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Brito TLD, Edson EA, Dias Florêncio KG, Machado-Neto JA, Garnique ADMB, Mesquita Luiz JP, Cunha FDQ, Alves-Filho JC, Haygood M, Wilke DV. Tartrolon D induces immunogenic cell death in melanoma. Chem Biol Interact 2024; 400:111177. [PMID: 39097071 DOI: 10.1016/j.cbi.2024.111177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Tartrolon D (TRL) is produced by Teredinibacter turnerae, a symbiotic cellulose-degrading bacteria in shipworm gills. Immunogenic cell death (ICD) induction contributes to a better and longer-lasting response to anticancer treatment. Tumor cells undergoing ICD trigger activation of the immune system, as a vaccine. AIMS This study aimed to evaluate ICD induction by TRL. MAIN METHODS Cell viability was evaluated by SRB assay. Cell stress, cell death, ICD features and antigen-presenting molecules were evaluated by flow cytometry and immunoblot. KEY FINDINGS TRL showed antiproliferative activity on 7 tumor cell lines (L929, HCT 116, B16-F10, WM293A, SK-MEL-28, PC-3M, and MCF-7) and a non-tumor cell (HEK293A), with an inhibition concentration mean (IC50) ranging from 0.03 μM to 13 μM. Metastatic melanomas, SK-MEL-28, B16-F10, and WM293A, were more sensitive cell lines, with IC50 ranging from 0.07 to 1.2 μM. TRL induced apoptosis along with autophagy and endoplasmic reticulum stress and release of typical damage-associated molecular patterns (DAMPs) of ICD such calreticulin, ERp57, and HSP70 exposure, and HMGB1 release. Additionally, melanoma B16-F10 exposed to TRL increased expression of antigen-presenting molecules MHC II and CD1d and induced activation of splenocytes of C57BL/6 mice. SIGNIFICANCE In spite of recent advances provided by target therapy and immunotherapy, advanced metastatic melanoma is incurable for more than half of patients. ICD inducers yield better and long-lasting responses to anticancer treatment. Our findings shed light on an anticancer candidate of marine origin that induces ICD in melanoma.
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Affiliation(s)
- Thaís Lima de Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceara, Ceara, Brazil.
| | - Evelline Araújo Edson
- Drug Research and Development Center, Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceara, Ceara, Brazil.
| | - Katharine Gurgel Dias Florêncio
- Drug Research and Development Center, Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceara, Ceara, Brazil.
| | | | | | - João Paulo Mesquita Luiz
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil.
| | - Fernando de Queiroz Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil.
| | - José Carlos Alves-Filho
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil.
| | | | - Diego Veras Wilke
- Drug Research and Development Center, Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceara, Ceara, Brazil.
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2
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Grams RJ, Santos WL, Scorei IR, Abad-García A, Rosenblum CA, Bita A, Cerecetto H, Viñas C, Soriano-Ursúa MA. The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology. Chem Rev 2024; 124:2441-2511. [PMID: 38382032 DOI: 10.1021/acs.chemrev.3c00663] [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: 02/23/2024]
Abstract
Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.
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Affiliation(s)
- R Justin Grams
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | | | - Antonio Abad-García
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
| | - Carol Ann Rosenblum
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Andrei Bita
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Hugo Cerecetto
- Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Marvin A Soriano-Ursúa
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
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3
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Chery-Karschney L, Patrapuvich R, Mudeppa DG, Kokkonda S, Chakrabarti R, Sriwichai P, O'Connor RM, Rathod PK, White J. Tartrolon E, a secondary metabolite of a marine symbiotic bacterium, is a potent inhibitor of asexual and sexual Plasmodium falciparum. Antimicrob Agents Chemother 2024; 68:e0068423. [PMID: 38193705 PMCID: PMC10848769 DOI: 10.1128/aac.00684-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/10/2023] [Indexed: 01/10/2024] Open
Abstract
Due to the spread of resistance to front-line artemisinin derivatives worldwide, there is a need for new antimalarials. Tartrolon E (TrtE), a secondary metabolite of a symbiotic bacterium of marine bivalve mollusks, is a promising antimalarial because it inhibits the growth of sexual and asexual blood stages of Plasmodium falciparum at sub-nanomolar levels. The potency of TrtE warrants further investigation into its mechanism of action, cytotoxicity, and ease with which parasites may evolve resistance to it.
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Affiliation(s)
| | - Rapatbhorn Patrapuvich
- Drug Research Unit for Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Sreekanth Kokkonda
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Rimi Chakrabarti
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Medicine, Goa Medical College and Hospital, Bambolim, Goa, India
| | - Patchara Sriwichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Roberta M. O'Connor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - John White
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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4
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Naka H, Haygood MG. The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae. Appl Environ Microbiol 2023; 89:e0074423. [PMID: 38009998 PMCID: PMC10734418 DOI: 10.1128/aem.00744-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/01/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE This study highlights diversity in iron acquisition and regulation in bacteria. The mechanisms of iron acquisition and its regulation in Teredinibacter turnerae, as well as its connection to cellulose utilization, a hallmark phenotype of T. turnerae, expand the paradigm of bacterial iron acquisition. Two of the four TonB genes identified in T. turnerae exhibit functional redundancy and play a crucial role in siderophore-mediated iron transport. Unlike typical TonB genes in bacteria, none of the TonB genes in T. turnerae are clearly iron regulated. This unusual regulation could be explained by another important finding in this study, namely, that the two TonB genes involved in iron transport are also essential for cellulose utilization as a carbon source, leading to the expression of TonB genes even under iron-rich conditions.
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Affiliation(s)
- Hiroaki Naka
- Department of Medicinal Chemistry, The University of Utah, Salt Lake City, Utah, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Margo G. Haygood
- Department of Medicinal Chemistry, The University of Utah, Salt Lake City, Utah, USA
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5
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Lim AL, Miller BW, Lin Z, Fisher MA, Barrows LR, Haygood MG, Schmidt EW. Resistance mechanisms for Gram-negative bacteria-specific lipopeptides, turnercyclamycins, differ from that of colistin. Microbiol Spectr 2023; 11:e0230623. [PMID: 37882570 PMCID: PMC10714751 DOI: 10.1128/spectrum.02306-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/13/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Bacterial resistance to antibiotics is a crisis. Acinetobacter baumannii is among the CDC urgent threat pathogens in part for this reason. Lipopeptides known as turnercyclamycins are produced by symbiotic bacteria that normally live in marine mollusks, where they may be involved in shaping their symbiotic niche. Turnercyclamycins killed Gram-negative pathogens including drug-resistant Acinetobacter, but how do the mechanisms of resistance compare to other lipopeptide drugs? Here, we define resistance from a truncation of MlaA, a protein involved in regulating bacterial membrane phospholipids. Intriguingly, this resistance mechanism only affected one turnercyclamycin variant, which differed only in two atoms in the lipid tail of the compounds. We could not obtain significant resistance to the second turnercyclamycin variant, which was also effective in an infection model. This study reveals an unexpected subtlety in resistance to lipopeptide antibiotics, which may be useful in the design and development of antibiotics to combat drug resistance.
