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Junier P, Cailleau G, Fatton M, Udriet P, Hashmi I, Bregnard D, Corona-Ramirez A, Francesco ED, Kuhn T, Mangia N, Zhioua S, Hunkeler D, Bindschedler S, Sieber S, Gonzalez D. A cohesive Microcoleus strain cluster causes benthic cyanotoxic blooms in rivers worldwide. WATER RESEARCH X 2024; 24:100252. [PMID: 39308956 PMCID: PMC11416633 DOI: 10.1016/j.wroa.2024.100252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024]
Abstract
Over the last two decades, proliferations of benthic cyanobacteria producing derivatives of anatoxin-a have been reported in rivers worldwide. Here, we follow up on such a toxigenic event happening in the Areuse river in Switzerland and investigate the diversity and genomics of major bloom-forming riverine benthic cyanobacteria. We show, using 16S rRNA-based community profiling, that benthic communities are dominated by Oscillatoriales. We correlate the detection of one Microcoleus sequence variant matching the Microcoleus anatoxicus species with the presence of anatoxin-a derivatives and use long-read metagenomics to assemble complete circular genomes of the strain. The main dihydro-anatoxin-a-producing strain in the Areuse is distinct from strains isolated in New Zealand, the USA, and Canada, but forms a monophyletic strain cluster with them with average nucleotide identity values close to the species threshold. Compared to the rest of the Microcoleus genus, the toxin-producing strains encode a 15 % smaller genome, lacking genes for the synthesis of some essential vitamins. Toxigenic mats harbor a distinct microbiome dominated by proteobacteria and bacteroidetes, which may support cyanobacterial growth by providing them with essential nutrients. We recommend that strains closely related to M. anatoxicus be monitored internationally in order to help predict and mitigate similar cyanotoxic events.
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Affiliation(s)
- Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | | | - Mathilda Fatton
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Pauline Udriet
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Isha Hashmi
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Danae Bregnard
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | | | - Eva di Francesco
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Naïma Mangia
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Sami Zhioua
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
| | - Daniel Hunkeler
- Centre for Hydrogeology and Geothermics, University of Neuchâtel, Switzerland
| | | | - Simon Sieber
- Department of Chemistry, University of Zürich, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, University of Neuchâtel, Switzerland
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2
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Nowruzi B, Porzani SJ. Toxic compounds produced by cyanobacteria belonging to several species of the order Nostocales: A review. J Appl Toxicol 2020; 41:510-548. [PMID: 33289164 DOI: 10.1002/jat.4088] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022]
Abstract
Cyanobacteria are well recognised as producers of a wide range of natural compounds that are in turn recognised as toxins that have potential and useful applications in the future as pharmaceutical agents. The order Nostocales, which is largely overlooked in this regard, has become increasingly recognised as a source of toxin producers including Anabaena, Nostoc, Hapalosiphon, Fischerella, Anabaenopsis, Aphanizomenon, Gloeotrichia, Cylindrospermopsis, Scytonema, Raphidiopsis, Cuspidothrix, Nodularia, Stigonema, Calothrix, Cylindrospermum and Desmonostoc species. The toxin compounds (i.e., microcystins, nodularin, anatoxins, ambiguines, fischerindoles and welwitindolinones) and metabolites are about to have a destructive effect on both inland and aquatic environment aspects. The present review gives an overview of the various toxins that are extracted by the order Nostocales. The current research suggests that these compounds that are produced by cyanobacterial species have promising future considerations as potentially harmful algae and as promising leads for drug discovery.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Samaneh Jafari Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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3
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Rubin GM, Ding Y. Recent advances in the biosynthesis of RiPPs from multicore-containing precursor peptides. J Ind Microbiol Biotechnol 2020; 47:659-674. [PMID: 32617877 PMCID: PMC7666021 DOI: 10.1007/s10295-020-02289-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) compose a large structurally and functionally diverse family of natural products. The biosynthesis system of RiPPs typically involves a precursor peptide comprising of a leader and core motif and nearby processing enzymes that recognize the leader and act on the core for producing modified peptides. Interest in RiPPs has increased substantially in recent years as improvements in genome mining techniques have dramatically improved access to these peptides and biochemical and engineering studies have supported their applications. A less understood, intriguing feature in the RiPPs biosynthesis is the precursor peptides of multiple RiPPs families produced by bacteria, fungi and plants carrying multiple core motifs, which we term "multicore". Herein, we present the prevalence of the multicore systems, their biosynthesis and engineering for applications.
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Affiliation(s)
- Garret M Rubin
- Department of Medicinal Chemistry, and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA.
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4
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Cegłowska M, Szubert K, Wieczerzak E, Kosakowska A, Mazur-Marzec H. Eighteen New Aeruginosamide Variants Produced by the Baltic Cyanobacterium Limnoraphis CCNP1324. Mar Drugs 2020; 18:E446. [PMID: 32867236 PMCID: PMC7551963 DOI: 10.3390/md18090446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Cyanobactins are a large family of ribosomally synthesized and post-translationally modified cyanopeptides (RiPPs). Thus far, over a hundred cyanobactins have been detected in different free-living and symbiotic cyanobacteria. The majority of these peptides have a cyclic structure. The occurrence of linear cyanobactins, aeruginosamides and virenamide, has been reported sporadically and in few cyanobacterial taxa. In the current work, the production of cyanobactins by Limnoraphis sp. CCNP1324, isolated from the brackish water Baltic Sea, has been studied for the first time. In the strain, eighteen new aeruginosamide (AEG) variants have been detected. These compounds are characterized by the presence of prenyl and thiazole groups. A common element of AEGs produced by Limnoraphis sp. CCNP1324 is the sequence of the three C-terminal residues containing proline, pyrrolidine and methyl ester of thiazolidyne-4-carboxylic acid (Pro-Pyr-TzlCOOMe) or thiazolidyne-4-carboxylic acid (Pro-Pyr-TzlCOOH). The aeruginosamides with methylhomotyrosine (MeHTyr1) and with the unidentified N-terminal amino acids showed strong cytotoxic activity against human breast cancer cells (T47D).
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Affiliation(s)
- Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81712 Sopot, Poland; (M.C.); (A.K.)
| | - Karolia Szubert
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland;
| | - Alicja Kosakowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81712 Sopot, Poland; (M.C.); (A.K.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
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5
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Chu L, Huang J, Muhammad M, Deng Z, Gao J. Genome mining as a biotechnological tool for the discovery of novel marine natural products. Crit Rev Biotechnol 2020; 40:571-589. [PMID: 32308042 DOI: 10.1080/07388551.2020.1751056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.
