancozeb, with no observable negative impacts on tomato leaves or root development. Furthermore, L75 EA extract had significantly lower aquatic toxicity than Mancozeb at the same concentrations. L75 EA extract targets germ tube elongation of A. solani conidia, with a fungistatic mode of action. Liquid chromatography-quadrupole time-of-flight mass spectrometry analysis identified two possible antifungal compounds, Alteramide A and the Heat-Stable Antifungal Factor, which together contribute partially to the bioactivity of L75 EA extract. On detached tomato leaves, coinoculation of A. solani with L75 EA extract of 50, 25, or 5 μg/ml reduced diseased areas by ∼98, ∼90, and ∼48%, respectively, relative to the control after 5 days. This study demonstrates the potential of natural products from mangrove rhizosphere bacteria in agricultural applications.
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Affiliation(s)
- Lingyun Hao
- 1 Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
- 2 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Xiaoli Zheng
- 1 Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
- 2 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Yu Wang
- 2 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Shuangfei Li
- 2 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Chenjing Shang
- 2 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Ying Xu
- 1 Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
- 2 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
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16
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Alanjary M, Cano-Prieto C, Gross H, Medema MH. Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines. Nat Prod Rep 2019; 36:1249-1261. [PMID: 31259995 DOI: 10.1039/c9np00021f] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their modular assembly line architecture potentially allows unlocking vast chemical space for biosynthesis. However, attempts thus far are often met with mixed success, due to limited molecular compatibility of the parts used for engineering. Now, new engineering strategies, increases in genomic data, and improved computational tools provide more opportunities for major progress. In this review we highlight some of the challenges and progressive strategies for the re-design of NRPSs & type I PKSs and survey useful computational tools and approaches to attain the ultimate goal of semi-automated and design-based engineering of novel peptide and polyketide products.
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Affiliation(s)
- Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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17
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Moss NA, Seiler G, Leão TF, Castro-Falcón G, Gerwick L, Hughes CC, Gerwick WH. Nature's Combinatorial Biosynthesis Produces Vatiamides A-F. Angew Chem Int Ed Engl 2019; 58:9027-9031. [PMID: 31071229 DOI: 10.1002/anie.201902571] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/18/2019] [Indexed: 12/11/2022]
Abstract
Hybrid type I PKS/NRPS biosynthetic pathways typically proceed in a collinear manner wherein one molecular building block is enzymatically incorporated in a sequence that corresponds to gene arrangement. In this work, genome mining combined with the use of a fluorogenic azide-based click probe led to the discovery and characterization of vatiamides A-F, three structurally diverse alkynylated lipopeptides, and their brominated analogues, from the cyanobacterium Moorea producens ASI16Jul14-2. These derive from a unique combinatorial non-collinear PKS/NRPS system encoded by a 90 kb gene cluster in which an upstream PKS cassette interacts with three separate cognate NRPS partners. This is facilitated by a series of promiscuous intermodule PKS-NRPS docking motifs possessing identical amino acid sequences. This interaction confers a new type of combinatorial capacity for creating molecular diversity in microbial systems.
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Affiliation(s)
- Nathan A Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Grant Seiler
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tiago F Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chambers C Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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18
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Moss NA, Seiler G, Leão TF, Castro‐Falcón G, Gerwick L, Hughes CC, Gerwick WH. Nature's Combinatorial Biosynthesis Produces Vatiamides A–F. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nathan A. Moss
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Grant Seiler
- Department of Chemistry and BiochemistryUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Tiago F. Leão
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Gabriel Castro‐Falcón
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Lena Gerwick
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Chambers C. Hughes
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - William H. Gerwick
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
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19
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Fournier J, Chen K, Mailyan AK, Jackson JJ, Buckman BO, Emayan K, Yuan S, Rajagopalan R, Misialek S, Adler M, Blaesse M, Griessner A, Zakarian A. Total Synthesis of Covalent Cysteine Protease Inhibitor N-Desmethyl Thalassospiramide C and Crystallographic Evidence for Its Mode of Action. Org Lett 2019; 21:508-512. [DOI: 10.1021/acs.orglett.8b03821] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy Fournier
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Karen Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Artur K. Mailyan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Jeffrey J. Jackson
