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Wang Y, Shi YN, Xiang H, Shi YM. Exploring nature's battlefield: organismic interactions in the discovery of bioactive natural products. Nat Prod Rep 2024. [PMID: 39316448 DOI: 10.1039/d4np00018h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Covering: up to March 2024.Microbial natural products have historically been a cornerstone for the discovery of therapeutic agents. Advanced (meta)genome sequencing technologies have revealed that microbes harbor far greater biosynthetic capabilities than previously anticipated. However, despite the application of CRISPR/Cas-based gene editing and high-throughput technologies to activate silent biosynthetic gene clusters, the rapid identification of new natural products has not led to a proportional increase in the discovery rate of lead compounds or drugs. A crucial issue in this gap may be insufficient knowledge about the inherent biological and physiological functions of microbial natural products. Addressing this gap necessitates recognizing that the generation of functional natural products is deeply rooted in the interactions between the producing microbes and other (micro)organisms within their ecological contexts, an understanding that is essential for harnessing their potential therapeutic benefits. In this review, we highlight the discovery of functional microbial natural products from diverse niches, including those associated with humans, nematodes, insects, fungi, protozoa, plants, and marine animals. Many of these findings result from an organismic-interaction-guided strategy using multi-omic approaches. The current importance of this topic lies in its potential to advance drug discovery in an era marked by increasing antimicrobial resistance.
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Affiliation(s)
- Yuyang Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yan-Ni Shi
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Hao Xiang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Ming Shi
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Zhou L, Höfte M, Hennessy RC. Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology? Front Bioeng Biotechnol 2024; 12:1363183. [PMID: 38476965 PMCID: PMC10928948 DOI: 10.3389/fbioe.2024.1363183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Lipopeptides (LPs) produced by Pseudomonas spp. are specialized metabolites with diverse structures and functions, including powerful biosurfactant and antimicrobial properties. Despite their enormous potential in environmental and industrial biotechnology, low yield and high production cost limit their practical use. While genome mining and functional genomics have identified a multitude of LP biosynthetic gene clusters, the regulatory mechanisms underlying their biosynthesis remain poorly understood. We propose that regulation holds the key to unlocking LP production in Pseudomonas for biotechnology. In this review, we summarize the structure and function of Pseudomonas-derived LPs and describe the molecular basis for their biosynthesis and regulation. We examine the global and specific regulator-driven mechanisms controlling LP synthesis including the influence of environmental signals. Understanding LP regulation is key to modulating production of these valuable compounds, both quantitatively and qualitatively, for industrial and environmental biotechnology.
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Affiliation(s)
- Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Rosanna C. Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Cai Y, Zhang X. The atypical organization of the luxI/R family genes in AHL-driven quorum-sensing circuits. J Bacteriol 2024; 206:e0043023. [PMID: 38240569 PMCID: PMC10882985 DOI: 10.1128/jb.00430-23] [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] [Indexed: 02/23/2024] Open
Abstract
Quorum sensing (QS) is an elaborate regulatory mechanism associated with virulence and bacterial adaptation to the changing environment. QS is widespread in Proteobacteria and acts primarily through N-acylhomoserine lactone (AHL) signals. At the core of the AHL-driven QS systems are the AHL synthase gene (luxI family) and its cognate transcriptional regulator gene (luxR family). Several QS systems display one or more genes intervening between the luxI and luxR, in which gene arrangements are notably different due to the relative position and the transcriptional orientation between the essential luxI/R and the genes of location correlation. These adjacent genes may exert a regulatory impact on the primary QS genes or contribute toward an extension of QS regulatory control. In this review, we describe the organization of AHL-driven QS genes based on previous research and specific genome databases and provide new insights into these atypical QS gene arrangements.
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Affiliation(s)
- Yuyuan Cai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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4
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Armstrong DW, Berthod A. Occurrence of D-amino acids in natural products. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:47. [PMID: 37932633 PMCID: PMC10628113 DOI: 10.1007/s13659-023-00412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023]
Abstract
Since the identified standard genetic code contains 61 triplet codons of three bases for the 20 L-proteinogenic amino acids (AAs), no D-AA should be found in natural products. This is not what is observed in the living world. D-AAs are found in numerous natural compounds produced by bacteria, algae, fungi, or marine animals, and even vertebrates. A review of the literature indicated the existence of at least 132 peptide natural compounds in which D-AAs are an essential part of their structure. All compounds are listed, numbered and described herein. The two biosynthetic routes leading to the presence of D-AA in natural products are: non-ribosomal peptide synthesis (NRPS), and ribosomally synthesized and post-translationally modified peptide (RiPP) synthesis which are described. The methods used to identify the AA chirality within naturally occurring peptides are briefly discussed. The biological activity of an all-L synthetic peptide is most often completely different from that of the D-containing natural compounds. Analyzing the selected natural compounds showed that D-Ala, D-Val, D-Leu and D-Ser are the most commonly encountered D-AAs closely followed by the non-proteinogenic D-allo-Thr. D-Lys and D-Met were the least prevalent D-AAs in naturally occurring compounds.
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Affiliation(s)
- Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, 76019, USA.
| | - Alain Berthod
- Institut des Sciences Analytiques, CNRS, University of Lyon 1, 69100, Villeurbanne, France
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5
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Pflanze S, Mukherji R, Ibrahim A, Günther M, Götze S, Chowdhury S, Reimer L, Regestein L, Stallforth P. Nonribosomal peptides protect Pseudomonas nunensis 4A2e from amoebal and nematodal predation. Chem Sci 2023; 14:11573-11581. [PMID: 37886094 PMCID: PMC10599466 DOI: 10.1039/d3sc03335j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/01/2023] [Indexed: 10/28/2023] Open
Abstract
The rhizosphere is a highly competitive environment forcing bacteria to evolve strategies to oppose their enemies. The production of toxic secondary metabolites allows bacteria to counteract predators. In this study, we describe the anti-predator armamentarium of the soil-derived bacterium Pseudomonas nunensis 4A2e. Based on a genome mining approach, we identified several biosynthetic gene clusters coding for nonribosomal peptide synthetases. Generation of gene deletion mutants of the respective clusters shows a loss of defense capabilities. We isolated the novel lipopeptides keanumycin D and nunapeptins B and C, and fully elucidated their structures by a combination of in-depth mass spectrometry experiments, stable isotope labelling, and chemical synthesis. Additionally, investigation of the quorum sensing-dependent biosynthesis allowed us to elucidate parts of the underlying regulation of the biosynthetic machinery. Ecology-inspired bioassays highlight the role of these peptides as a defence strategy against protozoans and led us to find a previously unknown function against the bacterivorous nematode Oscheius myriophilus.