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Affiliation(s)
- Leixia Chu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinping Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mustafa Muhammad
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Racine M, Saleem A, Pick FR. Metabolome Variation between Strains of Microcystis aeruginosa by Untargeted Mass Spectrometry. Toxins (Basel) 2019; 11:E723. [PMID: 31835794 PMCID: PMC6950387 DOI: 10.3390/toxins11120723] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are notorious for their potential to produce hepatotoxic microcystins (MCs), but other bioactive compounds synthesized in the cells could be as toxic, and thus present interest for characterization. Ultra performance liquid chromatography and high-resolution accurate mass spectrometry (UPLC-QTOF-MS/MS) combined with untargeted analysis was used to compare the metabolomes of five different strains of the common bloom-forming cyanobacterium, Microcystis aeruginosa. Even in microcystin-producing strains, other classes of oligopeptides including cyanopeptolins, aeruginosins, and aerucyclamides, were often the more dominant compounds. The distinct and large variation between strains of the same widespread species highlights the need to characterize the metabolome of a larger number of cyanobacteria, especially as several metabolites other than microcystins can affect ecological and human health.
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Affiliation(s)
- Marianne Racine
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (A.S.); (F.R.P.)
- Current address: Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, ON L7S 1A1, Canada
| | - Ammar Saleem
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (A.S.); (F.R.P.)
| | - Frances R. Pick
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (A.S.); (F.R.P.)
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7
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Wang Z, Song G, Li Y, Yu G, Hou X, Gan Z, Li R. The diversity, origin, and evolutionary analysis of geosmin synthase gene in cyanobacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 689:789-796. [PMID: 31280161 DOI: 10.1016/j.scitotenv.2019.06.468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 06/09/2023]
Abstract
The sesquiterpene geosmin, mainly originating from cyanobacteria, is considered one of the problematic odor compounds responsible for unpleasant-tasting and -smelling water episodes in freshwater supplies. The biochemistry and genetics of geosmin synthesis in cyanobacteria is well-elucidated and the geosmin synthase gene (geo) has been cloned and characterized in recent years. However, understanding the diversity, origin, and evolution of geo has been hindered by the limited availability of geo sequences to date. On the basis of the cloned geo sequences from16 filamentous geosmin-producing cyanobacterial species, representing 11 genera in Nostocales and Oscillatoriales, the diversity and evolution of geo in cyanobacteria was systematically analyzed in this study. Homologous alignment revealed that geo is highly conserved among the examined cyanobacterial species, with DNA sequence identities >0.72. Phylogenetic reconstruction and codon bias analysis based on geo suggest that cyanobacterial geo form a monophyletic branch with a common origin and ancestor for cyanobacteria, actinomycetes, and myxobacteria. The global ratio of nonsynonymous/synonymous nucleotide substitutions (dN/dS) was 0.125, which is substantially <1 and indicates strong purifying selection in the evolution of cyanobacterial geo. To add to further interest, horizontal gene transfer of cyanobacterial geo in evolutionary history was confirmed by the discovery of an incongruent coevolutionary relationship between geo and housekeeping genes 16S rDNA and rpoC. The present study enhances the fundamental understanding of cyanobacterial geo in diversity and evolution, and sheds light on the development of molecular assays for detection and molecular ecology research of geosmin-producing cyanobacteria.
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Affiliation(s)
- Zhongjie Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Gaofei Song
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Yeguang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Gongliang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Xiaoyu Hou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zixuan Gan
- Wuhan Foreign Language School Meiga Academy, Wuhan 430200, PR China
| | - Renhui Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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8
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Gu W, Dong SH, Sarkar S, Nair SK, Schmidt EW. The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis. Methods Enzymol 2018; 604:113-163. [PMID: 29779651 DOI: 10.1016/bs.mie.2018.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyanobactin biosynthetic enzymes have exceptional versatility in the synthesis of natural and unnatural products. Cyanobactins are ribosomally synthesized and posttranslationally modified peptides synthesized by multistep pathways involving a broad suite of enzymes, including heterocyclases/cyclodehydratases, macrocyclases, proteases, prenyltransferases, methyltransferases, and others. Here, we describe the enzymology and structural biology of cyanobactin biosynthetic enzymes, aiming at the twin goals of understanding biochemical mechanisms and biosynthetic plasticity. We highlight how this common suite of enzymes may be utilized to generate a large array or structurally and chemically diverse compounds.
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Affiliation(s)
- Wenjia Gu
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Snigdha Sarkar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States.
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9
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Morita M, Schmidt EW. Parallel lives of symbionts and hosts: chemical mutualism in marine animals. Nat Prod Rep 2018; 35:357-378. [PMID: 29441375 PMCID: PMC6025756 DOI: 10.1039/c7np00053g] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 Symbiotic microbes interact with animals, often by producing natural products (specialized metabolites; secondary metabolites) that exert a biological role. A major goal is to determine which microbes produce biologically important compounds, a deceptively challenging task that often rests on correlative results, rather than hypothesis testing. Here, we examine the challenges and successes from the perspective of marine animal-bacterial mutualisms. These animals have historically provided a useful model because of their technical accessibility. By comparing biological systems, we suggest a common framework for establishing chemical interactions between animals and microbes.
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Affiliation(s)
- Maho Morita
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA 84112.
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10
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Lin Z, Torres JP, Tianero MD, Kwan JC, Schmidt EW. Origin of Chemical Diversity in Prochloron-Tunicate Symbiosis. Appl Environ Microbiol 2016; 82:3450-60. [PMID: 27037119 PMCID: PMC4959158 DOI: 10.1128/aem.00860-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Diversity-generating metabolism leads to the evolution of many different chemicals in living organisms. Here, by examining a marine symbiosis, we provide a precise evolutionary model of how nature generates a family of novel chemicals, the cyanobactins. We show that tunicates and their symbiotic Prochloron cyanobacteria share congruent phylogenies, indicating that Prochloron phylogeny is related to host phylogeny and not to external habitat or geography. We observe that Prochloron exchanges discrete functional genetic modules for cyanobactin secondary metabolite biosynthesis in an otherwise conserved genetic background. The module exchange leads to gain or loss of discrete chemical functional groups. Because the underlying enzymes exhibit broad substrate tolerance, discrete exchange of substrates and enzymes between Prochloron strains leads to the rapid generation of chemical novelty. These results have implications in choosing biochemical pathways and enzymes for engineered or combinatorial biosynthesis. IMPORTANCE While most biosynthetic pathways lead to one or a few products, a subset of pathways are diversity generating and are capable of producing thousands to millions of derivatives. This property is highly useful in biotechnology since it enables biochemical or synthetic biological methods to create desired chemicals. A fundamental question has been how nature itself creates this chemical diversity. Here, by examining the symbiosis between coral reef animals and bacteria, we describe the genetic basis of chemical variation with unprecedented precision. New compounds from the cyanobactin family are created by either varying the substrate or importing needed enzymatic functions from other organisms or via both mechanisms. This natural process matches successful laboratory strategies to engineer the biosynthesis of new chemicals and teaches a new strategy to direct biosynthesis.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USAUniversity of Tennessee and Oak Ridge National Laboratory
| | - Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USAUniversity of Tennessee and Oak Ridge National Laboratory
| | - M Diarey Tianero
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USAUniversity of Tennessee and Oak Ridge National Laboratory
| | - Jason C Kwan
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USAUniversity of Tennessee and Oak Ridge National Laboratory
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USAUniversity of Tennessee and Oak Ridge National Laboratory
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11
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Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 415] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
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Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
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12
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Kurmayer R, Deng L, Entfellner E. Role of toxic and bioactive secondary metabolites in colonization and bloom formation by filamentous cyanobacteria Planktothrix. HARMFUL ALGAE 2016; 54:69-86. [PMID: 27307781 PMCID: PMC4892429 DOI: 10.1016/j.hal.2016.01.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 01/15/2016] [Accepted: 01/15/2016] [Indexed: 05/22/2023]
Abstract
Bloom-forming cyanobacteria Planktothrix agardhii and P. rubescens are regularly involved in the occurrence of cyanotoxin in lakes and reservoirs. Besides microcystins (MCs), which inhibit eukaryotic protein phosphatase 1 and 2A, several families of bioactive peptides are produced, thereby resulting in impressive secondary metabolite structural diversity. This review will focus on the current knowledge of the phylogeny, morphology, and ecophysiological adaptations of Planktothrix as well as the toxins and bioactive peptides produced. The relatively well studied ecophysiological adaptations (buoyancy, shade tolerance, nutrient storage capacity) can partly explain the invasiveness of this group of cyanobacteria that bloom within short periods (weeks to months). The more recent elucidation of the genetic basis of toxin and bioactive peptide synthesis paved the way for investigating its regulation both in the laboratory using cell cultures as well as under field conditions. The high frequency of several toxin and bioactive peptide synthesis genes observed within P. agardhii and P. rubescens, but not for other Planktothrix species (e.g. P. pseudagardhii), suggests a potential functional linkage between bioactive peptide production and the colonization potential and possible dominance in habitats. It is hypothesized that, through toxin and bioactive peptide production, Planktothrix act as a niche constructor at the ecosystem scale, possibly resulting in an even higher ability to monopolize resources, positive feedback loops, and resilience under stable environmental conditions. Thus, refocusing harmful algal bloom management by integrating ecological and phylogenetic factors acting on toxin and bioactive peptide synthesis gene distribution and concentrations could increase the predictability of the risks originating from Planktothrix blooms.