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Brad O. Buckman
- Blade Therapeutics, 442 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Kumar Emayan
- Bayside Pharma, 2600 Hilltop Drive, Richmond, California 94806, United States
| | - Shendong Yuan
- Bayside Pharma, 2600 Hilltop Drive, Richmond, California 94806, United States
| | - Ravi Rajagopalan
- Blade Therapeutics, 442 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Shawn Misialek
- Blade Therapeutics, 442 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Marc Adler
- ChemPartner, 280 Utah Avenue Suite 100, South San Francisco, California 94080, United States
| | - Michael Blaesse
- Proteros Biostructures GmbH, Bunsenstraße 7 a, 82152 Planegg-Martinsried, Germany
| | - Andreas Griessner
- Proteros Biostructures GmbH, Bunsenstraße 7 a, 82152 Planegg-Martinsried, Germany
| | - Armen Zakarian
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
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20
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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21
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Reddy KHV, Bédier M, Bouzbouz S. Efficient and Direct Synthesis of γ-Amino-α,β-Unsaturated Amides by Catalyzed Allylic Substitution of α-Fluoroenamides: Toward to Synthesis of Hybrid Peptides and Indolizidines. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Matthieu Bédier
- INSA, COBRA UMR 6014; CNRS, University of Rouen; 76183 Mont Saint Aignan cedex France
| | - Samir Bouzbouz
- INSA, COBRA UMR 6014; CNRS, University of Rouen; 76183 Mont Saint Aignan cedex France
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22
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Baars O, Zhang X, Gibson MI, Stone AT, Morel FMM, Seyedsayamdost MR. Crochelins: Siderophores with an Unprecedented Iron‐Chelating Moiety from the Nitrogen‐Fixing Bacterium
Azotobacter chroococcum. Angew Chem Int Ed Engl 2017; 57:536-541. [DOI: 10.1002/anie.201709720] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/04/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Oliver Baars
- Department of Geosciences Princeton University Princeton NJ 08544 USA
| | - Xinning Zhang
- Department of Geosciences Princeton University Princeton NJ 08544 USA
| | - Marcus I. Gibson
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Alan T. Stone
- Department of Environmental Health and Engineering Johns Hopkins University Baltimore MD 21218 USA
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23
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Baars O, Zhang X, Gibson MI, Stone AT, Morel FMM, Seyedsayamdost MR. Crochelins: Siderophores with an Unprecedented Iron‐Chelating Moiety from the Nitrogen‐Fixing Bacterium
Azotobacter chroococcum. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Oliver Baars
- Department of Geosciences Princeton University Princeton NJ 08544 USA
| | - Xinning Zhang
- Department of Geosciences Princeton University Princeton NJ 08544 USA
| | - Marcus I. Gibson
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Alan T. Stone
- Department of Environmental Health and Engineering Johns Hopkins University Baltimore MD 21218 USA
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24
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Tobias NJ, Wolff H, Djahanschiri B, Grundmann F, Kronenwerth M, Shi YM, Simonyi S, Grün P, Shapiro-Ilan D, Pidot SJ, Stinear TP, Ebersberger I, Bode HB. Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus. Nat Microbiol 2017; 2:1676-1685. [PMID: 28993611 DOI: 10.1038/s41564-017-0039-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/08/2017] [Indexed: 12/25/2022]
Abstract
Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria. Clustering the genes encoded in the individual genomes into hierarchical orthologous groups reveals a high-resolution picture of functional evolution in this clade. It identifies groups of genes-many of which are involved in secondary metabolite production-that may account for the niche specificity of these bacteria. Photorhabdus and Xenorhabdus appear very similar at the DNA sequence level, which indicates their close evolutionary relationship. Yet, high-resolution mass spectrometry analyses reveal a huge chemical diversity in the two taxa. Molecular network reconstruction identified a large number of previously unidentified metabolite classes, including the xefoampeptides and tilivalline. Here, we apply genomic and metabolomic methods in a complementary manner to identify and elucidate additional classes of natural products. We also highlight the ability to rapidly and simultaneously identify potentially interesting bioactive products from NRPSs and PKSs, thereby augmenting the contribution of molecular biology techniques to the acceleration of natural product discovery.
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Affiliation(s)
- Nicholas J Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Bardya Djahanschiri
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Florian Grundmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Max Kronenwerth
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Yi-Ming Shi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Svenja Simonyi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Peter Grün
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - David Shapiro-Ilan
- USDA-ARS, SEA, SE Fruit and Tree Nut Research Unit, 21 Dunbar Road, Byron, GA, 31008, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Ingo Ebersberger
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.,Senckenberg Climate and Research Centre (BIK-F), Frankfurt am Main, 60325, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.