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Affiliation(s)
- Sebastian Pflanze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Ruchira Mukherji
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Markus Günther
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Sebastian Götze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Lisa Reimer
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Lars Regestein
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University (FSU) Jena Germany
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6
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Götze S, Vij R, Burow K, Thome N, Urbat L, Schlosser N, Pflanze S, Müller R, Hänsch VG, Schlabach K, Fazlikhani L, Walther G, Dahse HM, Regestein L, Brunke S, Hube B, Hertweck C, Franken P, Stallforth P. Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block. J Am Chem Soc 2023; 145:2342-2353. [PMID: 36669196 PMCID: PMC9897216 DOI: 10.1021/jacs.2c11107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 01/22/2023]
Abstract
Investigating the ecological context of microbial predator-prey interactions enables the identification of microorganisms, which produce multiple secondary metabolites to evade predation or to kill the predator. In addition, genome mining combined with molecular biology methods can be used to identify further biosynthetic gene clusters that yield new antimicrobials to fight the antimicrobial crisis. In contrast, classical screening-based approaches have limitations since they do not aim to unlock the entire biosynthetic potential of a given organism. Here, we describe the genomics-based identification of keanumycins A-C. These nonribosomal peptides enable bacteria of the genus Pseudomonas to evade amoebal predation. While being amoebicidal at a nanomolar level, these compounds also exhibit a strong antimycotic activity in particular against the devastating plant pathogen Botrytis cinerea and they drastically inhibit the infection of Hydrangea macrophylla leaves using only supernatants of Pseudomonas cultures. The structures of the keanumycins were fully elucidated through a combination of nuclear magnetic resonance, tandem mass spectrometry, and degradation experiments revealing an unprecedented terminal imine motif in keanumycin C extending the family of nonribosomal amino acids by a highly reactive building block. In addition, chemical synthesis unveiled the absolute configuration of the unusual dihydroxylated fatty acid of keanumycin A, which has not yet been reported for this lipodepsipeptide class. Finally, a detailed genome-wide microarray analysis of Candida albicans exposed to keanumycin A shed light on the mode-of-action of this potential natural product lead, which will aid the development of new pharmaceutical and agrochemical antifungals.
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Affiliation(s)
- Sebastian Götze
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Raghav Vij
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Katja Burow
- Research
Centre for Horticultural Crops (FGK), Fachhochschule
Erfurt, Kühnhäuser
Straße 101, 99090 Erfurt, Germany
| | - Nicola Thome
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Lennart Urbat
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Nicolas Schlosser
- Bio
Pilot Plant, Leibniz Institute for Natural Product Research and Infection
Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sebastian Pflanze
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Rita Müller
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Veit G. Hänsch
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Kevin Schlabach
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Leila Fazlikhani
- Research
Centre for Horticultural Crops (FGK), Fachhochschule
Erfurt, Kühnhäuser
Straße 101, 99090 Erfurt, Germany
| | - Grit Walther
- National
Reference Center for Invasive Fungal Infections, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department
of Infection Biology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Lars Regestein
- Bio
Pilot Plant, Leibniz Institute for Natural Product Research and Infection
Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sascha Brunke
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Philipp Franken
- Research
Centre for Horticultural Crops (FGK), Fachhochschule
Erfurt, Kühnhäuser
Straße 101, 99090 Erfurt, Germany
- Molecular
Phytopathology, Friedrich Schiller University, 07745 Jena, Germany
| | - Pierre Stallforth
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Faculty
of Chemistry and Earth Sciences, Institute of Organic Chemistry and
Macromolecular Chemistry, Friedrich Schiller
University Jena, Humboldtstraße 10, 07743 Jena, Germany
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7
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Girard L, Lood C, De Mot R, van Noort V, Baudart J. Genomic diversity and metabolic potential of marine Pseudomonadaceae. Front Microbiol 2023; 14:1071039. [PMID: 37168120 PMCID: PMC10165715 DOI: 10.3389/fmicb.2023.1071039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/21/2023] [Indexed: 05/13/2023] Open
Abstract
Recent changes in the taxonomy of the Pseudomonadaceae family have led to the delineation of three new genera (Atopomonas, Halopseudomonas and Stutzerimonas). However, the genus Pseudomonas remains the most densely populated and displays a broad genetic diversity. Pseudomonas are able to produce a wide variety of secondary metabolites which drives important ecological functions and have a great impact in sustaining their lifestyles. While soilborne Pseudomonas are constantly examined, we currently lack studies aiming to explore the genetic diversity and metabolic potential of marine Pseudomonas spp. In this study, 23 Pseudomonas strains were co-isolated with Vibrio strains from three marine microalgal cultures and rpoD-based phylogeny allowed their assignment to the Pseudomonas oleovorans group (Pseudomonas chengduensis, Pseudomonas toyotomiensis and one new species). We combined whole genome sequencing on three selected strains with an inventory of marine Pseudomonas genomes to assess their phylogenetic assignations and explore their metabolic potential. Our results revealed that most strains are incorrectly assigned at the species level and half of them do not belong to the genus Pseudomonas but instead to the genera Halopseudomonas or Stutzerimonas. We highlight the presence of 26 new species (Halopseudomonas (n = 5), Stutzerimonas (n = 7) and Pseudomonas (n = 14)) and describe one new species, Pseudomonas chaetocerotis sp. nov. (type strain 536T = LMG 31766T = DSM 111343T). We used genome mining to identify numerous BGCs coding for the production of diverse known metabolites (i.e., osmoprotectants, photoprotectants, quorum sensing molecules, siderophores, cyclic lipopeptides) but also unknown metabolites (e.g., ARE, hybrid ARE-DAR, siderophores, orphan NRPS gene clusters) awaiting chemical characterization. Finally, this study underlines that marine environments host a huge diversity of Pseudomonadaceae that can drive the discovery of new secondary metabolites.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Léa Girard,
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Baudart
- Laboratoire de Biodiversité et Biotechnologie Microbiennes, Sorbonne Université, CNRS, Observatoire Océanologique, Banyuls-sur-Mer, France
- *Correspondence: Julia Baudart,
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8
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Dumack K, Feng K, Flues S, Sapp M, Schreiter S, Grosch R, Rose LE, Deng Y, Smalla K, Bonkowski M. What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes. Protist 2022; 173:125913. [PMID: 36257252 DOI: 10.1016/j.protis.2022.125913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022]
Abstract
In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.