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Affiliation(s)
- Rainer Kurmayer
- University of Innsbruck, Research Institute for Limnology, Mondseestrasse 9, 5310 Mondsee, Austria.
| | - Li Deng
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Elisabeth Entfellner
- University of Innsbruck, Research Institute for Limnology, Mondseestrasse 9, 5310 Mondsee, Austria
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13
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Sardar D, Tianero MD, Schmidt EW. Directing Biosynthesis: Practical Supply of Natural and Unnatural Cyanobactins. Methods Enzymol 2016; 575:1-20. [PMID: 27417922 DOI: 10.1016/bs.mie.2016.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The increasingly rapid accumulation of genomic information is revolutionizing natural products discovery. However, the translation of sequence data to chemical products remains a challenge. Here, we detail methods used to circumvent the supply problem of cyanobactin natural products, both by engineered synthesis in Escherichia coli and by using purified enzymes in vitro. Such methodologies exploit nature's strategies of combinatorial chemistry in the cyanobactin class of RiPP natural products. As a result, it is possible to synthesize a wide variety of natural and unnatural compounds.
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Affiliation(s)
- D Sardar
- University of Utah, Salt Lake City, UT, United States
| | - M D Tianero
- University of Utah, Salt Lake City, UT, United States
| | - E W Schmidt
- University of Utah, Salt Lake City, UT, United States.
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14
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Parajuli A, Kwak DH, Dalponte L, Leikoski N, Galica T, Umeobika U, Trembleau L, Bent A, Sivonen K, Wahlsten M, Wang H, Rizzi E, De Bellis G, Naismith J, Jaspars M, Liu X, Houssen W, Fewer DP. A Unique Tryptophan C-Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway. Angew Chem Int Ed Engl 2016; 55:3596-9. [PMID: 26846478 DOI: 10.1002/anie.201509920] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 11/07/2022]
Abstract
Cyanobactins are a rapidly growing family of linear and cyclic peptides produced by cyanobacteria. Kawaguchipeptins A and B, two macrocyclic undecapeptides reported earlier from Microcystis aeruginosa NIES-88, are shown to be products of the cyanobactin biosynthetic pathway. The 9 kb kawaguchipeptin (kgp) gene cluster was identified in a 5.26 Mb draft genome of Microcystis aeruginosa NIES-88. We verified that this gene cluster is responsible for the production of the kawaguchipeptins through heterologous expression of the kgp gene cluster in Escherichia coli. The KgpF prenyltransferase was overexpressed and was shown to prenylate C-3 of Trp residues in both linear and cyclic peptides in vitro. Our findings serve to further enhance the structural diversity of cyanobactins to include tryptophan-prenylated cyclic peptides.
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Affiliation(s)
- Anirudra Parajuli
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland
| | - Daniel H Kwak
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Luca Dalponte
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Niina Leikoski
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland
| | - Tomas Galica
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland.,Institute of Microbiology AS CR, v.v.i., Center ALGATECH, Třeboň, Czech Republic.,University of South Bohemia, Faculty of Science, Department of Ecosystem Biology, České Budějovice, Czech Republic
| | - Ugochukwu Umeobika
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
| | - Laurent Trembleau
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
| | - Andrew Bent
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland
| | - Matti Wahlsten
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland
| | - Hao Wang
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland
| | - Ermanno Rizzi
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), via F.lli Cervi 93, Segrate (MI), Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), via F.lli Cervi 93, Segrate (MI), Italy
| | - James Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
| | - Xinyu Liu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.
| | - Wael Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK. .,Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK. .,Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - David Peter Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, P.O.Box 56, Viikki Biocenter, Viikinkaari 9, 00014, University of Helsinki, Finland.