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25
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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26
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Rütschlin S, Gunesch S, Böttcher T. One Enzyme, Three Metabolites: Shewanella algae Controls Siderophore Production via the Cellular Substrate Pool. Cell Chem Biol 2017; 24:598-604.e10. [PMID: 28434877 DOI: 10.1016/j.chembiol.2017.03.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/25/2017] [Accepted: 03/24/2017] [Indexed: 11/16/2022]
Abstract
Shewanella algae B516 produces avaroferrin, an asymmetric hydroxamate siderophore, which has been shown to inhibit swarming motility of Vibrio alginolyticus. We aimed to elucidate the biosynthesis of this siderophore and to investigate how S. algae coordinates the production of avaroferrin and its two symmetric counterparts. We reconstituted the reaction in vitro with the main enzyme AvbD and the putative biosynthetic precursors, and demonstrate that multispecificity of this enzyme results in the production of all three cyclic hydroxamate siderophores that were previously isolated as natural products from S. algae. Surprisingly, purified AvbD exhibited a clear preference for the larger cadaverine-derived substrate. In live cells, however, siderophore ratios are maximized toward avaroferrin production, and we demonstrate that these siderophore ratios are the result of a regulation on substrate pool level, which may allow rapid evolutionary adaptation to environmental changes. Our results thereby give insights into a unique evolutionary strategy toward metabolite diversity.
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Affiliation(s)
- Sina Rütschlin
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sandra Gunesch
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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27
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Adamek M, Spohn M, Stegmann E, Ziemert N. Mining Bacterial Genomes for Secondary Metabolite Gene Clusters. Methods Mol Biol 2017; 1520:23-47. [PMID: 27873244 DOI: 10.1007/978-1-4939-6634-9_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
With the emergence of bacterial resistance against frequently used antibiotics, novel antibacterial compounds are urgently needed. Traditional bioactivity-guided drug discovery strategies involve laborious screening efforts and display high rediscovery rates. With the progress in next generation sequencing methods and the knowledge that the majority of antibiotics in clinical use are produced as secondary metabolites by bacteria, mining bacterial genomes for secondary metabolites with antimicrobial activity is a promising approach, which can guide a more time and cost-effective identification of novel compounds. However, what sounds easy to accomplish, comes with several challenges. To date, several tools for the prediction of secondary metabolite gene clusters are available, some of which are based on the detection of signature genes, while others are searching for specific patterns in gene content or regulation.Apart from the mere identification of gene clusters, several other factors such as determining cluster boundaries and assessing the novelty of the detected cluster are important. For this purpose, comparison of the predicted secondary metabolite genes with different cluster and compound databases is necessary. Furthermore, it is advisable to classify detected clusters into gene cluster families. So far, there is no standardized procedure for genome mining; however, different approaches to overcome all of these challenges exist and are addressed in this chapter. We give practical guidance on the workflow for secondary metabolite gene cluster identification, which includes the determination of gene cluster boundaries, addresses problems occurring with the use of draft genomes, and gives an outlook on the different methods for gene cluster classification. Based on comprehensible examples a protocol is set, which should enable the readers to mine their own genome data for interesting secondary metabolites.
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Affiliation(s)
- Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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28
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Cai X, Nowak S, Wesche F, Bischoff I, Kaiser M, Fürst R, Bode HB. Entomopathogenic bacteria use multiple mechanisms for bioactive peptide library design. Nat Chem 2016; 9:379-386. [DOI: 10.1038/nchem.2671] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 10/10/2016] [Indexed: 01/14/2023]
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29
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Zhang W, Lu L, Lai Q, Zhu B, Li Z, Xu Y, Shao Z, Herrup K, Moore BS, Ross AC, Qian PY. Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria. J Biol Chem 2016; 291:27228-27238. [PMID: 27875306 DOI: 10.1074/jbc.m116.756858] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
The thalassospiramide lipopeptides have great potential for therapeutic applications; however, their structural and functional diversity and biosynthesis are poorly understood. Here, by cultivating 130 Rhodospirillaceae strains sampled from oceans worldwide, we discovered 21 new thalassospiramide analogues and demonstrated their neuroprotective effects. To investigate the diversity of biosynthetic gene cluster (BGC) architectures, we sequenced the draft genomes of 28 Rhodospirillaceae strains. Our family-wide genomic analysis revealed three types of dysfunctional BGCs and four functional BGCs whose architectures correspond to four production patterns. This correlation allowed us to reassess the "diversity-oriented biosynthesis" proposed for the microbial production of thalassospiramides, which involves iteration of several key modules. Preliminary evolutionary investigation suggested that the functional BGCs could have arisen through module/domain loss, whereas the dysfunctional BGCs arose through horizontal gene transfer. Further comparative genomics indicated that thalassospiramide production is likely to be attendant on particular genes/pathways for amino acid metabolism, signaling transduction, and compound efflux. Our findings provide a systematic understanding of thalassospiramide production and new insights into the underlying mechanism.