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Affiliation(s)
- Kenneth Dumack
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | - Kai Feng
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Sebastian Flues
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Melanie Sapp
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Susanne Schreiter
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany; Helmholtz Centre for Environmental Research GmbH (UFZ), Deptartment Soil System Science, Theodor-Lieser-Str.4, 06120 Halle, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Laura E Rose
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Michael Bonkowski
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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9
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Ferrarini E, Špacapan M, Lam VB, McCann A, Cesa-Luna C, Marahatta BP, De Pauw E, De Mot R, Venturi V, Höfte M. Versatile role of Pseudomonas fuscovaginae cyclic lipopeptides in plant and microbial interactions. FRONTIERS IN PLANT SCIENCE 2022; 13:1008980. [PMID: 36426159 PMCID: PMC9679282 DOI: 10.3389/fpls.2022.1008980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Pseudomonas fuscovaginae is the most prominent bacterial sheath rot pathogen, causing sheath brown rot disease in rice. This disease occurs worldwide and it is characterized by typical necrotic lesions on the sheath, as well as a reduction in the number of emitted panicles and filled grains. P. fuscovaginae has been shown to produce syringotoxin and fuscopeptin cyclic lipopeptides (CLPs), which have been linked to pathogenicity. In this study, we investigated the role of P. fuscovaginae UPB0736 CLPs in plant pathogenicity, antifungal activity and swarming motility. To do so, we sequenced the strain to obtain a single-contig genome and we constructed deletion mutants in the biosynthetic gene clusters responsible for the synthesis of CLPs. We show that UPB0736 produces a third CLP of 13 amino acids, now named asplenin, and we link this CLP with the swarming activity of the strain. We could then show that syringotoxin is particularly active against Rhizoctonia solani in vitro. By testing the mutants in planta we investigated the role of both fuscopeptin and syringotoxin in causing sheath rot lesions. We proved that the presence of these two CLPs considerably affected the number of emitted panicles, although their number was still significantly affected in the mutants deficient in both fuscopeptin and syringotoxin. These results reveal the importance of CLPs in P. fuscovaginae pathogenicity, but also suggest that other pathogenicity factors may be involved.
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Affiliation(s)
- Enrico Ferrarini
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Mihael Špacapan
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Van Bach Lam
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Andrea McCann
- Department of Chemistry, Faculty of Sciences, University of Liège, Liège, Belgium
| | - Catherine Cesa-Luna
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Bishnu Prasad Marahatta
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Edwin De Pauw
- Department of Chemistry, Faculty of Sciences, University of Liège, Liège, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Monica Höfte
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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10
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Yellow polyketide pigment suppresses premature hatching in social amoeba. Proc Natl Acad Sci U S A 2022; 119:e2116122119. [PMID: 36252029 PMCID: PMC9618038 DOI: 10.1073/pnas.2116122119] [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: 11/18/2022] Open
Abstract
Low-molecular-weight natural products from microbes are indispensable in the development of potent drugs. However, their biological roles within an ecological context often remain elusive. Here, we shed light on natural products from eukaryotic microorganisms that have the ability to transition from single cells to multicellular organisms: the social amoebae. These eukaryotes harbor a large number of polyketide biosynthetic genes in their genomes, yet virtually none of the corresponding products can be isolated or characterized. Using complementary molecular biology approaches, including CRISPR-Cas9, we generated polyketide synthase (pks5) inactivation and overproduction strains of the social amoeba Dictyostelium discoideum. Differential, untargeted metabolomics of wild-type versus mutant fruiting bodies allowed us to pinpoint candidate metabolites derived from the amoebal PKS5. Extrachromosomal expression of the respective gene led to the identification of a yellow polyunsaturated fatty acid. Analysis of the temporospatial production pattern of this compound in conjunction with detailed bioactivity studies revealed the polyketide to be a spore germination suppressor.
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11
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Rivera-Chávez J, Ceapă CD, Figueroa M. Biological Dark Matter Exploration using Data Mining for the Discovery of Antimicrobial Natural Products. PLANTA MEDICA 2022; 88:702-720. [PMID: 35697058 DOI: 10.1055/a-1795-0562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of novel antimicrobials has significantly slowed down over the last three decades. At the same time, humans rely increasingly on antimicrobials because of the progressive antimicrobial resistance in medical practices, human communities, and the environment. Data mining is currently considered a promising option in the discovery of new antibiotics. Some of the advantages of data mining are the ability to predict chemical structures from sequence data, anticipation of the presence of novel metabolites, the understanding of gene evolution, and the corroboration of data from multiple omics technologies. This review analyzes the state-of-the-art for data mining in the fields of bacteria, fungi, and plant genomic data, as well as metabologenomics. It also summarizes some of the most recent research accomplishments in the field, all pinpointing to innovation through uncovering and implementing the next generation of antimicrobials.
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Affiliation(s)
- José Rivera-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Corina-Diana Ceapă
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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12
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Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH, Adhikari K, Weigt M, Schmeing TM, Li B. Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J Am Chem Soc 2022; 144:14057-14070. [PMID: 35895935 DOI: 10.1021/jacs.1c13404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (CmodAA). We also obtain the crystal structure of a CmodAA domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-CmodAA modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-CmodAA identify several key residues for activity, including four residues that are mostly conserved in the CmodAA subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for CmodAA domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of CmodAA domains. Understanding CmodAA domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.
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Affiliation(s)
- Jon B Patteson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Camille Marie Fortinez
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Andrew T Putz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Juan Rodriguez-Rivas
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - L Henry Bryant
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kamal Adhikari
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Bando Y, Hou Y, Seyfarth L, Probst J, Götze S, Bogacz M, Hellmich UA, Stallforth P, Mittag M, Arndt H. Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A. Chemistry 2022; 28:e202104417. [PMID: 35199896 PMCID: PMC9311703 DOI: 10.1002/chem.202104417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Indexed: 11/15/2022]
Abstract
A total synthesis of the cyclic lipodepsipeptide natural product orfamide A was achieved. By developing a synthesis format using an aminoacid ester building block and SPPS protocol adaptation, a focused library of target compounds was obtained, in high yield and purity. Spectral and LC-HRMS data of all library members with the isolated natural product identified the 5 Leu residue to be d- and the 3'-OH group to be R-configured. The structural correction of orfamide A by chemical synthesis and analysis was confirmed by biological activity comparison in Chlamydomonas reinhardtii, which indicated compound configuration to be important for bioactivity. Acute toxicity was also found against Trypanosoma brucei, the parasite causing African sleeping sickness.