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15
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Parajuli A, Kwak DH, Dalponte L, Leikoski N, Galica T, Umeobika U, Trembleau L, Bent A, Sivonen K, Wahlsten M, Wang H, Rizzi E, De Bellis G, Naismith J, Jaspars M, Liu X, Houssen W, Fewer DP. A Unique Tryptophan C-Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anirudra Parajuli
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
| | - Daniel H. Kwak
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Luca Dalponte
- Marine Biodiscovery Centre; Department of Chemistry; University of Aberdeen; Meston Walk Aberdeen AB24 3UE UK
- Institute of Medical Sciences; University of Aberdeen; Aberdeen AB25 2ZD UK
| | - Niina Leikoski
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
| | - Tomas Galica
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
- Institute of Microbiology AS CR, v.v.i., Center ALGATECH; Třeboň Czech Republic
- University of South Bohemia; Faculty of Science; Department of Ecosystem Biology; České Budějovice Czech Republic
| | - Ugochukwu Umeobika
- Marine Biodiscovery Centre; Department of Chemistry; University of Aberdeen; Meston Walk Aberdeen AB24 3UE UK
| | - Laurent Trembleau
- Marine Biodiscovery Centre; Department of Chemistry; University of Aberdeen; Meston Walk Aberdeen AB24 3UE UK
| | - Andrew Bent
- Biomedical Sciences Research Complex; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
| | - Matti Wahlsten
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
| | - Hao Wang
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
| | - Ermanno Rizzi
- Institute for Biomedical Technologies (ITB); National Research Council (CNR); via F.lli Cervi 93 Segrate (MI) Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies (ITB); National Research Council (CNR); via F.lli Cervi 93 Segrate (MI) Italy
| | - James Naismith
- Biomedical Sciences Research Complex; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre; Department of Chemistry; University of Aberdeen; Meston Walk Aberdeen AB24 3UE UK
| | - Xinyu Liu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Wael Houssen
- Marine Biodiscovery Centre; Department of Chemistry; University of Aberdeen; Meston Walk Aberdeen AB24 3UE UK
- Institute of Medical Sciences; University of Aberdeen; Aberdeen AB25 2ZD UK
- Pharmacognosy Department; Faculty of Pharmacy; Mansoura University; Mansoura 35516 Egypt
| | - David Peter Fewer
- Microbiology and Biotechnology Division; Department of Food and Environmental Sciences; P.O.Box 56, Viikki Biocenter Viikinkaari 9 00014, University of Helsinki Finland
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16
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Otten TG, Paerl HW. Health Effects of Toxic Cyanobacteria in U.S. Drinking and Recreational Waters: Our Current Understanding and Proposed Direction. Curr Environ Health Rep 2016; 2:75-84. [PMID: 26231244 DOI: 10.1007/s40572-014-0041-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cyanobacterial-derived water quality impairment issues are a growing concern worldwide. In addition to their ecological impacts, these organisms are prolific producers of bioactive secondary metabolites, many of which are known human intoxicants. To date only a handful of these compounds have been thoroughly studied and their toxicological risks estimated. While there are currently no national guidelines in place to deal with this issue, it is increasingly likely that within the next several years guidelines will be implemented. The intent of this review is to survey all relevant literature pertaining to cyanobacterial harmful algal bloom secondary metabolites, to inform a discussion on how best to manage this global public health threat.
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Affiliation(s)
- Timothy G Otten
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA,
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17
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Martins J, Vasconcelos V. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge. Mar Drugs 2015; 13:6910-46. [PMID: 26580631 PMCID: PMC4663559 DOI: 10.3390/md13116910] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/22/2015] [Accepted: 10/30/2015] [Indexed: 11/28/2022] Open
Abstract
Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.
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Affiliation(s)
- Joana Martins
- Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal.
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal.
| | - Vitor Vasconcelos
- Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal.
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal.
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18
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Genetic Basis for Geosmin Production by the Water Bloom-Forming Cyanobacterium, Anabaena ucrainica. WATER 2014. [DOI: 10.3390/w7010175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Houssen WE, Bent AF, McEwan AR, Pieiller N, Tabudravu J, Koehnke J, Mann G, Adaba RI, Thomas L, Hawas UW, Liu H, Schwarz-Linek U, Smith MCM, Naismith JH, Jaspars M. An efficient method for the in vitro production of azol(in)e-based cyclic peptides. Angew Chem Int Ed Engl 2014; 53:14171-4. [PMID: 25331823 PMCID: PMC4282754 DOI: 10.1002/anie.201408082] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Indexed: 11/11/2022]
Abstract
Heterocycle-containing cyclic peptides are promising scaffolds for the pharmaceutical industry but their chemical synthesis is very challenging. A new universal method has been devised to prepare these compounds by using a set of engineered marine-derived enzymes and substrates obtained from a family of ribosomally produced and post-translationally modified peptides called the cyanobactins. The substrate precursor peptide is engineered to have a non-native protease cleavage site that can be rapidly cleaved. The other enzymes used are heterocyclases that convert Cys or Cys/Ser/Thr into their corresponding azolines. A macrocycle is formed using a macrocyclase enzyme, followed by oxidation of the azolines to azoles with a specific oxidase. The work is exemplified by the production of 17 macrocycles containing 6-9 residues representing 11 out of the 20 canonical amino acids.
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Affiliation(s)
- Wael E Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE (UK); Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD (UK); Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516 (Egypt)
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20
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An Efficient Method for the In Vitro Production of Azol(in)e-Based Cyclic Peptides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408082] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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21
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Agha R, Quesada A. Oligopeptides as biomarkers of cyanobacterial subpopulations. Toward an understanding of their biological role. Toxins (Basel) 2014; 6:1929-50. [PMID: 24960202 PMCID: PMC4073138 DOI: 10.3390/toxins6061929] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/09/2014] [Accepted: 06/16/2014] [Indexed: 11/25/2022] Open
Abstract
Cyanobacterial oligopeptides comprise a wide range of bioactive and/or toxic compounds. While current research is strongly focused on exploring new oligopeptide variants and their bioactive properties, the biological role of these compounds remains elusive. Oligopeptides production abilities show a remarkably patchy distribution among conspecific strains. This observation has prompted alternative approaches to unveil their adaptive value, based on the use of cellular oligopeptide compositions as biomarkers of intraspecific subpopulations or chemotypes in freshwater cyanobacteria. Studies addressing the diversity, distribution, and dynamics of chemotypes in natural systems have provided important insights into the structure and ecology of cyanobacterial populations and the adaptive value of oligopeptides. This review presents an overview of the fundamentals of this emerging approach and its most relevant findings, and discusses our current understanding of the role of oligopeptides in the ecology of cyanobacteria.
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Affiliation(s)
- Ramsy Agha
- Departamento de Biología, Universidad Autónoma de Madrid, C/Darwin, 2, Madrid 28049, Spain.
| | - Antonio Quesada
- Departamento de Biología, Universidad Autónoma de Madrid, C/Darwin, 2, Madrid 28049, Spain.
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22
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Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology. ACTA ACUST UNITED AC 2013; 20:636-47. [PMID: 23706630 DOI: 10.1016/j.chembiol.2013.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/28/2013] [Accepted: 04/16/2013] [Indexed: 12/24/2022]
Abstract
Most biologically active microbial natural products are known from strains that can be isolated and cultivated in the laboratory. However, the genomics era has revealed that cultured bacteria represent a mere fraction of total estimated bacterial biodiversity. With the development of community genomics, termed metagenomics, the uncultivated majority became accessible for functional analysis. Through metagenomic studies, novel biocatalysts and biosynthetic pathways are being discovered at a pace previously not possible using traditional molecular biology techniques. Additionally, the study of uncultivated bacteria has provided valuable insights into previously overlooked biocatalysts from cultured strains. This perspective highlights recent discoveries from metagenomics of uncultivated bacteria and discusses the impact of those findings on the field of natural products.
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23
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Martins J, Leão PN, Ramos V, Vasconcelos V. N-terminal protease gene phylogeny reveals the potential for novel cyanobactin diversity in cyanobacteria. Mar Drugs 2013; 11:4902-16. [PMID: 24351973 PMCID: PMC3877893 DOI: 10.3390/md11124902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 11/21/2013] [Accepted: 11/21/2013] [Indexed: 11/29/2022] Open
Abstract
Cyanobactins are a recently recognized group of ribosomal cyclic peptides produced by cyanobacteria, which have been studied because of their interesting biological activities. Here, we have used a PCR-based approach to detect the N-terminal protease (A) gene from cyanobactin synthetase gene clusters, in a set of diverse cyanobacteria from our culture collection (Laboratory of Ecotoxicology, Genomics and Evolution (LEGE) CC). Homologues of this gene were found in Microcystis and Rivularia strains, and for the first time in Cuspidothrix, Phormidium and Sphaerospermopsis strains. Phylogenetic relationships inferred from available A-gene sequences, including those obtained in this work, revealed two new groups of phylotypes, harboring Phormidium, Sphaerospermopsis and Rivularia LEGE isolates. Thus, this study shows that, using underexplored cyanobacterial strains, it is still possible to expand the known genetic diversity of genes involved in cyanobactin biosynthesis.