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Affiliation(s)
- Weipeng Zhang
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Liang Lu
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Qiliang Lai
- the Third Institute of Oceanography, State Oceanic Administration, Xiamen 361000, China
| | - Beika Zhu
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Zhongrui Li
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Ying Xu
- the School of Life Science, Shenzhen University, Shenzhen, Guangdong Province 518060, China
| | - Zongze Shao
- the Third Institute of Oceanography, State Oceanic Administration, Xiamen 361000, China
| | - Karl Herrup
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Bradley S Moore
- the Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, and
| | - Avena C Ross
- the Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Pei-Yuan Qian
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong,
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30
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Nakashima Y, Egami Y, Kimura M, Wakimoto T, Abe I. Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'. PLoS One 2016; 11:e0164468. [PMID: 27732651 PMCID: PMC5061366 DOI: 10.1371/journal.pone.0164468] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an ‘Entotheonella’ sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.
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Affiliation(s)
- Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoko Egami
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Miki Kimura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
- * E-mail: (TW); (IA)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (TW); (IA)
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31
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Li ZR, Li J, Gu JP, Lai JYH, Duggan BM, Zhang WP, Li ZL, Li YX, Tong RB, Xu Y, Lin DH, Moore BS, Qian PY. Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin. Nat Chem Biol 2016; 12:773-5. [PMID: 27547923 PMCID: PMC5030165 DOI: 10.1038/nchembio.2157] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/14/2016] [Indexed: 12/25/2022]
Abstract
Colibactin is an as-yet-uncharacterized genotoxic secondary metabolite produced by human gut bacteria. Here we report the biosynthetic discovery of two new precolibactin molecules from Escherichia coli, including precolibactin-886, which uniquely incorporates the highly sought genotoxicity-associated aminomalonate building block into its unprecedented macrocyclic structure. This work provides new insights into the biosynthetic logic and mode of action of this colorectal-cancer-linked microbial chemical.
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Affiliation(s)
- Zhong-Rui Li
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States
| | - Jin-Ping Gu
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jennifer Y. H. Lai
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, United States
| | - Wei-Peng Zhang
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Zhi-Long Li
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Yong-Xin Li
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Rong-Biao Tong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource & Ecoenvironmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Dong-Hai Lin
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, United States
| | - Pei-Yuan Qian
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
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32
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Friestad GK, Banerjee K, Marié JC, Mali U, Yao L. Stereoselective access to tubuphenylalanine and tubuvaline: improved Mn-mediated radical additions and assembly of a tubulysin tetrapeptide analog. J Antibiot (Tokyo) 2016; 69:294-8. [PMID: 26883395 PMCID: PMC4924578 DOI: 10.1038/ja.2016.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 01/05/2023]
Abstract
Synthesis of tubuphenylalanine and tubuvaline (Tuv), α-substituted γ-amino acid building blocks for tubulysin family of antimitotic compounds, has been improved using a radical addition reaction in the presence of unprotected hydroxyl functionality. The key carbon-carbon bond construction entails stereoselective Mn-mediated photolytic additions of alkyl iodides to the C=N bond of chiral N-acylhydrazones, and generates the chiral amines in high yield with complete stereocontrol. Reductive N-N bond cleavage and alcohol oxidation converted these amino alcohols into the corresponding γ-amino acids. The route to Tuv proceeded via peptide coupling with serine methyl ester, followed by a high-yielding sequence to convert the serine amide to a thiazole. Finally, peptide bond construction established the tubulysin framework in the form of a C-terminal alcohol analog. Attempted oxidation to the C-terminal carboxylate was unsuccessful; control experiments with dipeptide 18 showed a cyclization interfered with the desired oxidation process.