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Affiliation(s)
- Albebson L. Lim
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Bailey W. Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Mark A. Fisher
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, Utah, USA
| | - Louis R. Barrows
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, USA
| | - Margo G. Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
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6
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Engelgeh T, Herrmann J, Jansen R, Müller R, Halbedel S. Tartrolon sensing and detoxification by the Listeria monocytogenes timABR resistance operon. Mol Microbiol 2023; 120:629-644. [PMID: 37804169 DOI: 10.1111/mmi.15178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
Listeria monocytogenes is a foodborne bacterium that naturally occurs in the soil. Originating from there, it contaminates crops and infects farm animals and their consumption by humans may lead to listeriosis, a systemic life-threatening infectious disease. The adaptation of L. monocytogenes to such contrastive habitats is reflected by the presence of virulence genes for host infection and other genes for survival under environmental conditions. Among the latter are ABC transporters for excretion of antibiotics produced by environmental competitors; however, most of these transporters have not been characterized. Here, we generated a collection of promoter-lacZ fusions for genes encoding ABC-type drug transporters of L. monocytogenes and screened this reporter strain collection for induction using a library of natural compounds produced by various environmental microorganisms. We found that the timABR locus (lmo1964-lmo1962) was induced by the macrodiolide antibiotic tartrolon B, which is synthesized by the soil myxobacterium Sorangium cellulosum. Tartrolon B resistance of L. monocytogenes was dependent on timAB, encoding the ATPase and the permease component of a novel ABC transporter. Moreover, transplantation of timAB was sufficient to confer tartrolon B resistance to Bacillus subtilis. Expression of the timABR locus was found to be auto-repressed by the TimR repressor, whose repressing activity was lost in the presence of tartrolon B. We also demonstrate that tartrolon sensitivity was suppressed by high external potassium concentrations, suggesting that tartrolon acts as potassium ionophore. Our results help to map the ecological interactions of an important human pathogen with its co-residing species within their joint natural reservoir.
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Affiliation(s)
- Tim Engelgeh
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken, Germany
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken, Germany
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
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7
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Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals. Mar Drugs 2023; 21:md21030174. [PMID: 36976223 PMCID: PMC10055925 DOI: 10.3390/md21030174] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Diverse ecologically important metabolites, such as allelochemicals, infochemicals and volatile organic chemicals, are involved in marine organismal interactions. Chemically mediated interactions between intra- and interspecific organisms can have a significant impact on community organization, population structure and ecosystem functioning. Advances in analytical techniques, microscopy and genomics are providing insights on the chemistry and functional roles of the metabolites involved in such interactions. This review highlights the targeted translational value of several marine chemical ecology-driven research studies and their impact on the sustainable discovery of novel therapeutic agents. These chemical ecology-based approaches include activated defense, allelochemicals arising from organismal interactions, spatio-temporal variations of allelochemicals and phylogeny-based approaches. In addition, innovative analytical techniques used in the mapping of surface metabolites as well as in metabolite translocation within marine holobionts are summarized. Chemical information related to the maintenance of the marine symbioses and biosyntheses of specialized compounds can be harnessed for biomedical applications, particularly in microbial fermentation and compound production. Furthermore, the impact of climate change on the chemical ecology of marine organisms—especially on the production, functionality and perception of allelochemicals—and its implications on drug discovery efforts will be presented.
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8
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Naka H, Haygood MG. The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529781. [PMID: 36865190 PMCID: PMC9980095 DOI: 10.1101/2023.02.23.529781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Teredinibacter turnerae is an intracellular bacterial symbiont that resides in the gills of shipworms, wood-eating bivalve mollusks. This bacterium produces a catechol siderophore, turnerbactin, required for the survival of this bacterium under iron limiting conditions. The turnerbactin biosynthetic genes are contained in one of the secondary metabolite clusters conserved among T. turnerae strains. However, Fe(III)-turnerbactin uptake mechanisms are largely unknown. Here, we show that the first gene of the cluster, fttA a homologue of Fe(III)-siderophore TonB-dependent outer membrane receptor (TBDR) genes is indispensable for iron uptake via the endogenous siderophore, turnerbactin, as well as by an exogenous siderophore, amphi-enterobactin, ubiquitously produced by marine vibrios. Furthermore, three TonB clusters containing four tonB genes were identified, and two of these genes, tonB1b and tonB2, functioned not only for iron transport but also for carbohydrate utilization when cellulose was a sole carbon source. Gene expression analysis revealed that none of the tonB genes and other genes in those clusters were clearly regulated by iron concentration while turnerbactin biosynthesis and uptake genes were up-regulated under iron limiting conditions, highlighting the importance of tonB genes even in iron rich conditions, possibly for utilization of carbohydrates derived from cellulose.
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Affiliation(s)
- Hiroaki Naka
- Department of Medicinal Chemistry, the University of Utah
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University
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9
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Ueoka R, Sondermann P, Leopold-Messer S, Liu Y, Suo R, Bhushan A, Vadakumchery L, Greczmiel U, Yashiroda Y, Kimura H, Nishimura S, Hoshikawa Y, Yoshida M, Oxenius A, Matsunaga S, Williamson RT, Carreira EM, Piel J. Genome-based discovery and total synthesis of janustatins, potent cytotoxins from a plant-associated bacterium. Nat Chem 2022; 14:1193-1201. [PMID: 36064972 PMCID: PMC7613652 DOI: 10.1038/s41557-022-01020-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Host-associated bacteria are increasingly being recognized as underexplored sources of bioactive natural products with unprecedented chemical scaffolds. A recently identified example is the plant-root-associated marine bacterium Gynuella sunshinyii of the chemically underexplored order Oceanospirillales. Its genome contains at least 22 biosynthetic gene clusters, suggesting a rich and mostly uncharacterized specialized metabolism. Here, in silico chemical prediction of a non-canonical polyketide synthase cluster has led to the discovery of janustatins, structurally unprecedented polyketide alkaloids with potent cytotoxicity that are produced in minute quantities. A combination of MS and two-dimensional NMR experiments, density functional theory calculations of 13C chemical shifts and semiquantitative interpretation of transverse rotating-frame Overhauser effect spectroscopy data were conducted to determine the relative configuration, which enabled the total synthesis of both enantiomers and assignment of the absolute configuration. Janustatins feature a previously unknown pyridodihydropyranone heterocycle and an unusual biological activity consisting of delayed, synchronized cell death at subnanomolar concentrations.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Philipp Sondermann
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Stefan Leopold-Messer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Yizhou Liu
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Rei Suo
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Lida Vadakumchery
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Ute Greczmiel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Yoko Yashiroda
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiromi Kimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Shinichi Nishimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yojiro Hoshikawa
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Annette Oxenius
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - R. Thomas Williamson
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Erick M. Carreira
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland,Correspondence and requests for materials should be addressed to J.P. or E.M.C.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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Biţă A, Scorei IR, Bălşeanu TA, Ciocîlteu MV, Bejenaru C, Radu A, Bejenaru LE, Rău G, Mogoşanu GD, Neamţu J, Benner SA. New Insights into Boron Essentiality in Humans and Animals. Int J Mol Sci 2022; 23:ijms23169147. [PMID: 36012416 PMCID: PMC9409115 DOI: 10.3390/ijms23169147] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 11/19/2022] Open
Abstract
Boron (B) is considered a prebiotic chemical element with a role in both the origin and evolution of life, as well as an essential micronutrient for some bacteria, plants, fungi, and algae. B has beneficial effects on the biological functions of humans and animals, such as reproduction, growth, calcium metabolism, bone formation, energy metabolism, immunity, and brain function. Naturally organic B (NOB) species may become promising novel prebiotic candidates. NOB-containing compounds have been shown to be essential for the symbiosis between organisms from different kingdoms. New insights into the key role of NOB species in the symbiosis between human/animal hosts and their microbiota will influence the use of natural B-based colon-targeting nutraceuticals. The mechanism of action (MoA) of NOB species is related to the B signaling molecule (autoinducer-2-borate (AI-2B)) as well as the fortification of the colonic mucus gel layer with NOB species from B-rich prebiotic diets. Both the microbiota and the colonic mucus gel layer can become NOB targets. This paper reviews the evidence supporting the essentiality of the NOB species in the symbiosis between the microbiota and the human/animal hosts, with the stated aim of highlighting the MoA and targets of these species.