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Affiliation(s)
- Joana Martins
- Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal; E-Mails: (J.M.); (V.R.)
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal; E-Mail:
| | - Pedro N. Leão
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal; E-Mail:
| | - Vitor Ramos
- Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal; E-Mails: (J.M.); (V.R.)
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal; E-Mail:
| | - Vitor Vasconcelos
- Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal; E-Mails: (J.M.); (V.R.)
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +351-22-340-18-37; Fax: +351-22-339-06-08
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24
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Genome Mining Expands the Chemical Diversity of the Cyanobactin Family to Include Highly Modified Linear Peptides. ACTA ACUST UNITED AC 2013; 20:1033-43. [DOI: 10.1016/j.chembiol.2013.06.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/20/2013] [Accepted: 06/30/2013] [Indexed: 11/19/2022]
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25
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McIntosh JA, Lin Z, Tianero MDB, Schmidt EW. Aestuaramides, a natural library of cyanobactin cyclic peptides resulting from isoprene-derived Claisen rearrangements. ACS Chem Biol 2013; 8:877-83. [PMID: 23411099 DOI: 10.1021/cb300614c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report 12 cyanobactin cyclic peptides, the aestuaramides, from the cultivated cyanobacterium Lyngbya aestuarii. We show that aestuaramides are synthesized enzymatically as reverse O-prenylated tyrosine ethers that subsequently undergo a Claisen rearrangement to produce forward C-prenylated tyrosine. These results reveal that a nonenzymatic Claisen rearrangement dictates isoprene regiochemistry in a natural system. They also reveal one of the mechanisms that organisms use to generate structurally diverse compound libraries starting from simple ribosomal peptide pathways (RiPPs).
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Affiliation(s)
- John A. McIntosh
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Zhenjian Lin
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Ma. Diarey B. Tianero
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Eric W. Schmidt
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
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26
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Synergistic effect between colistin and bacteriocins in controlling Gram-negative pathogens and their potential to reduce antibiotic toxicity in mammalian epithelial cells. Antimicrob Agents Chemother 2013; 57:2719-25. [PMID: 23571533 DOI: 10.1128/aac.02328-12] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogens resistant to most conventional antibiotics are a harbinger of the need to discover novel antimicrobials and anti-infective agents and develop innovative strategies to combat them. The aim of this study was to assess the in vitro activity of colistin alone or in combination with two bacteriocins, nisin A and pediocin PA-1/AcH, against Salmonella choleraesuis ATCC 14028, Pseudomonas aeruginosa ATCC 27853, Yersinia enterocolitica ATCC 9610, and Escherichia coli ATCC 35150 (O157:H7). The strain most sensitive to colistin was enterohemorrhagic E. coli O157:H7, which was inhibited at a concentration of about 0.12 μg/ml. When nisin A (1.70 μg/ml) or pediocin PA-1/AcH (1.56 μg/ml) was combined with colistin, the concentrations required to inhibit E. coli O157:H7 were 0.01 and 0.03 μg/ml, respectively. The in vitro antigenotoxic effect of colistin was determined by using the comet assay method to measure the level of DNA damage in freshly isolated human peripheral blood leukocytes (PBLs) incubated with colistin for 1 h at 37°C. Changes in the tail extents of PBLs of about 69.29 ± 0.08 μm were observed at a final colistin concentration of about 550 ng/ml. Besides the synergistic effect, the combination of colistin (1 mg/ml) and nisin (2 mg/ml) permitted us to re-evaluate the toxic effect of colistin on Vero (monkey kidney epithelial) cells.
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27
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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28
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1472] [Impact Index Per Article: 133.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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29
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Ahmed MZ, De Barro PJ, Ren SX, Greeff JM, Qiu BL. Evidence for horizontal transmission of secondary endosymbionts in the Bemisia tabaci cryptic species complex. PLoS One 2013; 8:e53084. [PMID: 23308142 PMCID: PMC3538644 DOI: 10.1371/journal.pone.0053084] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 11/27/2012] [Indexed: 11/18/2022] Open
Abstract
Bemisia tabaci (Hemiptera: Aleyrodidae) is a globally distributed pest composed of at least 34 morphologically indistinguishable cryptic species. At least seven species of endosymbiont have been found infecting some or all members of the complex. The origin(s) of the associations between specific endosymbionts and their whitefly hosts is unknown. Infection is normally vertical, but horizontal transmission does occur and is one way for new infections to be introduced into individuals. The relationships between the different members of the cryptic species complex and the endosymbionts have not been well explored. In this study, the phylogenies of different cryptic species of the host with those of their endosymbionts were compared. Of particular interest was whether there was evidence for both coevolution and horizontal transmission. Congruence was observed for the primary endosymbiont, Portiera aleyrodidarum, and partial incongruence in the case of two secondary endosymbionts, Arsenophonus and Cardinium and incongruence for a third, Wolbachia. The patterns observed for the primary endosymbiont supported cospeciation with the host while the patterns for the secondary endosymbionts, and especially Wolbachia showed evidence of host shifts and extinctions through horizontal transmission rather than cospeciation. Of particular note is the observation of several very recent host shift events in China between exotic invader and indigenous members of the complex. These shifts were from indigenous members of the complex to the invader as well as from the invader to indigenous relatives.