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Affiliation(s)
- Yuko Bando
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Yu Hou
- Friedrich Schiller University Jena Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular BotanyAm Planetarium 107743JenaGermany
| | - Lydia Seyfarth
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Jannik Probst
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Sebastian Götze
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll InstituteDepartment of PaleobiotechnologyBeutenbergstraße 11a07745JenaGermany
| | - Marta Bogacz
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Ute A. Hellmich
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Pierre Stallforth
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll InstituteDepartment of PaleobiotechnologyBeutenbergstraße 11a07745JenaGermany
| | - Maria Mittag
- Friedrich Schiller University Jena Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular BotanyAm Planetarium 107743JenaGermany
| | - Hans‐Dieter Arndt
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
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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: 37] [Impact Index Per Article: 18.5] [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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Iwumene NUN, Moseley DF, Pullin RDC, Willis MC. Diverse saturated heterocycles from a hydroacylation/conjugate addition cascade. Chem Sci 2022; 13:1504-1511. [PMID: 35222935 PMCID: PMC8809418 DOI: 10.1039/d1sc06900d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 11/21/2022] Open
Abstract
Rhodium-catalyzed hydroacylation using alkynes substituted with pendant nucleophiles, delivers linear α,β-unsaturated enone intermediates with excellent regioselectivity. These adducts are used to construct a broad range of diversely substituted, saturated O-, N- and S-heterocycles in a one-pot process. Judicious choice of cyclisation conditions enabled isolation of O-heterocycles with high levels of diastereoselectivity. A variety of derivatisation reactions are also performed, generating functionalised hydroacylation products. This sequence serves as a general approach for the synthesis of fully saturated heterocycles.
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Affiliation(s)
- Ndidi U N Iwumene
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Daniel F Moseley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Robert D C Pullin
- Vertex Pharmaceuticals (Europe) Ltd 86-88 Jubilee Avenue, Milton Park Abingdon OX14 4RW UK
| | - Michael C Willis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
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16
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Cui Y, Meng J, Zhang J, Wang L, Yan H, Xia H, Cao J, Wu L. Case Report: A Case of Sarocladium strictum Meningoencephalitis in an Immunocompetent Patient After Invasive Operation. Front Med (Lausanne) 2021; 8:762763. [PMID: 34859014 PMCID: PMC8631361 DOI: 10.3389/fmed.2021.762763] [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: 08/22/2021] [Accepted: 10/21/2021] [Indexed: 12/02/2022] Open
Abstract
As an opportunistic phytopathogen, Sarocladium strictum has only been shown to cause neurological disease in immunocompromised patients, where antifungal therapy was not effective. We report a case of Sarocladium strictum meningoencephalitis in an apparently immunocompetent young woman who presented with severe headache and slight fever after undergoing transnasal endoscopic repair of cerebrospinal fluid rhinorrhea. Chronic sinusitis and suspicious intracranial fungal lesions were observed on enhanced magnetic resonance imaging (MRI). Both culture and metagenomic next-generation sequencing of her cerebrospinal fluid were positive for Sarocladium strictum. After local debridement, treatment with amphotericin B plus voriconazole and Ommaya reservoir implantation, the patient improved significantly. Unfortunately, her symptoms worsened again despite plenty of antifungal therapy for a month.
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Affiliation(s)
- Yue Cui
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiali Meng
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jing Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lin Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Haihan Yan
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Jingrong Cao
- Department of Clinical Laboratory, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Liyong Wu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
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17
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Transporter Gene-mediated Typing for Detection and Genome Mining of Lipopeptide-producing Pseudomonas. Appl Environ Microbiol 2021; 88:e0186921. [PMID: 34731056 PMCID: PMC8788793 DOI: 10.1128/aem.01869-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Pseudomonas lipopeptides (LPs) are involved in diverse ecological functions and have biotechnological application potential associated with their antimicrobial and/or antiproliferative activities. They are synthesized by multimodular nonribosomal peptide synthetases which, together with transport and regulatory proteins, are encoded by large biosynthetic gene clusters (BGCs). These secondary metabolites are classified in distinct families based on the sequence and length of the oligopeptide and size of the macrocycle, if present. The phylogeny of PleB, the MacB-like transporter that is part of a dedicated ATP-dependent tripartite efflux system driving export of Pseudomonas LPs, revealed a strong correlation with LP chemical diversity. As each LP BGC carries its cognate pleB, PleB is suitable as a diagnostic sequence for genome mining, allowing assignment of the putative metabolite to a particular LP family. In addition, pleB proved to be a suitable target gene for an alternative PCR method for detecting LP-producing Pseudomonas sp. and did not rely on amplification of catalytic domains of the biosynthetic enzymes. Combined with amplicon sequencing, this approach enabled typing of Pseudomonas strains as potential producers of a LP belonging to one of the known LP families, underscoring its value for strain prioritization. This finding was validated by chemical characterization of known LPs from three different families secreted by novel producers isolated from the rice or maize rhizosphere, namely, the type strains of Pseudomonas fulva (putisolvin), Pseudomonas zeae (tensin), and Pseudomonas xantholysinigenes (xantholysin). In addition, a new member of the Bananamide family, prosekin, was discovered in the type strain of Pseudomonas prosekii, which is an Antarctic isolate. IMPORTANCEPseudomonas spp. are ubiquitous bacteria able to thrive in a wide range of ecological niches, and lipopeptides often support their lifestyle but also their interaction with other micro- and macro-organisms. Therefore, the production of lipopeptides is widespread among Pseudomonas strains. Consequently, Pseudomonas lipopeptide research not only affects chemists and microbiologists but also touches a much broader audience, including biochemists, ecologists, and plant biologists. In this study, we present a reliable transporter gene-guided approach for the detection and/or typing of Pseudomonas lipopeptide producers. Indeed, it allows us to readily assess the lipopeptide diversity among sets of Pseudomonas isolates and differentiate strains likely to produce known lipopeptides from producers of potentially novel lipopeptides. This work provides a valuable tool that can also be integrated in a genome mining strategy and adapted for the typing of other specialized metabolites.