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Affiliation(s)
| | - Koushik Banerjee
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242 USA
| | | | - Umesh Mali
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242 USA
| | - Lei Yao
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242 USA
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33
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Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 2015; 11:649-59. [PMID: 26284672 DOI: 10.1038/nchembio.1893] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022]
Abstract
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
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34
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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35
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Abstract
This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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36
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Marxen S, Stark TD, Rütschle A, Lücking G, Frenzel E, Scherer S, Ehling-Schulz M, Hofmann T. Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus. Sci Rep 2015; 5:10637. [PMID: 26013201 PMCID: PMC4445039 DOI: 10.1038/srep10637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/22/2015] [Indexed: 11/10/2022] Open
Abstract
Cereulide and isocereulides A-G are biosynthesized as emetic toxins by Bacillus cereus via a non-ribosomal peptide synthetase (NRPS) called Ces. Although a thiotemplate mechanisms involving cyclo-trimerization of ready-made D-O-Leu-D-Ala-L-O-Val-L-Val via a thioesterase (TE) domain is proposed for cereulide biosynthesis, the exact mechanism is far from being understood. UPLC-TOF MS analysis of B. cereus strains in combination with 13C-labeling experiments now revealed tetra-, octa-, and dodecapeptides of a different sequence, namely (L-O-Val-L-Val-D-O-Leu-D-Ala)1-3, as intermediates of cereulide biosynthesis. Surprisingly, also di-, hexa-, and decadepsipeptides were identified which, together with the structures of the previously reported isocereulides E, F, and G, do not correlate to the currently proposed mechanism for cereulide biosynthesis and violate the canonical NRPS biosynthetic logic. UPLC-TOF MS metabolite analysis and bioinformatic gene cluster analysis highlighted dipeptides rather than single amino or hydroxy acids as the basic modules in tetradepsipeptide assembly and proposed the CesA C-terminal C* domain and the CesB C-terminal TE domain to function as a cooperative esterification and depsipeptide elongation center repeatedly recruiting the action of the C* domain to oligomerize tetradepsipeptides prior to the release of cereulide from the TE domain by macrocyclization.
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Affiliation(s)
- Sandra Marxen
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Straße 34, Freising, 85354, Germany
| | - Timo D Stark
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Straße 34, Freising, 85354, Germany
| | - Andrea Rütschle
- Department of Microbiology, Central Institute for Food and Nutrition Research, Technische Universität München, Freising, 85350
| | - Genia Lücking
- Department of Microbiology, Central Institute for Food and Nutrition Research, Technische Universität München, Freising, 85350
| | - Elrike Frenzel
- Institute of Microbiology Department of Pathobiology, Functional Microbiology, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Siegfried Scherer
- Department of Microbiology, Central Institute for Food and Nutrition Research, Technische Universität München, Freising, 85350.,Department of Biosciences, Chair of Microbial Ecology, WZW, Technische Universität München, Freising, 85350, Germany
| | - Monika Ehling-Schulz
- Institute of Microbiology Department of Pathobiology, Functional Microbiology, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Straße 34, Freising, 85354, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Gregor-Mendel Strasse 4, 85354, Freising, Germany
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37
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Awakawa T, Crüsemann M, Munguia J, Ziemert N, Nizet V, Fenical W, Moore BS. Salinipyrone and Pacificanone Are Biosynthetic By-products of the Rosamicin Polyketide Synthase. Chembiochem 2015; 16:1443-7. [PMID: 25930739 DOI: 10.1002/cbic.201500177] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Indexed: 11/12/2022]
Abstract
Salinipyrones and pacificanones are structurally related polyketides from Salinispora pacifica CNS-237 that are proposed to arise from the same modular polyketide synthase (PKS) assembly line. Genome sequencing revealed a large macrolide PKS gene cluster that codes for the biosynthesis of rosamicin A and a series of new macrolide antibiotics. Mutagenesis experiments unexpectedly correlated salinipyrone and pacificanone biosynthesis to the rosamicin octamodule Spr PKS. Remarkably, this bifurcated polyketide pathway illuminates a series of enzymatic domain- and module-skipping reactions that give rise to natural polyketide product diversity. Our findings enlarge the growing knowledge of polyketide biochemistry and illuminate potential challenges in PKS bioengineering.
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Affiliation(s)
- Takayoshi Awakawa
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA).,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Max Crüsemann
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA)
| | - Jason Munguia
- Pediatrics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Nadine Ziemert
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA)
| | - Victor Nizet
- Pediatrics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA).,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - William Fenical
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA)
| | - Bradley S Moore
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA). .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA).
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38
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Mechanism of action of thalassospiramides, a new class of calpain inhibitors. Sci Rep 2015; 5:8783. [PMID: 25740631 PMCID: PMC4350077 DOI: 10.1038/srep08783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022] Open
Abstract
Thalassospiramides comprise a large family of lipopeptide natural products produced by Thalassospira and Tistrella marine bacteria. Here we provide further evidence of their nanomolar inhibitory activity against the human calpain 1 protease. Analysis of structure-activity relationship data supported our hypothesis that the rigid 12-membered ring containing an α,β-unsaturated carbonyl moiety is the pharmacologically active functional group, in contrast to classic electrophilic “warheads” in known calpain inhibitors. Using a combination of chemical modifications, mass spectrometric techniques, site-directed mutagenesis, and molecular modeling, we show the covalent binding of thalassospiramide's α,β-unsaturated carbonyl moiety to the thiol group of calpain's catalytic Cys115 residue by a Michael 1,4-addition reaction. As nanomolar calpain inhibitors with promising selectivity and low toxicity from natural sources are rare, we consider thalassospiramides as promising drug leads.