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Affiliation(s)
- Muhammad Z. Ahmed
- Department of Entomology, South China Agricultural University, Guangzhou, People's Republic of China
- Department of Genetics, University of Pretoria, Pretoria , South Africa
| | | | - Shun-Xiang Ren
- Department of Entomology, South China Agricultural University, Guangzhou, People's Republic of China
| | - Jaco M. Greeff
- Department of Genetics, University of Pretoria, Pretoria , South Africa
| | - Bao-Li Qiu
- Department of Entomology, South China Agricultural University, Guangzhou, People's Republic of China
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Houssen WE, Koehnke J, Zollman D, Vendome J, Raab A, Smith MCM, Naismith JH, Jaspars M. The Discovery of New Cyanobactins fromCyanothecePCC 7425 Defines a New Signature for Processing of Patellamides. Chembiochem 2012; 13:2683-9. [DOI: 10.1002/cbic.201200661] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Indexed: 11/07/2022]
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Wang H, Sivonen K, Rouhiainen L, Fewer DP, Lyra C, Rantala-Ylinen A, Vestola J, Jokela J, Rantasärkkä K, Li Z, Liu B. Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90. BMC Genomics 2012; 13:613. [PMID: 23148582 PMCID: PMC3542288 DOI: 10.1186/1471-2164-13-613] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 11/05/2012] [Indexed: 11/15/2022] Open
Abstract
Background Cyanobacteria can form massive toxic blooms in fresh and brackish bodies of water and are frequently responsible for the poisoning of animals and pose a health risk for humans. Anabaena is a genus of filamentous diazotrophic cyanobacteria commonly implicated as a toxin producer in blooms in aquatic ecosystems throughout the world. The biology of bloom-forming cyanobacteria is poorly understood at the genome level. Results Here, we report the complete sequence and comprehensive annotation of the bloom-forming Anabaena sp. strain 90 genome. It comprises two circular chromosomes and three plasmids with a total size of 5.3 Mb, encoding a total of 4,738 genes. The genome is replete with mobile genetic elements. Detailed manual annotation demonstrated that almost 5% of the gene repertoire consists of pseudogenes. A further 5% of the genome is dedicated to the synthesis of small peptides that are the products of both ribosomal and nonribosomal biosynthetic pathways. Inactivation of the hassallidin (an antifungal cyclic peptide) biosynthetic gene cluster through a deletion event and a natural mutation of the buoyancy-permitting gvpG gas vesicle gene were documented. The genome contains a large number of genes encoding restriction-modification systems. Two novel excision elements were found in the nifH gene that is required for nitrogen fixation. Conclusions Genome analysis demonstrated that this strain invests heavily in the production of bioactive compounds and restriction-modification systems. This well-annotated genome provides a platform for future studies on the ecology and biology of these important bloom-forming cyanobacteria.
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Affiliation(s)
- Hao Wang
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, FIN-00014, Finland
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Pérez-Gómez B, Mendoza-Hernández G, Cabellos-Avelar T, Leyva-Castillo LE, Gutiérrez-Cirlos EB, Gómez-Lojero C. A proteomic approach to the analysis of the components of the phycobilisomes from two cyanobacteria with complementary chromatic adaptation: Fremyella diplosiphon UTEX B590 and Tolypothrix PCC 7601. PHOTOSYNTHESIS RESEARCH 2012; 114:43-58. [PMID: 22965313 DOI: 10.1007/s11120-012-9779-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 08/29/2012] [Indexed: 06/01/2023]
Abstract
Tolypothrix PCC 7601 and Fremyella diplosiphon UTEX B590 can produce two alternative phycobilisome (PBS) rods. PE-PBSs with one phycocyanin (PC) disk and multiple phycoerythrin (PE) disks are found in cells grown under green light (GL). PC-PBSs with only PC disks are obtained from cells grown under red light (RL). In this manuscript, we show the localization of the linker proteins and ferredoxin-NADP(+) oxidoreductase (FNR) in the PC-PBS and of PE-PBS rods using visible spectroscopy and mass spectrometry. PE-PBSs with different [PE]/[PC] ratios and PC-PBSs with different [PC]/[AP] (AP, allophycocyanin) ratios were isolated. CpeC was the primary rod linker protein found in the PBSs with a [PE]/[PC] ratio of 1.1, which indicates that this is the rod linker at the interphase PC-PE. CpeC and CpeD were identified in the PBSs with a [PE]/[PC] ratio of 1.6, which indicates that CpcD is the linker between the first and the second PE hexamers. Finally, CpeC, CpeD, and CpeE were found in the PBSs with a [PE]/[PC] ratio of 2.9, indicating the position of CpeE between the second and third PE moieties. CpcI2 was identified in the two PC-PBSs obtained from cells grown under RL, which indicates that CpcI2 is the linker between the first and second PC hexamers. CpcH2 was identified only in the PC-PBSs from Tolypothrix with a high [PC]/[AP] ratio of 1.92, which indicates that CpcH2 is the linker between the second and third PC hexamers. The PC-PBSs contained the rod cap protein L(R)(10) (CpcD), but this protein was absent in the PE-PBSs. PE-PBSs (lacking L(R)(10)) incorporated exogenous rFNR in a stoichiometry of up to five FNRs per PBS. A maximum of two FNRs per PBS were found in PC-PBSs (with L(R)(10)). These observations support the hypothesis that FNR binds at the distal ends of the PBS rods in the vacant site of CpcD L(R)(10). Finally, the molecular mass of the core membrane linker (L(CM)) was determined to be 102 kDa from a mass spectrometry analysis.
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Affiliation(s)
- Bertha Pérez-Gómez
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados-IPN, Apartado Postal 14-740, 07000 Mexico, DF, Mexico
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Leikoski N, Fewer DP, Jokela J, Alakoski P, Wahlsten M, Sivonen K. Analysis of an inactive cyanobactin biosynthetic gene cluster leads to discovery of new natural products from strains of the genus Microcystis. PLoS One 2012; 7:e43002. [PMID: 22952627 PMCID: PMC3428304 DOI: 10.1371/journal.pone.0043002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 07/16/2012] [Indexed: 11/26/2022] Open
Abstract
Cyanobactins are cyclic peptides assembled through the cleavage and modification of short precursor proteins. An inactive cyanobactin gene cluster has been described from the genome Microcystis aeruginosa NIES843. Here we report the discovery of active counterparts in strains of the genus Microcystis guided by this silent cyanobactin gene cluster. The end products of the gene clusters were structurally diverse cyclic peptides, which we named piricyclamides. Some of the piricyclamides consisted solely of proteinogenic amino acids while others contained disulfide bridges and some were prenylated or geranylated. The piricyclamide gene clusters encoded between 1 and 4 precursor genes. They encoded highly diverse core peptides ranging in length from 7–17 amino acids with just a single conserved amino acid. Heterologous expression of the pir gene cluster from Microcystis aeruginosa PCC7005 in Escherichia coli confirmed that this gene cluster is responsible for the biosynthesis of piricyclamides. Chemical analysis demonstrated that Microcystis strains could produce an array of piricyclamides some of which are geranylated or prenylated. The genetic diversity of piricyclamides in a bloom sample was explored and 19 different piricyclamide precursor genes were found. This study provides evidence for a stunning array of piricyclamides in Microcystis, a worldwide occurring bloom forming cyanobacteria.
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Affiliation(s)
- Niina Leikoski
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - David P. Fewer
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jouni Jokela
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pirita Alakoski
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Matti Wahlsten
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kaarina Sivonen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
- * E-mail:
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Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J. Origin and variation of tunicate secondary metabolites. JOURNAL OF NATURAL PRODUCTS 2012; 75:295-304. [PMID: 22233390 PMCID: PMC3288725 DOI: 10.1021/np200665k] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ascidians (tunicates) are rich sources of structurally elegant, pharmaceutically potent secondary metabolites and, more recently, potential biofuels. It has been demonstrated that some of these compounds are made by symbiotic bacteria and not by the animals themselves, and for a few other compounds evidence exists supporting a symbiotic origin. In didemnid ascidians, compounds are highly variable even in apparently identical animals. Recently, we have explained this variation at the genomic and metagenomic levels and have applied the basic scientific findings to drug discovery and development. This review discusses what is currently known about the origin and variation of symbiotically derived metabolites in ascidians, focusing on the family Didemnidae, where most research has occurred. Applications of our basic studies are also described.