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Affiliation(s)
- Andrei Biţă
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., 31B Dunării Street, 207465 Podari, Romania
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Ion Romulus Scorei
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., 31B Dunării Street, 207465 Podari, Romania
- Correspondence: ; Tel.: +40-351-407-543
| | - Tudor Adrian Bălşeanu
- Department of Physiology, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Maria Viorica Ciocîlteu
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Cornelia Bejenaru
- Department of Pharmaceutical Botany, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Antonia Radu
- Department of Pharmaceutical Botany, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Ludovic Everard Bejenaru
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Gabriela Rău
- Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - George Dan Mogoşanu
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Johny Neamţu
- Department of Physics, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Avenue, Room N112, Alachua, FL 32615, USA
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11
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Toopaang W, Bunnak W, Srisuksam C, Wattananukit W, Tanticharoen M, Yang YL, Amnuaykanjanasin A. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat Prod Rep 2022; 39:2008-2029. [PMID: 35822627 DOI: 10.1039/d1np00058f] [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
Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.
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Affiliation(s)
- Wachiraporn Toopaang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand. .,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Warapon Bunnak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Chettida Srisuksam
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Wilawan Wattananukit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Morakot Tanticharoen
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Alongkorn Amnuaykanjanasin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
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12
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Mupparapu N, Brewster L, Ostrom KF, Elshahawi SI. Late-Stage Chemoenzymatic Installation of Hydroxy-Bearing Allyl Moiety on the Indole Ring of Tryptophan-Containing Peptides. Chemistry 2022; 28:e202104614. [PMID: 35178791 PMCID: PMC9314954 DOI: 10.1002/chem.202104614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Indexed: 01/08/2023]
Abstract
The late‐stage functionalization of indole‐ and tryptophan‐containing compounds with reactive moieties facilitates downstream diversification and leads to changes in their biological properties. Here, the synthesis of two hydroxy‐bearing allyl pyrophosphates is described. A chemoenzymatic method is demonstrated which uses a promiscuous indole prenyltransferase enzyme to install a dual reactive hydroxy‐bearing allyl moiety directly on the indole ring of tryptophan‐containing peptides. This is the first report of late‐stage indole modifications with this reactive group.
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Affiliation(s)
- Nagaraju Mupparapu
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Lauren Brewster
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Katrina F Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
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13
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Miller B, Schmidt EW, Concepcion GP, Haygood MG. Halogenated Metal-Binding Compounds from Shipworm Symbionts. JOURNAL OF NATURAL PRODUCTS 2022; 85:479-484. [PMID: 35196451 PMCID: PMC8961882 DOI: 10.1021/acs.jnatprod.1c01049] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Indexed: 06/02/2023]
Abstract
Bacteria use small molecules to impose strict regulation over the acquisition, uptake, and sequestration of transition metal ions. Low-abundance nutrient metals, such as Fe(III), need to be scavenged from the environment by high-affinity chelating molecules called siderophores. Conversely, metal ions that become toxic at high concentrations need to be sequestered and detoxified. Often, bacteria produce a suite of compounds that bind various metal ions at different affinities in order to maintain homeostasis. Turnerbactin, a triscatecholate siderophore isolated from the intracellular shipworm symbiont Teredinibacter turnerae T7901, is responsible for iron regulation and uptake. Herein, another series of compounds are described that complex with iron, copper, and molybdenum in solution. Teredinibactins belong to a class of metal-binding molecules that utilize a phenolate-thiazoline moiety in the coordination of metal ions. In contrast to other compounds in this class, such as yersiniabactin, the phenyl ring is decorated with a 2,4-dihydroxy-3-halo substitution pattern. UV-vis absorption spectroscopy based titration experiments with CuCl2 show the formation of an intermediate complex at substoichiometric concentrations and conversion to a copper-bound complex at 1:1 molar equiv.
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Affiliation(s)
- Bailey
W. Miller
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Gisela P. Concepcion
- The
Marine Science Institute, University of
the Philippines, Diliman, Quezon
City 1101, Philippines
| | - Margo G. Haygood
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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14
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Hemmerling F, Piel J. Strategies to access biosynthetic novelty in bacterial genomes for drug discovery. Nat Rev Drug Discov 2022; 21:359-378. [PMID: 35296832 DOI: 10.1038/s41573-022-00414-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.
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Affiliation(s)
- Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
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15
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Falco R, Appiah-Madson HJ, Distel DL. The Ocean Genome Legacy: A Genomic Resource Repository for Marine Life. Biopreserv Biobank 2022; 20:104-106. [PMID: 35108094 DOI: 10.1089/bio.2021.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rosalia Falco
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts, USA
| | - Hannah J Appiah-Madson
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts, USA
| | - Daniel L Distel
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts, USA
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16
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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17
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Inducible boron resistance via active efflux in Lysinibacillus and Enterococcus isolates from boron-contaminated agricultural soil. Biometals 2022; 35:215-228. [PMID: 35037170 DOI: 10.1007/s10534-021-00359-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/08/2021] [Indexed: 11/02/2022]
Abstract
Phylogenetically diverse bacteria tolerate high boron concentrations while others require it for metabolic purposes despite the metalloid being toxic beyond a threshold. Boron resistance and plant growth promoting attributes of two bacterial strains, Lysinibacillus sp. OL1 and a novel Enterococcus sp. OL5, isolated from boron-fertilizer-amended cauliflower fields were investigated in this study. OL1 and OL5 grew efficiently in the presence of 210-230 mM boron, and resistance was found to be inducible by small amounts of the element: 5 to 50 mM boron pre-exposure progressively shortened the lag phase of growth in the presence of 200 mM boron. Intracellular boron accumulation was also found to be regulated by the level of pre-exposure: no induction or induction by small amounts led to higher levels of intracellular accumulation, whereas induction by high concentrations led to lower accumulation. These data, in the context of the strains' overall resistance towards 200 mM boron, indicated that induction by higher boron concentrations turned potential efflux mechanisms on, while resistance was eventually achieved by continuous cellular entry and exit of the ions. Involvement of solute efflux in boron resistance was corroborated by the genome content of the isolates (genes encoding proteins of the ATP-binding cassette, major facilitator, small multidrug resistance, multi antimicrobial extrusion, and resistance-nodulation-cell division, family/superfamily). Bacteria such as OL1 and OL5, which resist boron via influx-efflux, potentially lower boron bioavailability, and therefore toxicity, for the soil microbiota at large. These bacteria, by virtue of their plant-growth-promoting attributes, can also be used as biofertilizers.
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18
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Miller BW, Lim AL, Lin Z, Bailey J, Aoyagi KL, Fisher MA, Barrows LR, Manoil C, Schmidt EW, Haygood MG. Shipworm symbiosis ecology-guided discovery of an antibiotic that kills colistin-resistant Acinetobacter. Cell Chem Biol 2021; 28:1628-1637.e4. [PMID: 34146491 PMCID: PMC8605984 DOI: 10.1016/j.chembiol.2021.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
Teredinibacter turnerae is an intracellular bacterial symbiont in the gills of wood-eating shipworms, where it is proposed to use antibiotics to defend itself and its animal host. Several biosynthetic gene clusters are conserved in T. turnerae and their host shipworms around the world, implying that they encode defensive compounds. Here, we describe turnercyclamycins, lipopeptide antibiotics encoded in the genomes of all sequenced T. turnerae strains. Turnercyclamycins are bactericidal against challenging Gram-negative pathogens, including colistin-resistant Acinetobacter baumannii. Phenotypic screening identified the outer membrane as the likely target. Turnercyclamycins and colistin operate by similar cellular, although not necessarily molecular, mechanisms, but turnercyclamycins kill colistin-resistant A. baumannii, potentially filling an urgent clinical need. Thus, by exploring environments that select for the properties we require, we harvested the fruits of evolution to discover compounds with potential to target unmet health needs. Investigating the symbionts of shipworms is a powerful example of this principle.