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39
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Magnetotactic bacteria as potential sources of bioproducts. Mar Drugs 2015; 13:389-430. [PMID: 25603340 PMCID: PMC4306944 DOI: 10.3390/md13010389] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/17/2014] [Indexed: 11/16/2022] Open
Abstract
Magnetotactic bacteria (MTB) produce intracellular organelles called magnetosomes which are magnetic nanoparticles composed of magnetite (Fe3O4) or greigite (Fe3S4) enveloped by a lipid bilayer. The synthesis of a magnetosome is through a genetically controlled process in which the bacterium has control over the composition, direction of crystal growth, and the size and shape of the mineral crystal. As a result of this control, magnetosomes have narrow and uniform size ranges, relatively specific magnetic and crystalline properties, and an enveloping biological membrane. These features are not observed in magnetic particles produced abiotically and thus magnetosomes are of great interest in biotechnology. Most currently described MTB have been isolated from saline or brackish environments and the availability of their genomes has contributed to a better understanding and culturing of these fastidious microorganisms. Moreover, genome sequences have allowed researchers to study genes related to magnetosome production for the synthesis of magnetic particles for use in future commercial and medical applications. Here, we review the current information on the biology of MTB and apply, for the first time, a genome mining strategy on these microorganisms to search for secondary metabolite synthesis genes. More specifically, we discovered that the genome of the cultured MTB Magnetovibrio blakemorei, among other MTB, contains several metabolic pathways for the synthesis of secondary metabolites and other compounds, thereby raising the possibility of the co-production of new bioactive molecules along with magnetosomes by this species.
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40
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Lu L, Wang J, Xu Y, Wang K, Hu Y, Tian R, Yang B, Lai Q, Li Y, Zhang W, Shao Z, Lam H, Qian PY. A high-resolution LC-MS-based secondary metabolite fingerprint database of marine bacteria. Sci Rep 2014; 4:6537. [PMID: 25298017 PMCID: PMC5377448 DOI: 10.1038/srep06537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/04/2014] [Indexed: 01/01/2023] Open
Abstract
Marine bacteria are the most widely distributed organisms in the ocean environment and produce a wide variety of secondary metabolites. However, traditional screening for bioactive natural compounds is greatly hindered by the lack of a systematic way of cataloguing the chemical profiles of bacterial strains found in nature. Here we present a chemical fingerprint database of marine bacteria based on their secondary metabolite profiles, acquired by high-resolution LC-MS. Till now, 1,430 bacterial strains spanning 168 known species collected from different marine environments were cultured and profiled. Using this database, we demonstrated that secondary metabolite profile similarity is approximately, but not always, correlated with taxonomical similarity. We also validated the ability of this database to find species-specific metabolites, as well as to discover known bioactive compounds from previously unknown sources. An online interface to this database, as well as the accompanying software, is provided freely for the community to use.
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Affiliation(s)
- Liang Lu
- 1] Environmental Science Program, School of Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China [2]
| | - Jijie Wang
- 1] Division of Biomedical Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China [2]
| | - Ying Xu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Kailing Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yingwei Hu
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Renmao Tian
- Environmental Science Program, School of Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Bo Yang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Qiliang Lai
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Yongxin Li
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Weipeng Zhang
- Environmental Science Program, School of Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Zongze Shao
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Henry Lam
- 1] Division of Biomedical Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China [2] Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Pei-Yuan Qian
- 1] Environmental Science Program, School of Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China [2] Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
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41
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Schieferdecker S, König S, Weigel C, Dahse HM, Werz O, Nett M. Structure and biosynthetic assembly of gulmirecins, macrolide antibiotics from the predatory bacterium Pyxidicoccus fallax. Chemistry 2014; 20:15933-40. [PMID: 25287056 DOI: 10.1002/chem.201404291] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 01/28/2023]
Abstract
The gulmirecins constitute a new class of glycosylated macrolides that were isolated from the predatory bacterium Pyxidicoccus fallax HKI 727. Their structures were solved by a combination of NMR spectroscopic experiments and chemical derivatization. Analysis of the annotated gulmirecin gene cluster complemented the configurational assignment and provided insights into the stereochemical course of the biosynthetic assembly. The gulmirecins exhibit strong activity against staphylococci, including methicillin-resistant Staphylococcus aureus, but no cytotoxic effects on human cells.