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Affiliation(s)
- Eric W Schmidt
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, USA.
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Abstract
Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology. In the case of natural product research, phylogenetic relationships are proving to be highly informative in terms of delineating the architecture and function of the genes involved in secondary metabolite biosynthesis. Polyketide synthases and nonribosomal peptide synthetases provide model examples in which individual domain phylogenies display different predictive capacities, resolving features ranging from substrate specificity to structural motifs associated with the final metabolic product. This chapter provides examples in which phylogeny has proven effective in terms of predicting functional or structural aspects of secondary metabolism. The basics of how to build a reliable phylogenetic tree are explained along with information about programs and tools that can be used for this purpose. Furthermore, it introduces the Natural Product Domain Seeker, a recently developed Web tool that employs phylogenetic logic to classify ketosynthase and condensation domains based on established enzyme architecture and biochemical function.
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Affiliation(s)
- Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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36
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Zapomělová E, Hrouzek P, Řezanka T, Jezberová J, Řeháková K, Hisem D, Komárková J. POLYPHASIC CHARACTERIZATION OF DOLICHOSPERMUM SPP. AND SPHAEROSPERMOPSIS SPP. (NOSTOCALES, CYANOBACTERIA): MORPHOLOGY, 16S rRNA GENE SEQUENCES AND FATTY ACID AND SECONDARY METABOLITE PROFILES(1). JOURNAL OF PHYCOLOGY 2011; 47:1152-1163. [PMID: 27020196 DOI: 10.1111/j.1529-8817.2011.01034.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The genera Dolichospermum (Ralfs ex Bornet et Flahault) Wacklin, L. Hoffm. et Komárek and Sphaerospermopsis Zapomělová, Jezberová, Hrouzek, Hisem, K. Řeháková et Komárk.-Legn. represent a highly diversified group of planktonic cyanobacteria that have been recently separated from the traditional genus Anabaena Bory ex Bornet et Flahault. In this study, morphological diversity, phylogeny of the 16S rRNA gene, production of fatty acids, and secondary metabolite profiles were evaluated in 33 strains of 14 morphospecies isolated from the Czech Republic. Clustering of the strains based on 16S rRNA gene sequences corresponded to wider groups of species in terms of morphology. The overall secondary metabolite and fatty acid profiles, however, were not correlated to each other and neither were they correlated to the 16S rRNA phylogeny nor the morphology of the strains. Nevertheless, a minor part of the detected secondary metabolites (19% of all compounds) was present only in close relatives and can be thus considered as autapomorphic features.
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Affiliation(s)
- Eliška Zapomělová
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Pavel Hrouzek
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Tomáš Řezanka
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Jitka Jezberová
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Klára Řeháková
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Daniel Hisem
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Jaroslava Komárková
- Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic Institute of Physical Biology, Zámek 136, CZ-37333 Nové Hrady, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech RepublicInstitute of Microbiology, AS CR, Vídeňská 1083, CZ-14220 Prague, Czech RepublicBiology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic Institute of Microbiology, AS CR, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-379 81 Třeboň, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-37005 České Budějovice, Czech Republic Biology Centre of AS CR, Institute of Hydrobiology, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic Institute of Botany, AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
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Linking chemistry and genetics in the growing cyanobactin natural products family. ACTA ACUST UNITED AC 2011; 18:508-19. [PMID: 21513887 DOI: 10.1016/j.chembiol.2011.01.019] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/31/2010] [Accepted: 01/10/2011] [Indexed: 11/22/2022]
Abstract
Ribosomal peptide natural products are ubiquitous, yet relatively few tools exist to predict structures and clone new pathways. Cyanobactin ribosomal peptides are found in ~30% of all cyanobacteria, but the connection between gene sequence and structure was not defined, limiting the rapid identification of new compounds and pathways. Here, we report discovery of four orphan cyanobactin gene clusters by genome mining and an additional pathway by targeted cloning, which represented a tyrosine O-prenylating biosynthetic pathway. Genome mining enabled discovery of five cyanobactins, including peptide natural products from Spirulina supplements. A phylogenetic model defined four cyanobactin genotypes, which explain the synthesis of multiple cyanobactin structural classes and help direct pathway cloning and structure prediction efforts. These strategies were applied to DNA isolated from a mixed cyanobacterial bloom containing cyanobactins.
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McIntosh JA, Donia MS, Nair SK, Schmidt EW. Enzymatic basis of ribosomal peptide prenylation in cyanobacteria. J Am Chem Soc 2011; 133:13698-705. [PMID: 21766822 DOI: 10.1021/ja205458h] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic basis of ribosomal peptide natural product prenylation has not been reported. Here, we characterize a prenyltransferase, LynF, from the TruF enzyme family. LynF is the first characterized representative of the TruF protein family, which is responsible for both reverse- and forward-O-prenylation of tyrosine, serine, and threonine in cyclic peptides known as cyanobactins. We show that LynF reverse O-prenylates tyrosine in macrocyclic peptides. Based upon these results, we propose that the TruF family prenylates mature cyclic peptides, from which the leader sequence and other enzyme recognition elements have been excised. This differs from the common model of ribosomal peptide biosynthesis, in which a leader sequence is required to direct post-translational modifications. In addition, we find that reverse O-prenylated tyrosine derivatives undergo a facile Claisen rearrangement at 'physiological' temperature in aqueous buffers, leading to forward C-prenylated products. Although the Claisen rearrangement route to natural products has been chemically anticipated for at least 40 years, it has not been demonstrated as a route to prenylated natural products. Here, we show that the Claisen rearrangement drives phenolic C-prenylation in at least one case, suggesting that this route should be reconsidered as a mechanism for the biosynthesis of prenylated phenolic compounds.
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Affiliation(s)
- John A McIntosh
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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Granaticins and their biosynthetic gene cluster from Streptomyces vietnamensis: evidence of horizontal gene transfer. Antonie van Leeuwenhoek 2011; 100:607-17. [DOI: 10.1007/s10482-011-9615-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
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40
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Melby JO, Nard NJ, Mitchell DA. Thiazole/oxazole-modified microcins: complex natural products from ribosomal templates. Curr Opin Chem Biol 2011; 15:369-78. [PMID: 21429787 PMCID: PMC3947797 DOI: 10.1016/j.cbpa.2011.02.027] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/10/2011] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
Abstract
With billions of years of evolution under its belt, Nature has been expanding and optimizing its biosynthetic capabilities. Chemically complex secondary metabolites continue to challenge and inspire today's most talented synthetic chemists. A brief glance at these natural products, especially the substantial structural variation within a class of compounds, clearly demonstrates that Nature has long played the role of medicinal chemist. The recent explosion in genome sequencing has expanded our appreciation of natural product space and the vastness of uncharted territory that remains. One small corner of natural product chemical space is occupied by the recently dubbed thiazole/oxazole-modified microcins (TOMMs), which are ribosomally produced peptides with posttranslationally installed heterocycles derived from cysteine, serine and threonine residues. As with other classes of natural products, the genetic capacity to synthesize TOMMs has been widely disseminated among bacteria. Over the evolutionary timescale, Nature has tested countless random mutations and selected for gain of function in TOMM biosynthetic gene clusters, yielding several privileged molecular scaffolds. Today, this burgeoning class of natural products encompasses a structurally and functionally diverse set of molecules (i.e. microcin B17, cyanobactins, and thiopeptides). TOMMs presumably provide their producers with an ecological advantage. This advantage can include chemical weapons wielded in the battle for nutrients, disease-promoting virulence factors, or compounds presumably beneficial for symbiosis. Despite this plethora of functions, many TOMMs await experimental interrogation. This review will focus on the biosynthesis and natural combinatorial diversity of the TOMM family.