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Affiliation(s)
- Bailey W Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA
| | - Albebson L Lim
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA
| | - Jeannie Bailey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kari L Aoyagi
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark A Fisher
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT 84112, USA
| | - Louis R Barrows
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA.
| | - Margo G Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA.
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19
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Identification of Translocation Inhibitors Targeting the Type III Secretion System of Enteropathogenic Escherichia coli. Antimicrob Agents Chemother 2021; 65:e0095821. [PMID: 34543097 DOI: 10.1128/aac.00958-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections with enteropathogenic Escherichia coli (EPEC) cause severe diarrhea in children. The noninvasive bacteria adhere to enterocytes of the small intestine and use a type III secretion system (T3SS) to inject effector proteins into host cells to modify and exploit cellular processes in favor of bacterial survival and replication. Several studies have shown that the T3SSs of bacterial pathogens are essential for virulence. Furthermore, the loss of T3SS-mediated effector translocation results in increased immune recognition and clearance of the bacteria. The T3SS is, therefore, considered a promising target for antivirulence strategies and novel therapeutics development. Here, we report the results of a high-throughput screening assay based on the translocation of the EPEC effector protein Tir (translocated intimin receptor). Using this assay, we screened more than 13,000 small molecular compounds of six different compound libraries and identified three substances which showed a significant dose-dependent effect on translocation without adverse effects on bacterial or eukaryotic cell viability. In addition, these substances reduced bacterial binding to host cells, effector-dependent cell detachment, and abolished attaching and effacing lesion formation without affecting the expression of components of the T3SS or associated effector proteins. Moreover, no effects of the inhibitors on bacterial motility or Shiga-toxin expression were observed. In summary, we have identified three new compounds that strongly inhibit T3SS-mediated translocation of effectors into mammalian cells, which could be valuable as lead substances for treating EPEC and enterohemorrhagic E. coli infections.
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20
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Pesante G, Sabbadin F, Elias L, Steele-King C, Shipway JR, Dowle AA, Li Y, Busse-Wicher M, Dupree P, Besser K, Cragg SM, Bruce NC, McQueen-Mason SJ. Characterisation of the enzyme transport path between shipworms and their bacterial symbionts. BMC Biol 2021; 19:233. [PMID: 34724941 PMCID: PMC8561940 DOI: 10.1186/s12915-021-01162-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022] Open
Abstract
Background Shipworms are marine xylophagus bivalve molluscs, which can live on a diet solely of wood due to their ability to produce plant cell wall-degrading enzymes. Bacterial carbohydrate-active enzymes (CAZymes), synthesised by endosymbionts living in specialised shipworm cells called bacteriocytes and located in the animal’s gills, play an important role in wood digestion in shipworms. However, the main site of lignocellulose digestion within these wood-boring molluscs, which contains both endogenous lignocellulolytic enzymes and prokaryotic enzymes, is the caecum, and the mechanism by which bacterial enzymes reach the distant caecum lumen has remained so far mysterious. Here, we provide a characterisation of the path through which bacterial CAZymes produced in the gills of the shipworm Lyrodus pedicellatus reach the distant caecum to contribute to the digestion of wood. Results Through a combination of transcriptomics, proteomics, X-ray microtomography, electron microscopy studies and in vitro biochemical characterisation, we show that wood-digesting enzymes produced by symbiotic bacteria are localised not only in the gills, but also in the lumen of the food groove, a stream of mucus secreted by gill cells that carries food particles trapped by filter feeding to the mouth. Bacterial CAZymes are also present in the crystalline style and in the caecum of their shipworm host, suggesting a unique pathway by which enzymes involved in a symbiotic interaction are transported to their site of action. Finally, we characterise in vitro four new bacterial glycosyl hydrolases and a lytic polysaccharide monooxygenase identified in our transcriptomic and proteomic analyses as some of the major bacterial enzymes involved in this unusual biological system. Conclusion Based on our data, we propose that bacteria and their enzymes are transported from the gills along the food groove to the shipworm’s mouth and digestive tract, where they aid in wood digestion. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01162-6.
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Affiliation(s)
- Giovanna Pesante
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Luisa Elias
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Clare Steele-King
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - J Reuben Shipway
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Adam A Dowle
- Bioscience Technology Facility, Department, of Biology, University of York, York, YO10 5DD, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Marta Busse-Wicher
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Katrin Besser
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Simon M Cragg
- Institute of Marine Sciences Laboratories, Langstone Harbour, Ferry Road, Eastney, Portsmouth, PO4 9LY, UK
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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21
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Stravoravdis S, Shipway JR, Goodell B. How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes. Front Microbiol 2021; 12:665001. [PMID: 34322098 PMCID: PMC8312274 DOI: 10.3389/fmicb.2021.665001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.
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Affiliation(s)
- Stefanos Stravoravdis
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - J Reuben Shipway
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Barry Goodell
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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22
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Abstract
Spirocyclic scaffolds are incorporated in various approved drugs and drug candidates. The increasing interest in less planar bioactive compounds has given rise to the development of synthetic methodologies for the preparation of spirocyclic scaffolds. In this Perspective, we summarize the diverse synthetic routes to obtain spirocyclic systems. The impact of spirocycles on potency and selectivity, including the aspect of stereochemistry, is discussed. Furthermore, we examine the changes in physicochemical properties as well as in in vitro and in vivo ADME using selected studies that compare spirocyclic compounds to their nonspirocyclic counterparts. In conclusion, the value of spirocyclic scaffolds in medicinal chemistry is discussed.
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Affiliation(s)
- Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue Straße 9, D-60348 Frankfurt am Main, Germany
| | - Dmitry Dar'in
- Institute of Chemistry, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue Straße 9, D-60348 Frankfurt am Main, Germany
| | - Mikhail Krasavin
- Institute of Chemistry, Saint Petersburg State University, 199034 Saint Petersburg, Russia
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23
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Lacerna NM, Ramones CMV, Robes JMD, Picart MRD, Tun JO, Miller BW, Haygood MG, Schmidt EW, Salvador-Reyes LA, Concepcion GP. Inhibition of Biofilm Formation by Modified Oxylipins from the Shipworm Symbiont Teredinibacter turnerae. Mar Drugs 2020; 18:md18120656. [PMID: 33419303 PMCID: PMC7766104 DOI: 10.3390/md18120656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
The bioactivity-guided purification of the culture broth of the shipworm endosymbiont Teredinibacter turnerae strain 991H.S.0a.06 yielded a new fatty acid, turneroic acid (1), and two previously described oxylipins (2–3). Turneroic acid (1) is an 18-carbon fatty acid decorated by a hydroxy group and an epoxide ring. Compounds 1–3 inhibited bacterial biofilm formation in Staphylococcus epidermidis, while only 3 showed antimicrobial activity against planktonic S. epidermidis. Comparison of the bioactivity of 1–3 with structurally related compounds indicated the importance of the epoxide moiety for selective and potent biofilm inhibition.
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Affiliation(s)
- Noel M. Lacerna
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Cydee Marie V. Ramones
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Jose Miguel D. Robes
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Myra Ruth D. Picart
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Jortan O. Tun
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Bailey W. Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (B.W.M.); (M.G.H.); (E.W.S.)
| | - Margo G. Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (B.W.M.); (M.G.H.); (E.W.S.)