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Affiliation(s)
- Sebastian Schieferdecker
- Junior Research Group, "Secondary Metabolism of Predatory Bacteria", Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena (Germany), Fax: (+49) 3641-5320811
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42
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Lai Q, Liu Y, Yuan J, Du J, Wang L, Sun F, Shao Z. Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments. PLoS One 2014; 9:e106353. [PMID: 25198177 PMCID: PMC4157779 DOI: 10.1371/journal.pone.0106353] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/02/2014] [Indexed: 11/23/2022] Open
Abstract
Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16–97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76–97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments.
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Affiliation(s)
- Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Jun Yuan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Liping Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
- * E-mail:
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Still PC, Johnson TA, Theodore CM, Loveridge ST, Crews P. Scrutinizing the scaffolds of marine biosynthetics from different source organisms: Gram-negative cultured bacterial products enter center stage. JOURNAL OF NATURAL PRODUCTS 2014; 77:690-702. [PMID: 24571234 PMCID: PMC4095796 DOI: 10.1021/np500041x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Compounds from macro marine organisms are presumed to owe their biosynthetic origins to associated microbial symbionts, although few definitive examples exist. An upsurge in the recent literature from 2012 to 2013 has shown that four compounds previously reported from macro marine organisms are in fact biosynthesized by non-photosynthetic Gram-negative bacteria (NPGNB). Structural parallels between compounds isolated from macro marine organisms and NPGNB producers form the basis of this review. Although less attention has been given to investigating the chemistry of NPGNB sources, there exists a significant list of structural parallels between NPGNB and macro marine organism-derived compounds. Alternatively, of the thousands of compounds isolated from Gram-positive actinomycetes, few structural parallels with macro marine organisms are known. A summary of small molecules isolated from marine NPGNB sources is presented, including compounds isolated from marine myxobacteria. From this assemblage of structural parallels and diverse chemical structures, it is hypothesized that the potential for the discovery of inspirational molecules from NPGNB sources is vast and that the recent spike in the literature of macro marine compounds owing their biosynthetic origin to NPGNB producers represents a turning point in the field.
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Affiliation(s)
- Patrick C. Still
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95060, United States
| | - Tyler A. Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95060, United States
| | - Christine M. Theodore
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95060, United States
| | - Steven T. Loveridge
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95060, United States
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95060, United States
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Schorn M, Zettler J, Noel JP, Dorrestein PC, Moore BS, Kaysser L. Genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors. ACS Chem Biol 2014; 9:301-9. [PMID: 24168704 DOI: 10.1021/cb400699p] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The epoxyketone proteasome inhibitors are an established class of therapeutic agents for the treatment of cancer. Their unique α',β'-epoxyketone pharmacophore allows binding to the catalytic β-subunits of the proteasome with extraordinary specificity. Here, we report the characterization of the first gene clusters for the biosynthesis of natural peptidyl-epoxyketones. The clusters for epoxomicin, the lead compound for the anticancer drug Kyprolis, and for eponemycin were identified in the actinobacterial producer strains ATCC 53904 and Streptomyces hygroscopicus ATCC 53709, respectively, using a modified protocol for Ion Torrent PGM genome sequencing. Both gene clusters code for a hybrid nonribosomal peptide synthetase/polyketide synthase multifunctional enzyme complex and homologous redox enzymes. Epoxomicin and eponemycin were heterologously produced in Streptomyces albus J1046 via whole pathway expression. Moreover, we employed mass spectral molecular networking for a new comparative metabolomics approach in a heterologous system and discovered a number of putative epoxyketone derivatives. With this study, we have definitively linked epoxyketone proteasome inhibitors and their biosynthesis genes for the first time in any organism, which will now allow for their detailed biochemical investigation.