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18
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Biology and applications of co-produced, synergistic antimicrobials from environmental bacteria. Nat Microbiol 2021; 6:1118-1128. [PMID: 34446927 DOI: 10.1038/s41564-021-00952-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/21/2021] [Indexed: 02/07/2023]
Abstract
Environmental bacteria, such as Streptomyces spp., produce specialized metabolites that are potent antibiotics and therapeutics. Selected specialized antimicrobials are co-produced and function together synergistically. Co-produced antimicrobials comprise multiple chemical classes and are produced by a wide variety of bacteria in different environmental niches, suggesting that their combined functions are ecologically important. Here, we highlight the exquisite mechanisms that underlie the simultaneous production and functional synergy of 16 sets of co-produced antimicrobials. To date, antibiotic and antifungal discovery has focused mainly on single molecules, but we propose that methods to target co-produced antimicrobials could widen the scope and applications of discovery programs.
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19
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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20
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Pérez-Victoria I. Co-occurring Congeners Reveal the Position of Enantiomeric Amino Acids in Nonribosomal Peptides. Chembiochem 2021; 22:2087-2092. [PMID: 33440038 DOI: 10.1002/cbic.202000805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/11/2021] [Indexed: 11/09/2022]
Abstract
The absolute configuration of the constituent amino acids in microbial nonribosomal peptides is typically determined by Marfey's method after total hydrolysis of the peptide. A challenge to structure elucidation arises when both d and l enantiomeric configurations of an amino acid are present. Determining the actual position of each amino acid enantiomer within the peptide sequence typically requires laborious approaches based on peptide partial hydrolysis or even total synthesis of the possible diastereomers. Herein, an alternative solution is discussed based on the homogeneous backbone chirality that governs all peptides biosynthesized by a common nonribosomal peptide synthetase. The information on configuration provided by Marfey's analysis of co-occurring minor congeners can reveal unequivocally the stereochemical sequence of the whole peptide family.
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Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain
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21
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Abstract
Bacteria are inherently social organisms whose actions should ideally be studied within an interactive ecological context. We show that the exchange and modification of natural products enables two unrelated bacteria to defend themselves against a common predator. Amoebal predation is a major cause of death in soil bacteria and thus it exerts a strong selective pressure to evolve defensive strategies. A systematic analysis of binary combinations of coisolated bacteria revealed strains that were individually susceptible to predation but together killed their predator. This cooperative defense relies on a Pseudomonas species producing syringafactin, a lipopeptide, which induces the production of peptidases in a Paenibacillus strain. These peptidases then degrade the innocuous syringafactin into compounds, which kill the predator. A combination of bioprospecting, coculture experiments, genome modification, and transcriptomics unravel this novel natural product-based defense strategy.
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22
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Schlembach I, Grünberger A, Rosenbaum MA, Regestein L. Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes. Trends Biotechnol 2021; 39:1093-1109. [PMID: 33573846 PMCID: PMC7612867 DOI: 10.1016/j.tibtech.2021.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial mixed cultures are gaining increasing attention as biotechnological production systems, since they offer a large but untapped potential for future bioprocesses. Effects of secondary metabolite induction and advantages of labor division for the degradation of complex substrates offer new possibilities for process intensification. However, mixed cultures are highly complex, and, consequently, many biotic and abiotic parameters are required to be identified, characterized, and ideally controlled to establish a stable bioprocess. In this review, we discuss the advantages and disadvantages of existing measurement techniques for identifying, characterizing, monitoring, and controlling mixed cultures and highlight promising examples. Moreover, existing challenges and emerging technologies are discussed, which lay the foundation for novel analytical workflows to monitor mixed-culture bioprocesses.
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Affiliation(s)
- Ivan Schlembach
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Lars Regestein
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
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23
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Girard L, Höfte M, De Mot R. Lipopeptide families at the interface between pathogenic and beneficial Pseudomonas-plant interactions. Crit Rev Microbiol 2020; 46:397-419. [PMID: 32885723 DOI: 10.1080/1040841x.2020.1794790] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipopeptides (LPs) are a prominent class of molecules among the steadily growing spectrum of specialized metabolites retrieved from Pseudomonas, in particular soil-dwelling and plant-associated isolates. Among the multiple LP families, pioneering research focussed on phytotoxic and antimicrobial cyclic lipopeptides (CLPs) of the ubiquitous plant pathogen Pseudomonas syringae (syringomycin and syringopeptin). Their non-ribosomal peptide synthetases (NRPSs) are embedded in biosynthetic gene clusters (BGCs) that are tightly co-clustered on a pathogenicity island. Other members of the P. syringae group (Pseudomonas cichorii) and some species of the Pseudomonas asplenii group and Pseudomonas fluorescens complex have adopted these biosynthetic strategies to co-produce their own mycin and peptin variants, in some strains supplemented with an analogue of the P. syringae linear LP (LLP), syringafactin. This capacity is not confined to phytopathogens but also occurs in some biocontrol strains, which indicates that these LP families not solely function as general virulence factors. We address this issue by scrutinizing the structural diversity and bioactivities of LPs from the mycin, peptin, and factin families in a phylogenetic and evolutionary perspective. BGC functional organization (including associated regulatory and transport genes) and NRPS modular architectures in known and candidate LP producers were assessed by genome mining.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
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24
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Grab HA, Kirsch VC, Sieber SA, Bach T. Total Synthesis of the Cyclic Depsipeptide Vioprolide D via its (Z)-Diastereoisomer. Angew Chem Int Ed Engl 2020; 59:12357-12361. [PMID: 32126146 PMCID: PMC7383572 DOI: 10.1002/anie.202002328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Indexed: 12/15/2022]
Abstract
The first total synthesis of vioprolide D was accomplished in an overall yield of 2.0 % starting from methyl (2S)-3-benzyloxy-2-hydroxypropanoate (16 steps in the longest linear sequence). The cyclic depsipeptide was assembled from two building blocks of similar size and complexity in a modular, highly convergent approach. Peptide bond formation at the C-terminal dehydrobutyrine amino acid of the northern fragment was possible via its (Z)-diastereoisomer. After macrolactamization and formation of the thiazoline ring, the (Z)-double bond of the dehydrobutyrine unit was isomerized to the (E)-double bond of the natural product. The cytotoxicity of vioprolide D is significantly higher than that of its (Z)-diastereoisomer.