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (B.W.M.); (M.G.H.); (E.W.S.)
| | - Lilibeth A. Salvador-Reyes
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Gisela P. Concepcion
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
- Correspondence: ; Tel.: +632-8275-2877
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Summer K, Browne J, Liu L, Benkendorff K. Molluscan Compounds Provide Drug Leads for the Treatment and Prevention of Respiratory Disease. Mar Drugs 2020; 18:md18110570. [PMID: 33228163 PMCID: PMC7699502 DOI: 10.3390/md18110570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Respiratory diseases place an immense burden on global health and there is a compelling need for the discovery of new compounds for therapeutic development. Here, we identify research priorities by critically reviewing pre-clinical and clinical studies using extracts and compounds derived from molluscs, as well as traditional molluscan medicines, used in the treatment of respiratory diseases. We reviewed 97 biomedical articles demonstrating the anti-inflammatory, antimicrobial, anticancer, and immunomodulatory properties of >320 molluscan extracts/compounds with direct relevance to respiratory disease, in addition to others with promising bioactivities yet to be tested in the respiratory context. Of pertinent interest are compounds demonstrating biofilm inhibition/disruption and antiviral activity, as well as synergism with approved antimicrobial and chemotherapeutic agents. At least 100 traditional medicines, incorporating over 300 different mollusc species, have been used to treat respiratory-related illness in cultures worldwide for thousands of years. These medicines provide useful clues for the discovery of bioactive components that likely underpin their continued use. There is particular incentive for investigations into anti-inflammatory compounds, given the extensive application of molluscan traditional medicines for symptoms of inflammation, and shells, which are the principal molluscan product used in these preparations. Overall, there is a need to target research toward specific respiratory disease-related hypotheses, purify bioactive compounds and elucidate their chemical structures, and develop an evidence base for the integration of quality-controlled traditional medicines.
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Affiliation(s)
- Kate Summer
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, GPO Box 157, Lismore, NSW 2480, Australia;
| | - Jessica Browne
- School of Health and Human Sciences, Southern Cross University, Terminal Drive, Bilinga, QLD 4225, Australia;
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, GPO Box 157, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- National Marine Science Centre, Southern Cross University, 2 Bay Drive, Coffs Harbour, NSW 2450, Australia
- Correspondence: ; Tel.: +61-429-520-589
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Bowden GD, Reis PM, Rogers MB, Bone Relat RM, Brayton KA, Wilson SK, Di Genova BM, Knoll LJ, Nepveux V FJ, Tai AK, Ramadhar TR, Clardy J, O'Connor RM. A conserved coccidian gene is involved in Toxoplasma sensitivity to the anti-apicomplexan compound, tartrolon E. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:1-7. [PMID: 32738587 PMCID: PMC7394737 DOI: 10.1016/j.ijpddr.2020.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/23/2022]
Abstract
New treatments for the diseases caused by apicomplexans are needed. Recently, we determined that tartrolon E (trtE), a secondary metabolite derived from a shipworm symbiotic bacterium, has broad-spectrum anti-apicomplexan parasite activity. TrtE inhibits apicomplexans at nM concentrations in vitro, including Cryptosporidium parvum, Toxoplasma gondii, Sarcocystis neurona, Plasmodium falciparum, Babesia spp. and Theileria equi. To investigate the mechanism of action of trtE against apicomplexan parasites, we examined changes in the transcriptome of trtE-treated T. gondii parasites. RNA-Seq data revealed that the gene, TGGT1_272370, which is broadly conserved in the coccidia, is significantly upregulated within 4 h of treatment. Using bioinformatics and proteome data available on ToxoDB, we determined that the protein product of this tartrolon E responsive gene (trg) has multiple transmembrane domains, a phosphorylation site, and localizes to the plasma membrane. Deletion of trg in a luciferase-expressing T. gondii strain by CRISPR/Cas9 resulted in a 68% increase in parasite resistance to trtE treatment, supporting a role for the trg protein product in the response of T. gondii to trtE treatment. Trg is conserved in the coccidia, but not in more distantly related apicomplexans, indicating that this response to trtE may be unique to the coccidians, and other mechanisms may be operating in other trtE-sensitive apicomplexans. Uncovering the mechanisms by which trtE inhibits apicomplexans may identify shared pathways critical to apicomplexan parasite survival and advance the search for new treatments.
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Affiliation(s)
- Gregory D Bowden
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, P.O. Box 647040, Pullman, WA, 99164-7040, USA
| | - Patricia M Reis
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, P.O. Box 647040, Pullman, WA, 99164-7040, USA
| | - Maxwell B Rogers
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, P.O. Box 647040, Pullman, WA, 99164-7040, USA
| | - Rachel M Bone Relat
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, P.O. Box 647040, Pullman, WA, 99164-7040, USA
| | - Kelly A Brayton
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, P.O. Box 647040, Pullman, WA, 99164-7040, USA
| | - Sarah K Wilson
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, 1550 Linden Dr Madison, WI, 53706, USA
| | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, 1550 Linden Dr Madison, WI, 53706, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, 1550 Linden Dr Madison, WI, 53706, USA
| | - Felix J Nepveux V
- Division of Geographic Medicine and Infectious Disease, Tufts Medical Center, 60 Tremont St 3rd Fl, Boston, MA, 02116, USA
| | - Albert K Tai
- Department of Immunology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Timothy R Ramadhar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue C-213, Boston, MA, 02115, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue C-213, Boston, MA, 02115, USA
| | - Roberta M O'Connor
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, P.O. Box 647040, Pullman, WA, 99164-7040, USA.
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26
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Yang S, Wu L, Wu B, Zhang Y, Wang H, Tan X. Diversity and structure of soil microbiota of the Jinsha earthen relic. PLoS One 2020; 15:e0236165. [PMID: 32697804 PMCID: PMC7375591 DOI: 10.1371/journal.pone.0236165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/30/2020] [Indexed: 12/02/2022] Open
Abstract
In order to define the diversity and composition of the microbial communities colonizing of the soil microbiome of the Jinsha earthen relic, we used high-throughput sequencing technology to identify and characterize the microbiota in 22 samples collected from the Jinsha earthen relic in China during 2017 and 2018. We compared the taxonomy of the microbial communities from samples taken at different times and different sites. Our results showed that the identity of the dominant bacterial phyla differed among the samples. Proteobacteria (23–86.2%) were the predominant bacterial phylum in all samples taken from site A in both 2017 and 2018. However, Actinobacteria (21–92.3%) were the most popular bacterial phylum in samples from sites B and C in 2017 and 2018. Ascomycota were identified as the only fungal phyla in samples in 2017. However, the group varied drastically in relative abundance between 2017 and 2018. Functional analysis of the soil bacterial community suggested that abundant members of the microbiota may be associated with metabolism and the specific environment. This report was the first high-throughput sequencing study of the soil of the Jinsha earthen relic microbiome. Since soil microbiota can damage soil and archeological structures, comprehensive analyses of the microbiomes at archeological sites may contribute to the understand of the influence of microorganisms on the degradation of soil, as well as to the identification of potentially beneficial or undesirable members of these microbial communities in archeological sites. The study will be helpful to provide effective data and guidance for the prevention and control of microbial corrosion of the Jinsha earthen relic.
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Affiliation(s)
- Sheng Yang
- Chengdu Institute of Cultural Relics, Chengdu, PR China
| | - Linfeng Wu
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Bin Wu
- Jinsha Site Museum, Chengdu, PR China
| | - Yizheng Zhang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Haiyan Wang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Xuemei Tan
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
- * E-mail:
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27
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Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes. mSystems 2020; 5:5/3/e00261-20. [PMID: 32606027 PMCID: PMC7329324 DOI: 10.1128/msystems.00261-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis. Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites. IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.