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Affiliation(s)
- Michelle Schorn
- Scripps
Institution of Oceanography, University of California, San Diego, California 92093, United States of America
| | - Judith Zettler
- Pharmaceutical
Biology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Center
for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Joseph P. Noel
- Jack
H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States of America
| | - Pieter C. Dorrestein
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States of America
| | - Bradley S. Moore
- Scripps
Institution of Oceanography, University of California, San Diego, California 92093, United States of America
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States of America
| | - Leonard Kaysser
- Scripps
Institution of Oceanography, University of California, San Diego, California 92093, United States of America
- Pharmaceutical
Biology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Center
for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
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Challenges and triumphs to genomics-based natural product discovery. J Ind Microbiol Biotechnol 2013; 41:203-9. [PMID: 24104399 DOI: 10.1007/s10295-013-1353-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022]
Abstract
Genome sequencing is rapidly changing the field of natural products research by providing opportunities to assess the biosynthetic potential of strains prior to chemical analysis or biological testing. Ready access to sequence data is driving the development of new bioinformatic tools and methods to identify the products of silent or cryptic pathways. While genome mining has fast become a useful approach to natural product discovery, it has also become clear that identifying pathways of interest is much easier than finding the associated products. This has led to bottlenecks in the discovery process that must be overcome for the potential of genomics-based natural product discovery to be fully realized. In this perspective, we address some of these challenges in the context of our work with the marine actinomycete genus Salinispora, which is proving to be a useful model with which to apply genome mining as an approach to natural product discovery.
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Reimer D, Cowles KN, Proschak A, Nollmann FI, Dowling AJ, Kaiser M, ffrench-Constant R, Goodrich-Blair H, Bode HB. Rhabdopeptides as insect-specific virulence factors from entomopathogenic bacteria. Chembiochem 2013; 14:1991-7. [PMID: 24038745 DOI: 10.1002/cbic.201300205] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Indexed: 12/17/2022]
Abstract
Six novel linear peptides, named "rhabdopeptides", have been identified in the entomopathogenic bacterium Xenorhabdus nematophila after the discovery of the corresponding rdp gene cluster by using a promoter trap strategy for the detection of insect-inducible genes. The structures of these rhabdopeptides were deduced from labeling experiments combined with detailed MS analysis. Detailed analysis of an rdp mutant revealed that these compounds participate in virulence towards insects and are produced upon bacterial infection of a suitable insect host. Furthermore, two additional rhabdopeptide derivatives produced by Xenorhabdus cabanillasii were isolated, these showed activity against insect hemocytes thereby confirming the virulence of this novel class of compounds.
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Affiliation(s)
- Daniela Reimer
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main (Germany)
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Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses. Proc Natl Acad Sci U S A 2013; 110:E3129-37. [PMID: 23898213 DOI: 10.1073/pnas.1305867110] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bacteria are a major source of natural products that provide rich opportunities for both chemical and biological investigation. Although the vast majority of known bacterial metabolites derive from free-living organisms, increasing evidence supports the widespread existence of chemically prolific bacteria living in symbioses. A strategy based on bioinformatic prediction, symbiont cultivation, isotopic enrichment, and advanced analytics was used to characterize a unique polyketide, nosperin, from a lichen-associated Nostoc sp. cyanobacterium. The biosynthetic gene cluster and the structure of nosperin, determined from 30 μg of compound, are related to those of the pederin group previously known only from nonphotosynthetic bacteria associated with beetles and marine sponges. The presence of this natural product family in such highly dissimilar associations suggests that some bacterial metabolites may be specific to symbioses with eukaryotes and encourages exploration of other symbioses for drug discovery and better understanding of ecological interactions mediated by complex bacterial metabolites.
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Um S, Pyee Y, Kim EH, Lee SK, Shin J, Oh DC. Thalassospiramide G, a new γ-amino-acid-bearing peptide from the marine bacterium Thalassospira sp. Mar Drugs 2013; 11:611-22. [PMID: 23442790 PMCID: PMC3705361 DOI: 10.3390/md11030611] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/29/2013] [Accepted: 02/06/2013] [Indexed: 01/05/2023] Open
Abstract
In the chemical investigation of marine unicellular bacteria, a new peptide, thalassospiramide G (1), along with thalassospiramides A and D (2–3), was discovered from a large culture of Thalassospira sp. The structure of thalassospiramide G, bearing γ-amino acids, such as 4-amino-5-hydroxy-penta-2-enoic acid (AHPEA), 4-amino-3,5-dihydroxy-pentanoic acid (ADPA), and unique 2-amino-1-(1H-indol-3-yl)ethanone (AIEN), was determined via extensive spectroscopic analysis. The absolute configuration of thalassospiramide D (3), including 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA), was rigorously determined by 1H–1H coupling constant analysis and chemical derivatization. Thalassospiramides A and D (2–3) inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated mouse macrophage RAW 264.7 cells, with IC50 values of 16.4 and 4.8 μM, respectively.
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Affiliation(s)
- Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Yuna Pyee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Korea; E-Mail:
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-2-880-2491; Fax: +82-2-762-8322
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