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Affiliation(s)
- Hanusch A. Grab
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| | - Volker C. Kirsch
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| | - Stephan A. Sieber
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| | - Thorsten Bach
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
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25
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Grab HA, Kirsch VC, Sieber SA, Bach T. Totalsynthese des cyclischen Depsipeptids Vioprolid D über sein (
Z
)‐Diastereomer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hanusch A. Grab
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| | - Volker C. Kirsch
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| | - Thorsten Bach
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
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26
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Mukherji R, Zhang S, Chowdhury S, Stallforth P. Chimeric LuxR Transcription Factors Rewire Natural Product Regulation. Angew Chem Int Ed Engl 2020; 59:6192-6195. [PMID: 31943579 PMCID: PMC7187462 DOI: 10.1002/anie.201914449] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/12/2019] [Indexed: 01/17/2023]
Abstract
LuxR-type transcriptional activator proteins frequently regulate the expression of biosynthetic gene clusters (BGCs). With only a fraction of bacterial BGCs being expressed under standard culturing conditions, modulation of LuxRs would provide a powerful approach to activate silent clusters. We show that by exploiting the modular nature of LuxR proteins, it is possible to construct functional chimeric LuxRs, which enables both the rewiring of quorum sensing systems and the activation of silent BGCs. Importantly, our strategy allowed us to identify the novel natural product pseudomonol from a bacterium of the genus Pseudomonas.
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Affiliation(s)
- Ruchira Mukherji
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Shuaibing Zhang
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Somak Chowdhury
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Pierre Stallforth
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstrasse 11a07745JenaGermany
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Mukherji R, Zhang S, Chowdhury S, Stallforth P. Chimeric LuxR Transcription Factors Rewire Natural Product Regulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ruchira Mukherji
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Shuaibing Zhang
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Somak Chowdhury
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Pierre Stallforth
- Independent Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
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28
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Klapper M, Schlabach K, Paschold A, Zhang S, Chowdhury S, Menzel K, Rosenbaum MA, Stallforth P. Biosynthesis of Pseudomonas-Derived Butenolides. Angew Chem Int Ed Engl 2020; 59:5607-5610. [PMID: 31880848 PMCID: PMC7154651 DOI: 10.1002/anie.201914154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/29/2019] [Indexed: 11/06/2022]
Abstract
Butenolides are well-known signaling molecules in Gram-positive bacteria. Here, we describe a novel class of butenolides isolated from a Gram-negative Pseudomonas strain, the styrolides. Structure elucidation was aided by the total synthesis of styrolide A. Transposon mutagenesis enabled us to identify the styrolide biosynthetic gene cluster, and by using a homology search, we discovered the related and previously unknown acaterin biosynthetic gene cluster in another Pseudomonas species. Mutagenesis, heterologous expression, and identification of key shunt and intermediate products were crucial to propose a biosynthetic pathway for both Pseudomonas-derived butenolides. Comparative transcriptomics suggests a link between styrolide formation and the regulatory networks of the bacterium.
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Affiliation(s)
- Martin Klapper
- Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstraße 11a07745JenaGermany
| | - Kevin Schlabach
- Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstraße 11a07745JenaGermany
| | - André Paschold
- Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstraße 11a07745JenaGermany
| | - Shuaibing Zhang
- Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstraße 11a07745JenaGermany
| | - Somak Chowdhury
- Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstraße 11a07745JenaGermany
| | - Klaus‐Dieter Menzel
- Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology, HKIGermany
| | - Miriam A. Rosenbaum
- Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology, HKIGermany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial CommunicationLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstraße 11a07745JenaGermany
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29
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Klapper M, Schlabach K, Paschold A, Zhang S, Chowdhury S, Menzel K, Rosenbaum MA, Stallforth P. Biosynthesis of
Pseudomonas
‐Derived Butenolides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Martin Klapper
- Junior Research Group Chemistry of Microbial Communication Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstraße 11a 07745 Jena Germany
| | - Kevin Schlabach
- Junior Research Group Chemistry of Microbial Communication Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstraße 11a 07745 Jena Germany
| | - André Paschold
- Junior Research Group Chemistry of Microbial Communication Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstraße 11a 07745 Jena Germany
| | - Shuaibing Zhang
- Junior Research Group Chemistry of Microbial Communication Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstraße 11a 07745 Jena Germany
| | - Somak Chowdhury
- Junior Research Group Chemistry of Microbial Communication Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstraße 11a 07745 Jena Germany
| | - Klaus‐Dieter Menzel
- Bio Pilot Plant Leibniz Institute for Natural Product Research and Infection Biology, HKI Germany
| | - Miriam A. Rosenbaum
- Bio Pilot Plant Leibniz Institute for Natural Product Research and Infection Biology, HKI Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstraße 11a 07745 Jena Germany
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30
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Liu C, Kakeya H. Cryptic Chemical Communication: Secondary Metabolic Responses Revealed by Microbial Co‐culture. Chem Asian J 2020; 15:327-337. [DOI: 10.1002/asia.201901505] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/15/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University Sakyo-ku Kyoto 606-8501 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University Sakyo-ku Kyoto 606-8501 Japan
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31
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Antimicrobial Activity of Metabolites Secreted by the Endophytic Bacterium Frateuria defendens. PLANTS 2020; 9:plants9010072. [PMID: 31935875 PMCID: PMC7020481 DOI: 10.3390/plants9010072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 01/28/2023]
Abstract
Candidatus Phytoplasma, the causative agent of yellows disease, inflicts substantial damage on several hundred plant species including perennials and annual plants. The endophytic bacterium Frateuria defendens reduces the symptoms of yellows disease in a number of agricultural crops. One possible mode of action is that the bacterium secretes antimicrobial metabolites. To test this hypothesis, the substances secreted by the endophyte during 10 days of growth in an artificial medium were identified by GC-MS (gas chromatography-mass spectrometry). Synthetic analogues to these substances were then used on periwinkle, a nurse culture plant infected by phytoplasma. Phytoplasma quantities were evaluated by quantitative PCR, and disease symptoms were monitored and recorded. It was found that specific compounds identified by the biochemical analysis caused a significant reduction in both the titer of phytoplasma and the disease symptoms in periwinkle when compared to untreated infected plants. Further research is required to examine the potential of these compounds as an effective treatment against yellows disease.