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O’Connor RM, Nepveux V FJ, Abenoja J, Bowden G, Reis P, Beaushaw J, Bone Relat RM, Driskell I, Gimenez F, Riggs MW, Schaefer DA, Schmidt EW, Lin Z, Distel DL, Clardy J, Ramadhar TR, Allred DR, Fritz HM, Rathod P, Chery L, White J. A symbiotic bacterium of shipworms produces a compound with broad spectrum anti-apicomplexan activity. PLoS Pathog 2020; 16:e1008600. [PMID: 32453775 PMCID: PMC7274485 DOI: 10.1371/journal.ppat.1008600] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/05/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Apicomplexan parasites cause severe disease in both humans and their domesticated animals. Since these parasites readily develop drug resistance, development of new, effective drugs to treat infection caused by these parasites is an ongoing challenge for the medical and veterinary communities. We hypothesized that invertebrate-bacterial symbioses might be a rich source of anti-apicomplexan compounds because invertebrates are susceptible to infections with gregarines, parasites that are ancestral to all apicomplexans. We chose to explore the therapeutic potential of shipworm symbiotic bacteria as they are bona fide symbionts, are easily grown in axenic culture and have genomes rich in secondary metabolite loci [1,2]. Two strains of the shipworm symbiotic bacterium, Teredinibacter turnerae, were screened for activity against Toxoplasma gondii and one strain, T7901, exhibited activity against intracellular stages of the parasite. Bioassay-guided fractionation identified tartrolon E (trtE) as the source of the activity. TrtE has an EC50 of 3 nM against T. gondii, acts directly on the parasite itself and kills the parasites after two hours of treatment. TrtE exhibits nanomolar to picomolar level activity against Cryptosporidium, Plasmodium, Babesia, Theileria, and Sarcocystis; parasites representing all branches of the apicomplexan phylogenetic tree. The compound also proved effective against Cryptosporidium parvum infection in neonatal mice, indicating that trtE may be a potential lead compound for preclinical development. Identification of a promising new compound after such limited screening strongly encourages further mining of invertebrate symbionts for new anti-parasitic therapeutics.
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Affiliation(s)
- Roberta M. O’Connor
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| | - Felix J. Nepveux V
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Jaypee Abenoja
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Gregory Bowden
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Patricia Reis
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Josiah Beaushaw
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Rachel M. Bone Relat
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Iwona Driskell
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Fernanda Gimenez
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Michael W. Riggs
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Deborah A. Schaefer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Northeastern University, Nahant, Massachusetts, United States of America
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Timothy R. Ramadhar
- Department of Chemistry, Howard University, Washington DC, United States of America
| | - David R. Allred
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Heather M. Fritz
- California Animal Health and Food Safety Lab, University of California, Davis, California, United States of America
| | - Pradipsinh Rathod
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Laura Chery
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - John White
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
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Abstract
The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host–microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies. The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. This Perspective article outlines research priorities to strengthen our current knowledge of host-microbiome interactions, to help predict responses to anthropogenic stressors and to inform future management strategies.
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Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Automated structure prediction of trans-acyltransferase polyketide synthase products. Nat Chem Biol 2019; 15:813-821. [PMID: 31308532 PMCID: PMC6642696 DOI: 10.1038/s41589-019-0313-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/23/2019] [Indexed: 12/01/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex known enzymes from secondary metabolism and are responsible for the biosynthesis of highly diverse bioactive polyketides. However, most of these metabolites remain uncharacterized, since trans-AT PKSs frequently occur in poorly studied microbes and feature a remarkable array of non-canonical biosynthetic components with poorly understood functions. As a consequence, genome-guided natural product identification has been challenging. To enable de novo structural predictions for trans-AT PKS-derived polyketides, we developed the trans-AT PKS polyketide predictor (TransATor). TransATor is a versatile bio- and chemoinformatics web application that suggests informative chemical structures for even highly aberrant trans-AT PKS biosynthetic gene clusters, thus permitting hypothesis-based, targeted biotechnological discovery and biosynthetic studies. We demonstrate the applicative scope in several examples, including the characterization of new variants of bioactive natural products as well as structurally new polyketides from unusual bacterial sources.
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Affiliation(s)
- Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Alon Dolev
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Gianmaria Califano
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - Pablo Moreno
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.
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31
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Lacerna NM, Miller BW, Lim AL, Tun JO, Robes JMD, Cleofas MJB, Lin Z, Salvador-Reyes LA, Haygood MG, Schmidt EW, Concepcion GP. Mindapyrroles A-C, Pyoluteorin Analogues from a Shipworm-Associated Bacterium. JOURNAL OF NATURAL PRODUCTS 2019; 82:1024-1028. [PMID: 30793902 PMCID: PMC8188622 DOI: 10.1021/acs.jnatprod.8b00979] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Three new pyoluteorin analogues, mindapyrroles A-C (1-3), were purified from Pseudomonas aeruginosa strain 1682U.R.0a.27, a gill-associated bacterium isolated from the tissue homogenate of the giant shipworm Kuphus polythalamius. Mindapyrroles B and C inhibit the growth of multiple pathogenic bacteria, with mindapyrrole B (2) showing the most potent antimicrobial activity and widest selectivity index over mammalian cells. Preliminary structure-activity relationship analysis showed that dimerization of the pyoluteorin moiety through a C-C linkage is detrimental to the antimicrobial activity, but addition of an aerugine unit in the methylene bridge is favorable for both the antimicrobial activity and selectivity index.
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Affiliation(s)
- Noel M. Lacerna
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Bailey W. Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Albebson L. Lim
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Jortan O. Tun
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Jose Miguel D. Robes
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Mark Jeremiah B. Cleofas
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | | | - Margo G. Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Gisela P. Concepcion
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Corresponding Author Tel: (+632) 275-2877.
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32
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Brito TL, Campos AB, Bastiaan von Meijenfeldt FA, Daniel JP, Ribeiro GB, Silva GGZ, Wilke DV, de Moraes DT, Dutilh BE, Meirelles PM, Trindade-Silva AE. The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei. PLoS One 2018; 13:e0200437. [PMID: 30427852 PMCID: PMC6235255 DOI: 10.1371/journal.pone.0200437] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/08/2018] [Indexed: 12/02/2022] Open
Abstract
Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae “clade I” strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills’ metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.
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Affiliation(s)
- Thais L. Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Amanda B. Campos
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Julio P. Daniel
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Gabriella B. Ribeiro
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Genivaldo G. Z. Silva
- Computational Science Research Center, San Diego State University, San Diego, California, United States of America
| | - Diego V. Wilke
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Pedro M. Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Federal University of Bahia, Salvador, Brazil
| | - Amaro E. Trindade-Silva
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- * E-mail:
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Surup F, Chauhan D, Niggemann J, Bartok E, Herrmann J, Keck M, Zander W, Stadler M, Hornung V, Müller R. Activation of the NLRP3 Inflammasome by Hyaboron, a New Asymmetric Boron-Containing Macrodiolide from the Myxobacterium Hyalangium minutum. ACS Chem Biol 2018; 13:2981-2988. [PMID: 30183250 DOI: 10.1021/acschembio.8b00659] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A Natural Compound Library containing myxobacterial secondary metabolites was screened in murine macrophages for novel activators of IL-1β maturation and secretion. The most potent of three hits in total was a so far undescribed metabolite, which was identified from the myxobacterium Hyalangium minutum strain Hym3. While the planar structure of 1 was elucidated by high resolution mass spectrometry and NMR data yielding an asymmetric boron containing a macrodiolide core structure, its relative stereochemistry of all 20 stereocenters of the 42-membered ring was assigned by rotating frame Overhause effect spectroscopy correlations, 1H,1H, and 1H,13C coupling constants, and by comparison of 13C chemical shifts to those of the structurally related metabolites tartrolon B-D. The absolute stereochemistry was subsequently assigned by Mosher's and Marfey's methods. Further functional studies revealed that hyaboron and other boronated natural compounds resulted in NLRP3 inflammasome dependent IL-1β maturation, which is most likely due to their ability to act as potassium ionophores. Moreover, besides its inflammasome-stimulatory activity in human and mouse cells, hyaboron (1) showed additional diverse biological activities, including antibacterial and antiparasitic effects.