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Affiliation(s)
- Joel O Melby
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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41
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Velásquez JE, van der Donk W. Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol 2011; 15:11-21. [PMID: 21095156 PMCID: PMC3090663 DOI: 10.1016/j.cbpa.2010.10.027] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/20/2010] [Accepted: 10/25/2010] [Indexed: 11/20/2022]
Abstract
In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides. In this review, we describe the strategies used for the identification of these ribosomally synthesized and posttranslationally modified peptides (RiPPs) and the structures of newly identified compounds. The increasing number of chemical entities and their remarkable structural and functional diversity may lead to novel pharmaceutical applications.
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Affiliation(s)
- Juan E. Velásquez
- Department of Chemistry, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
| | - Wilfred van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
- Howard Hughes Medical Institute; University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
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Jones AC, Monroe EA, Eisman EB, Gerwick L, Sherman DH, Gerwick WH. The unique mechanistic transformations involved in the biosynthesis of modular natural products from marine cyanobacteria. Nat Prod Rep 2010; 27:1048-65. [PMID: 20442916 DOI: 10.1039/c000535e] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cyanobacteria are abundant producers of natural products well recognized for their bioactivity and utility in drug discovery and biotechnology applications. In the last decade, characterization of several modular gene clusters that code for the biosynthesis of these compounds has revealed a number of unusual enzymatic reactions. In this article, we review several mechanistic transformations identified in marine cyanobacterial biosynthetic pathways, with an emphasis on modular polyketide synthase(PKS)/non-ribosomal peptide synthetase (NRPS) gene clusters. In selected instances, we also make comparisons between cyanobacterial gene clusters derived from marine and freshwater strains. We then provide an overview of recent developments in cyanobacterial natural products biosynthesis made available through genome sequencing and new advances in bioinformatics and genetics.
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Affiliation(s)
- Adam C Jones
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA 92093, USA
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Exploiting the natural diversity of microviridin gene clusters for discovery of novel tricyclic depsipeptides. Appl Environ Microbiol 2010; 76:3568-74. [PMID: 20363789 DOI: 10.1128/aem.02858-09] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Microviridins are ribosomally synthesized tricyclic depsipeptides produced by different genera of cyanobacteria. The prevalence of the microviridin gene clusters and the natural diversity of microviridin precursor sequences are currently unknown. Screening of laboratory strains and field samples of the bloom-forming freshwater cyanobacterium Microcystis via PCR revealed global occurrence of the microviridin pathway and an unexpected natural variety. We could detect 15 new variants of the precursor gene mdnA encoding microviridin backbones that differ in up to 4 amino acid positions from known isoforms of the peptide. The survey not only provides insights into the versatility of the biosynthetic enzymes in a closely related group of cyanobacteria, but also facilitates the discovery and characterization of cryptic microviridin variants. This is demonstrated for microviridin L in Microcystis aeruginosa strain NIES843 and heterologously produced variants.
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Sivonen K, Leikoski N, Fewer DP, Jokela J. Cyanobactins-ribosomal cyclic peptides produced by cyanobacteria. Appl Microbiol Biotechnol 2010; 86:1213-25. [PMID: 20195859 PMCID: PMC2854353 DOI: 10.1007/s00253-010-2482-x] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 01/29/2010] [Accepted: 01/29/2010] [Indexed: 11/30/2022]
Abstract
Cyanobactins are small cyclic peptides that are produced by a diverse selection of cyanobacteria living in symbioses as well as terrestrial, marine, or freshwater environments. They include compounds with antimalarial, antitumor, and multidrug reversing activities and potential as pharmaceutical leads. Cyanobactins are produced through the proteolytic cleavage and cyclization of precursor peptides coupled with further posttranslational modifications such as heterocyclization, oxidation, or prenylation of amino acids. Cyanobactin gene clusters encode two proteases which cleave and cyclisize the precursor peptide as well as proteins participating in posttranslational modifications. The bioinformatic mining of cyanobacterial genomes has led to the discovery of novel cyanobactins. Heterologous expression of these gene clusters provided insights into the role of the genes participating in the biosynthesis of cyanobactins and facilitated the rational design of novel peptides. Enzymes participating in the biosynthesis of cyanobactins may prove useful as catalysts for producing novel cyclic peptides in the future. The recent discovery of the cyanobactin biosynthetic pathway in cyanobacteria extends our knowledge of their potential as producers of interesting metabolites.
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Affiliation(s)
- Kaarina Sivonen
- Department of Food and Environmental Sciences, Division of Microbiology, Viikki Biocenter, University of Helsinki, Helsinki, P.O. Box 56, Viikinkaari 9, FIN-00014, Finland.
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Abstract
Cyanobactins are small, cyclic peptides recently found in cyanobacteria. They are formed through proteolytic cleavage and posttranslational modification of short precursor proteins and exhibit antitumor, cytotoxic, or multi-drug-reversing activities. Using genome project data, bioinformatics, stable isotope labeling, and mass spectrometry, we discovered novel cyclic peptides, anacyclamides, in 27 Anabaena strains. The lengths of the anacylamides varied greatly, from 7 to 20 amino acids. Pronounced sequence variation was also detected, and only one amino acid, proline, was present in all anacyclamides. The anacyclamides identified included unmodified proteinogenic or prenylated amino acids. We identified an 11-kb gene cluster in the genome of Anabaena sp. 90, and heterologous expression in Escherichia coli confirmed that this cluster was responsible for anacyclamide production. The discovery of anacyclamides greatly increases the structural diversity of cyanobactins.
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Abstract
Natural products researchers are increasingly employing evolutionary analyses of genes and gene products that rely on phylogenetic trees. The field of phylogenetic inference and of evolutionary analyses based on phylogenies is growing at an amazing rate, making it difficult to keep up with the latest methodologies. Here, we summarize phylogenetic applications in natural products research, and review methods and software useful for carrying out analyses inferring or using phylogenetic trees. We include an updated overview of available alignment methods and programs, as well as a selection of some useful phylogenetic analysis tools. This review covers primarily the period 2000-2009 for applications of phylogenetic methods in natural product research, and 1990-2009 for phylogenetic methods, with some references going back to the 1960s.
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Affiliation(s)
- Imke Schmitt
- Department of Plant Biology and Bell Museum of Natural History, University of Minnesota, 250 Biological Sciences Center, 1445 Gortner Ave., St. Paul, MN 55108, USA.
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