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32
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Götze S, Stallforth P. Structure elucidation of bacterial nonribosomal lipopeptides. Org Biomol Chem 2020; 18:1710-1727. [DOI: 10.1039/c9ob02539a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
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Affiliation(s)
- Sebastian Götze
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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33
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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34
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Götze S, Arp J, Lackner G, Zhang S, Kries H, Klapper M, García-Altares M, Willing K, Günther M, Stallforth P. Structure elucidation of the syringafactin lipopeptides provides insight in the evolution of nonribosomal peptide synthetases. Chem Sci 2019; 10:10979-10990. [PMID: 32953002 PMCID: PMC7472662 DOI: 10.1039/c9sc03633d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Modular biosynthetic machineries such as polyketide synthases (PKSs) or nonribosomal peptide synthetases (NRPSs) give rise to a vast structural diversity of bioactive metabolites indispensable in the treatment of cancer or infectious diseases. Here, we provide evidence for different evolutionary processes leading to the diversification of modular NRPSs and thus, their respective products. Discovery of a novel lipo-octapeptide family from Pseudomonas, the virginiafactins, and detailed structure elucidation of closely related peptides, the cichofactins and syringafactins, allowed retracing recombinational diversification of the respective NRPS genes. Bioinformatics analyses allowed us to spot an evolutionary snapshot of these processes, where recombination occurred both within the same and between different biosynthetic gene clusters. Our systems feature a recent diversification process, which may represent a typical paradigm to variations in modular biosynthetic machineries.
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Affiliation(s)
- Sebastian Götze
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Johannes Arp
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Gerald Lackner
- Independent Junior Research Group Synthetic Microbiology , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Shuaibing Zhang
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Hajo Kries
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Martin Klapper
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - María García-Altares
- Department Biomolecular Chemistry , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Karsten Willing
- Department Bio Pilot Plant , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Markus Günther
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Pierre Stallforth
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
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35
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Stanišić A, Hüsken A, Kries H. HAMA: a multiplexed LC-MS/MS assay for specificity profiling of adenylate-forming enzymes. Chem Sci 2019; 10:10395-10399. [PMID: 32110329 PMCID: PMC6988596 DOI: 10.1039/c9sc04222a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/13/2019] [Indexed: 01/04/2023] Open
Abstract
Adenylation enzymes are engineering targets in ribosomal and nonribosomal peptide synthesis. Through multiplexed LC-MS/MS measurement of hydroxamates, the HAMA assay records specificity profiles of these enzymes in a snap.
Adenylation enzymes selecting substrates for ribosomal and nonribosomal protein and peptide biosynthesis have been popular targets of enzyme engineering. Previous standard assays for adenylation specificity have been cumbersome and failed to reflect the competition conditions inside a cell because they measure substrates one at a time. We have developed an adenylation assay based on hydroxamate quenching and LC-MS/MS detection of hydroxamate products testing dozens of competing amino acid substrates in parallel. Streamlined specificity profiling of adenylation enzymes will facilitate engineering and directed evolution of ribosomal and nonribosomal peptide synthesis.
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Affiliation(s)
- Aleksa Stanišić
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology e.V. , Hans Knöll Institute (HKI Jena) , Beutenbergstr. 11a , 07745 Jena , Germany .
| | - Annika Hüsken
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology e.V. , Hans Knöll Institute (HKI Jena) , Beutenbergstr. 11a , 07745 Jena , Germany .
| | - Hajo Kries
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology e.V. , Hans Knöll Institute (HKI Jena) , Beutenbergstr. 11a , 07745 Jena , Germany .
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36
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Sugiyama R, Nakatani T, Nishimura S, Takenaka K, Ozaki T, Asamizu S, Onaka H, Kakeya H. Chemical Interactions of Cryptic Actinomycete Metabolite 5‐Alkyl‐1,2,3,4‐tetrahydroquinolines through Aggregate Formation. Angew Chem Int Ed Engl 2019; 58:13486-13491. [DOI: 10.1002/anie.201905970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
- Present address: Department of PharmacyNational University of Singapore 18 Science Drive 4 Singapore 117543 Singapore
| | - Takahiro Nakatani
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Kei Takenaka
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
| | - Taro Ozaki
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Present address: Department of ChemistryFaculty of ScienceHokkaido University Sapporo 060-0810 Hokkaido Japan
| | - Shumpei Asamizu
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
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37
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Klapper M, Paschold A, Zhang S, Weigel C, Dahse HM, Götze S, Pace S, König S, Rao Z, Reimer L, Werz O, Stallforth P. Bioactivity and Mode of Action of Bacterial Tetramic Acids. ACS Chem Biol 2019; 14:1693-1697. [PMID: 31294961 DOI: 10.1021/acschembio.9b00388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microbially produced 3-acyltetramic acids display a diverse range of biological activities. The pyreudiones are new members of this class that were isolated from bacteria of the genus Pseudomonas. Here, we performed a structure-activity relationship study and determined their mode of action. An efficient biomimetic synthesis was developed to synthesize pyreudione A. Pyreudiones and synthetic analogs thereof were tested for their amoebicidal, antibacterial, antiproliferative, and cytotoxic activities. The length of the alkyl side chain and the nature of the amino acid residues within the tetramic acid moiety strongly affected activity, in particular against mycobacteria. The mode of action was shown to correlate with the ability of pyreudiones to act as protonophores. Removal of the acidic proton by methylation of pyreudione A resulted in a loss of bioactivity.
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Affiliation(s)
- Martin Klapper
- Independent Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - André Paschold
- Independent Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Shuaibing Zhang
- Independent Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christiane Weigel
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sebastian Götze
- Independent Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Simona Pace
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Stefanie König
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Zhigang Rao
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Lisa Reimer
- Independent Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Pierre Stallforth
- Independent Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
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38
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Sugiyama R, Nakatani T, Nishimura S, Takenaka K, Ozaki T, Asamizu S, Onaka H, Kakeya H. Chemical Interactions of Cryptic Actinomycete Metabolite 5‐Alkyl‐1,2,3,4‐tetrahydroquinolines through Aggregate Formation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
- Present address: Department of PharmacyNational University of Singapore 18 Science Drive 4 Singapore 117543 Singapore
| | - Takahiro Nakatani
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Kei Takenaka
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
| | - Taro Ozaki
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Present address: Department of ChemistryFaculty of ScienceHokkaido University Sapporo 060-0810 Hokkaido Japan
| | - Shumpei Asamizu
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of BiotechnologyGraduate School of Agricultural and Life SciencesThe University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University, Sakyo-ku Kyoto 606-8501 Japan
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39
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Wencewicz TA. Crossroads of Antibiotic Resistance and Biosynthesis. J Mol Biol 2019; 431:3370-3399. [PMID: 31288031 DOI: 10.1016/j.jmb.2019.06.033] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.