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Affiliation(s)
- Frank Surup
- Department Microbial Drugs, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Dhruv Chauhan
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Jutta Niggemann
- Department Microbial Drugs, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Eva Bartok
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Sigmund-Freud-Straße 25, Bonn, 53127, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University Campus, Building E8.1, Saarbrücken, 66123, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Matthias Keck
- Department Microbial Drugs, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Wiebke Zander
- Department Microbial Drugs, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
- Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Rolf Müller
- Department Microbial Drugs, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University Campus, Building E8.1, Saarbrücken, 66123, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, Braunschweig, 38124, Germany
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Senra MVX, Sung W, Ackerman M, Miller SF, Lynch M, Soares CAG. An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae. Genome Biol Evol 2018; 10:723-730. [PMID: 29415256 PMCID: PMC5833318 DOI: 10.1093/gbe/evy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 12/14/2022] Open
Abstract
Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.
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Affiliation(s)
- Marcus V X Senra
- Departamento de Zoologia, Universidade Federal de Juiz de Fora, Brazil
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte
| | - Matthew Ackerman
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Carlos Augusto G Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil
- Corresponding author: E-mail:
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Ueoka R, Bhushan A, Probst SI, Bray WM, Lokey RS, Linington RG, Piel J. Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Agneya Bhushan
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Silke I. Probst
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Walter M. Bray
- Chemistry & Biochemistry Department; University of California Santa Cruz; 1156 High Street 95064 Santa Cruz California USA
| | - R. Scott Lokey
- Chemistry & Biochemistry Department; University of California Santa Cruz; 1156 High Street 95064 Santa Cruz California USA
| | - Roger G. Linington
- Department of Chemistry; Simon Fraser University; 8888 University Drive Bumaby BC V5A 1S6 Canada
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
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Ueoka R, Bhushan A, Probst SI, Bray WM, Lokey RS, Linington RG, Piel J. Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. Angew Chem Int Ed Engl 2018; 57:14519-14523. [PMID: 30025185 DOI: 10.1002/anie.201805673] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/12/2018] [Indexed: 01/14/2023]
Abstract
The large number of sequenced bacterial genomes provides the opportunity to bioinformatically identify rich natural product sources among previously neglected microbial groups. Testing this discovery strategy, unusually high biosynthetic potential was suggested for the Oceanospirillales member Gynuella sunshinyii, a Gram-negative marine bacterium from the rhizosphere of the halophilic plant Carex scabrifolia. Its genome contains numerous unusual biosynthetic gene clusters for diverse types of metabolites. Genome-guided isolation yielded representatives of four different natural product classes, of which only alteramide A was known. Cytotoxic lacunalides were identified as products of a giant trans-acyltransferase polyketide synthase gene cluster, one of six present in this strain. Cytological profiling against HeLa cells suggested that lacunalide A disrupts CDK signaling in the cell cycle. In addition, chemical studies on model compounds were conducted, suggesting the structurally unusual ergoynes as products of a conjugated diyne-thiourea cyclization reaction.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Silke I Probst
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Walter M Bray
- Chemistry & Biochemistry Department, University of California Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
| | - R Scott Lokey
- Chemistry & Biochemistry Department, University of California Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Bumaby, BC, V5A 1S6, Canada
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
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Extending the "One Strain Many Compounds" (OSMAC) Principle to Marine Microorganisms. Mar Drugs 2018; 16:md16070244. [PMID: 30041461 PMCID: PMC6070831 DOI: 10.3390/md16070244] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 02/07/2023] Open
Abstract
Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as “silent”, meaning that they are not expressed under laboratory conditions. Triggering expression of these “silent” clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these “silent” genes. The principles behind the cultivation based approaches have been conceptualized in the “one strain many compounds” (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate “silent” clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken “silent” gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms.
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de Moraes Akamine DT, de Almeida Cozendey da Silva D, de Lima Câmara G, Carvalho TV, Brienzo M. Endoglucanase activity in Neoteredo reynei (Bivalvia, Teredinidae) digestive organs and its content. World J Microbiol Biotechnol 2018; 34:84. [DOI: 10.1007/s11274-018-2468-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 05/31/2018] [Indexed: 11/25/2022]
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Morita M, Schmidt EW. Parallel lives of symbionts and hosts: chemical mutualism in marine animals. Nat Prod Rep 2018; 35:357-378. [PMID: 29441375 PMCID: PMC6025756 DOI: 10.1039/c7np00053g] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 Symbiotic microbes interact with animals, often by producing natural products (specialized metabolites; secondary metabolites) that exert a biological role. A major goal is to determine which microbes produce biologically important compounds, a deceptively challenging task that often rests on correlative results, rather than hypothesis testing. Here, we examine the challenges and successes from the perspective of marine animal-bacterial mutualisms. These animals have historically provided a useful model because of their technical accessibility. By comparing biological systems, we suggest a common framework for establishing chemical interactions between animals and microbes.
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Affiliation(s)
- Maho Morita
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA 84112.
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Reed KB, Alper HS. Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering. Synth Syst Biotechnol 2018; 3:20-33. [PMID: 29911196 PMCID: PMC5884228 DOI: 10.1016/j.synbio.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/08/2017] [Accepted: 12/09/2017] [Indexed: 12/15/2022] Open
Abstract
Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially) be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.
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Affiliation(s)
- Kevin B. Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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41
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Evolutionary stability of antibiotic protection in a defensive symbiosis. Proc Natl Acad Sci U S A 2018; 115:E2020-E2029. [PMID: 29444867 DOI: 10.1073/pnas.1719797115] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The increasing resistance of human pathogens severely limits the efficacy of antibiotics in medicine, yet many animals, including solitary beewolf wasps, successfully engage in defensive alliances with antibiotic-producing bacteria for millions of years. Here, we report on the in situ production of 49 derivatives belonging to three antibiotic compound classes (45 piericidin derivatives, 3 streptochlorin derivatives, and nigericin) by the symbionts of 25 beewolf host species and subspecies, spanning 68 million years of evolution. Despite a high degree of qualitative stability in the antibiotic mixture, we found consistent quantitative differences between species and across geographic localities, presumably reflecting adaptations to combat local pathogen communities. Antimicrobial bioassays with the three main components and in silico predictions based on the structure and specificity in polyketide synthase domains of the piericidin biosynthesis gene cluster yield insights into the mechanistic basis and ecoevolutionary implications of producing a complex mixture of antimicrobial compounds in a natural setting.
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Jennifer Kan SB, Huang X, Gumulya Y, Chen K, Arnold FH. Genetically programmed chiral organoborane synthesis. Nature 2017; 552:132-136. [PMID: 29186119 PMCID: PMC5819735 DOI: 10.1038/nature24996] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 11/02/2017] [Indexed: 12/20/2022]
Abstract
Recent advances in enzyme engineering and design have expanded nature's catalytic repertoire to functions that are new to biology. However, only a subset of these engineered enzymes can function in living systems. Finding enzymatic pathways that form chemical bonds that are not found in biology is particularly difficult in the cellular environment, as this depends on the discovery not only of new enzyme activities, but also of reagents that are both sufficiently reactive for the desired transformation and stable in vivo. Here we report the discovery, evolution and generalization of a fully genetically encoded platform for producing chiral organoboranes in bacteria. Escherichia coli cells harbouring wild-type cytochrome c from Rhodothermus marinus (Rma cyt c) were found to form carbon-boron bonds in the presence of borane-Lewis base complexes, through carbene insertion into boron-hydrogen bonds. Directed evolution of Rma cyt c in the bacterial catalyst provided access to 16 novel chiral organoboranes. The catalyst is suitable for gram-scale biosynthesis, providing up to 15,300 turnovers, a turnover frequency of 6,100 h-1, a 99:1 enantiomeric ratio and 100% chemoselectivity. The enantiopreference of the biocatalyst could also be tuned to provide either enantiomer of the organoborane products. Evolved in the context of whole-cell catalysts, the proteins were more active in the whole-cell system than in purified forms. This study establishes a DNA-encoded and readily engineered bacterial platform for borylation; engineering can be accomplished at a pace that rivals the development of chemical synthetic methods, with the ability to achieve turnovers that are two orders of magnitude (over 400-fold) greater than those of known chiral catalysts for the same class of transformation. This tunable method for manipulating boron in cells could expand the scope of boron chemistry in living systems.
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Affiliation(s)
| | | | - Yosephine Gumulya
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, United States
| | - Kai Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, United States
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Yan X, Huang G, Liu Q, Zheng J, Chen H, Huang Q, Chen J, Huang H. Withaferin A protects against spinal cord injury by inhibiting apoptosis and inflammation in mice. PHARMACEUTICAL BIOLOGY 2017; 55:1171-1176. [PMID: 28228044 PMCID: PMC6130570 DOI: 10.1080/13880209.2017.1288262] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/22/2016] [Accepted: 01/13/2017] [Indexed: 05/31/2023]
Abstract
CONTEXT Withaferin A (WFA) exhibits diverse pharmaceutical applications on human diseases, including rheumatoid arthritis, cancers and microbial infection. OBJECTIVE We evaluated the neuroprotective role of WFA using a mouse model of spinal cord injury (SCI). MATERIALS AND METHODS BALB/c mice were administrated 10 mg/kg of WFA. Gene expression was measured by real-time PCR, western blot and immunohistochemistry. Cell morphology and apoptosis were determined by H&E staining and TUNEL assay. Motor function was evaluated by the BBB functional scale for continuous 7 weeks. RESULTS WFA significantly improved neurobehavioural function and alleviated histological alteration of spinal cord tissues in traumatized mice. Brain-derived neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF) significantly increased in WFA-treated mice. Meanwhile, the expression of Nogo-A and RhoA remarkably decreased in the presence of WFA. Furthermore, the apoptotic cell death was attenuated in mice treated with WFA (31.48 ± 2.50% vs. 50.08 ± 2.08%) accompanied by decreased bax and increased bcl-2. In addition, WFA decreased the expression of pro-inflammatory mediators such as IL-1β (11.20 ± 1.96 ng/mL vs. 17.59 ± 1.42 ng/mL) and TNF-α (57.38 ± 3.57 pg/mL vs. 95.06 ± 9.13 pg/mL). The anti-inflammatory cytokines including TGF-β1 (14.32 ± 1.04 pg/mL vs. 9.37 ± 1.17 pg/mL) and IL-10 (116.80 ± 6.91 pg/mL vs. 72.33 ± 9.35 pg/mL) were elevated after WFA administration. DISCUSSION AND CONCLUSION This study demonstrated that WFA has a neuroprotective role by inhibition of apoptosis and inflammation after SCI in mice.
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Affiliation(s)
- Xianlei Yan
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Guangxiang Huang
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Quan Liu
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Jiemin Zheng
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Hongmou Chen
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Qidan Huang
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Jiakang Chen
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Heqing Huang
- Department of Neurosurgery, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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45
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Elshahawi SI, Cao H, Shaaban KA, Ponomareva LV, Subramanian T, Farman ML, Spielmann HP, Phillips GN, Thorson JS, Singh S. Structure and specificity of a permissive bacterial C-prenyltransferase. Nat Chem Biol 2017; 13:366-368. [PMID: 28166207 PMCID: PMC5362326 DOI: 10.1038/nchembio.2285] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/01/2016] [Indexed: 11/21/2022]
Abstract
This study highlights the biochemical and structural characterization of the L-tryptophan C6 C-prenyltransferase (C-PT) PriB from Streptomyces sp. RM-5-8. PriB was found to be uniquely permissive to a diverse array of prenyl donors and acceptors including daptomycin. Two additional PTs also produced novel prenylated daptomycins with improved antibacterial activities over the parent drug.
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Affiliation(s)
- Sherif I. Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536
- Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, KY 40536
| | - Hongnan Cao
- Department of Biosciences, Rice University, Houston, TX 77005
| | - Khaled A. Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536
- Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, KY 40536
| | - Larissa V. Ponomareva
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536
- Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, KY 40536
| | - Thangaiah Subramanian
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536
| | - Mark L. Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - H. Peter Spielmann
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536
- Department of Chemistry, Markey Cancer Center, Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536
| | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536
- Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, KY 40536
| | - Shanteri Singh
- Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, KY 40536
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Meusel M, Hufsky F, Panter F, Krug D, Müller R, Böcker S. Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns. Anal Chem 2016; 88:7556-66. [DOI: 10.1021/acs.analchem.6b01015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Marvin Meusel
- Chair
for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Franziska Hufsky
- Chair
for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany
- RNA
Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Fabian Panter
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Daniel Krug
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Sebastian Böcker
- Chair
for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany
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47
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DeFrancesco H, Dudley J, Coca A. Boron Chemistry: An Overview. BORON REAGENTS IN SYNTHESIS 2016. [DOI: 10.1021/bk-2016-1236.ch001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Heather DeFrancesco
- Chemistry Department, Southern Connecticut State University, 501 Crescent St., New Haven, Connecticut 06515, United States
| | - Joshua Dudley
- Chemistry Department, Southern Connecticut State University, 501 Crescent St., New Haven, Connecticut 06515, United States
| | - Adiel Coca
- Chemistry Department, Southern Connecticut State University, 501 Crescent St., New Haven, Connecticut 06515, United States
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48
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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49
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Metal and metalloid containing natural products and a brief overview of their applications in biology, biotechnology and biomedicine. Biometals 2015; 29:1-13. [DOI: 10.1007/s10534-015-9892-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
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50
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Wolkenstein K, Sun H, Falk H, Griesinger C. Structure and Absolute Configuration of Jurassic Polyketide-Derived Spiroborate Pigments Obtained from Microgram Quantities. J Am Chem Soc 2015; 137:13460-3. [PMID: 26443920 DOI: 10.1021/jacs.5b08191] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Complete structural elucidation of natural products is often challenging due to structural complexity and limited availability. This is true for present-day secondary metabolites, but even more for exceptionally preserved secondary metabolites of ancient organisms that potentially provide insights into the evolutionary history of natural products. Here, we report the full structure and absolute configuration of the borolithochromes, enigmatic boron-containing pigments from a Jurassic putative red alga, from samples of less than 50 μg using microcryoprobe NMR, circular dichroism spectroscopy, and density functional theory calculations and reveal their polyketide origin. The pigments are identified as spiroborates with two pentacyclic sec-butyl-trihydroxy-methyl-benzo[gh]tetraphen-one ligands and less-substituted derivatives. The configuration of the sec-butyl group is found to be (S). Because the exceptional benzo[gh]tetraphene scaffold is otherwise only observed in the recently discovered polyketide clostrubin from a present-day Clostridium bacterium, the Jurassic borolithochromes now can be unambiguously linked to the modern polyketide, providing evidence that the fossil pigments are almost originally preserved secondary metabolites and suggesting that the pigments in fact may have been produced by an ancient bacterium. The borolithochromes differ fundamentally from previously described boronated polyketides and represent the first boronated aromatic polyketides found so far. Our results demonstrate the potential of microcryoprobe NMR in the analysis of previously little-explored secondary metabolites from ancient organisms and reveal the evolutionary significance of clostrubin-type polyketides.
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Affiliation(s)
- Klaus Wolkenstein
- Department of Geobiology, Geoscience Centre, University of Göttingen , Goldschmidtstraße 3, 37077 Göttingen, Germany
| | - Han Sun
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Heinz Falk
- Institute of Organic Chemistry, University of Linz , Altenbergerstraße 69, 4040 Linz, Austria
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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