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Affiliation(s)
- Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA.
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40
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Niu G, Li W. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends Biochem Sci 2019; 44:961-972. [PMID: 31256981 DOI: 10.1016/j.tibs.2019.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022]
Abstract
The widespread emergence of antibiotic-resistant pathogens poses a severe threat to public health. This problem becomes even worse with a coincident decline in the supply of new antibiotics. Conventional bioactivity-guided natural product discovery has failed to meet the urgent need for new antibiotics, largely due to limited resources and high rediscovery rates. Recent advances in cultivation techniques, analytical technologies, and genomics-based approaches have greatly expanded our access to previously underexploited microbial sources. These strategies will enable us to access new reservoirs of microorganisms and unleash their chemical potentials, thus opening new opportunities for the discovery of next-generation drugs to address the growing concerns of antimicrobial resistance.
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Affiliation(s)
- Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Braddock AA, Theodorakis EA. Marine Spirotetronates: Biosynthetic Edifices That Inspire Drug Discovery. Mar Drugs 2019; 17:md17040232. [PMID: 31010150 PMCID: PMC6521127 DOI: 10.3390/md17040232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022] Open
Abstract
Spirotetronates are actinomyces-derived polyketides that possess complex structures and exhibit potent and unexplored bioactivities. Due to their anticancer and antimicrobial properties, they have potential as drug hits and deserve further study. In particular, abyssomicin C and tetrocarcin A have shown significant promise against antibiotic-resistant S. aureus and tuberculosis, as well as for the treatment of various lymphomas and solid tumors. Improved synthetic routes to these compounds, particularly the class II spirotetronates, are needed to access sufficient quantities for structure optimization and clinical applications.
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Affiliation(s)
- Alexander A Braddock
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
| | - Emmanuel A Theodorakis
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
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Comparison of structures and cytotoxicity of mupirocin and batumin against melanoma and several other cancer cell lines. Future Med Chem 2019; 11:677-691. [PMID: 30947530 DOI: 10.4155/fmc-2018-0333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: To determine the computer-predicted anticancer activity of mupirocin and to compare its activities with those determined for another polyene antibiotic, batumin. Materials & methods: Molecular docking, cytotoxicity assays, cell microscopy and cell cycle progression were studied in cancer and nontumorigenic cell lines. Results & conclusion: Cytotoxicity of mupirocin against several cancerous cell lines was detected with the highest one (IC50 = 5.4 μg/ml) against melanoma cell line. The profile of cytotoxicity of mupirocin was similar to that reported for batumin. Nevertheless, the morphology of cells treated with these antibiotics and alterations in cell cycle progression suggested possible dissimilarity in their mechanisms of action. Selective cytotoxicity of mupirocin against melanoma cells potentiates further studies to discover nontoxic drugs for melanoma prevention.
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Song B, Li LY, Shang H, Liu Y, Yu M, Ding G, Zou ZM. Trematosphones A and B, Two Unique Dimeric Structures from the Desert Plant Endophytic Fungus Trematosphaeria terricola. Org Lett 2019; 21:2139-2142. [DOI: 10.1021/acs.orglett.9b00454] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Bo Song
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
- College of Pharmacy, Qiqihar Medical University, Qiqihar 161006, Heilongjiang, People’s Republic of China
| | - Ling-Yu Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
| | - Hai Shang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
| | - Yang Liu
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
| | - Meng Yu
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
| | - Gang Ding
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
| | - Zhong-Mei Zou
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, People’s Republic of China
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Abstract
The medical treatment of infectious diseases often requires combination therapies that blend two molecules to enhance drug efficacy. Nature does the same. In a new article, Mrak et al. identify and functionally characterize natural products from Streptomyces rapamycinicus that show synergistic antifungal activity with the well-known immunosuppressant metabolite rapamycin, produced by the same strain. The genomic co-association of the two biosynthetic gene clusters paves the way toward new strategies to discover synergistic pairs of antibiotics through large-scale genome mining.
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Affiliation(s)
- Mohammad Alanjary
- From the Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Marnix H Medema
- From the Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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Mrak P, Krastel P, Pivk Lukančič P, Tao J, Pistorius D, Moore CM. Discovery of the actinoplanic acid pathway in Streptomyces rapamycinicus reveals a genetically conserved synergism with rapamycin. J Biol Chem 2018; 293:19982-19995. [PMID: 30327433 DOI: 10.1074/jbc.ra118.005314] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/11/2018] [Indexed: 01/11/2023] Open
Abstract
Actinobacteria possess a great wealth of pathways for production of bioactive compounds. Following advances in genome mining, dozens of natural product (NP) gene clusters are routinely found in each actinobacterial genome; however, the modus operandi of this large arsenal is poorly understood. During investigations of the secondary metabolome of Streptomyces rapamycinicus, the producer of rapamycin, we observed accumulation of two compounds never before reported from this organism. Structural elucidation revealed actinoplanic acid A and its demethyl analogue. Actinoplanic acids (APLs) are potent inhibitors of Ras farnesyltransferase and therefore represent bioactive compounds of medicinal interest. Supported with the unique structure of these polyketides and using genome mining, we identified a gene cluster responsible for their biosynthesis in S. rapamycinicus Based on experimental evidence and genetic organization of the cluster, we propose a stepwise biosynthesis of APL, the first bacterial example of a pathway incorporating the rare tricarballylic moiety into an NP. Although phylogenetically distant, the pathway shares some of the biosynthetic principles with the mycotoxins fumonisins. Namely, the core polyketide is acylated with the tricarballylate by an atypical nonribosomal peptide synthetase-catalyzed ester formation. Finally, motivated by the conserved colocalization of the rapamycin and APL pathway clusters in S. rapamycinicus and all other rapamycin-producing actinobacteria, we confirmed a strong synergism of these compounds in antifungal assays. Mining for such evolutionarily conserved coharboring of pathways would likely reveal further examples of NP sets, attacking multiple targets on the same foe. These could then serve as a guide for development of new combination therapies.
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Affiliation(s)
- Peter Mrak
- From the Novartis Technical Operations, Antiinfectives, SI-1234 Mengeš, Slovenia,; University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Petra Pivk Lukančič
- From the Novartis Technical Operations, Antiinfectives, SI-1234 Mengeš, Slovenia
| | - Jianshi Tao
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, and
| | - Dominik Pistorius
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Charles M Moore
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland,.
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