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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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2
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Bownik A, Pawlik-Skowrońska B, Wlodkowic D, Mieczan T. Interactive effects of cyanobacterial metabolites aeruginosin-98B, anabaenopeptin-B and cylindrospermopsin on physiological parameters and novel in vivo fluorescent indicators in Chironomus aprilinus larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169846. [PMID: 38185144 DOI: 10.1016/j.scitotenv.2023.169846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
We aimed to determine the effects of single cyanobacterial metabolites aeruginosin-B (AER-B), anabaenopeptin-B (ANA-B), cylindrospermopsin (CYL), their binary and ternary mixtures on biomarkers of Chironomus aprilinus larvae: oxygen consumption, fat body structure and two novel fluorescent indicators: imaging of nuclei in cells of body integument, and the catecholamine level. The obtained results showed that oxygen consumption was inhibited by single tested cyanobacterial metabolites except for ANA-B at the lowest concentration (250 μg/L). Although the mixtures of the metabolites inhibited oxygen consumption with antagonistic interactions between the components stimulation was noted in the group exposed to the lowest concentrations of AER-B + CYL (125 μg/L + 125 μg/L, respectively) and the ternary mixture of AER-B + ANA-B + CYL (83.3 μg/L + 83.3 μg/L + 83.3 μg/L, respectively). In vivo fluorescent staining with Hoechst 34580 showed that single AER-B had lower cytotoxic potential on body integument cells than ANA-B and CYL and most binary mixtures except for AER-B + CYL induced synergistic toxicity. Catecholamine level was decreased in animals exposed to single metabolites, their binary and ternary mixtures; however, the interactions between the components in the ternary mixture were antagonistic. Fat body was found to be disrupted in the larvae exposed to single metabolites and their combinations. Antagonistic toxic interactions between the oligopeptide components were found in most binary and the ternary mixtures; however, synergistic effect was noted in the binary mixture of AER-B + CYL. The results suggest that in natural conditions Chironomus larvae and possibly other benthic invertebrates may be affected by cyanobacterial metabolites, however various components and in mixtures and their concentrations may determine varied physiological effects and diverse interactions.
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Affiliation(s)
- Adam Bownik
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262 Lublin, Poland.
| | - Barbara Pawlik-Skowrońska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262 Lublin, Poland
| | - Donald Wlodkowic
- The Neurotox Lab, School of Science, RMIT University, Plenty Road, P.O. Box 71, Bundoora, VIC 3083, Australia
| | - Tomasz Mieczan
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262 Lublin, Poland
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3
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Entfellner E, Baumann KBL, Edwards C, Kurmayer R. High Structural Diversity of Aeruginosins in Bloom-Forming Cyanobacteria of the Genus Planktothrix as a Consequence of Multiple Recombination Events. Mar Drugs 2023; 21:638. [PMID: 38132959 PMCID: PMC10744761 DOI: 10.3390/md21120638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Many compounds produced by cyanobacteria act as serine protease inhibitors, such as the tetrapeptides aeruginosins (Aer), which are found widely distributed. The structural diversity of Aer is intriguingly high. However, the genetic basis of this remains elusive. In this study, we explored the genetic basis of Aer synthesis among the filamentous cyanobacteria Planktothrix spp. In total, 124 strains, isolated from diverse freshwater waterbodies, have been compared regarding variability within Aer biosynthesis genes and the consequences for structural diversity. The high structural variability could be explained by various recombination processes affecting Aer synthesis, above all, the acquisition of accessory enzymes involved in post synthesis modification of the Aer peptide (e.g., halogenases, glycosyltransferases, sulfotransferases) as well as a large-range recombination of Aer biosynthesis genes, probably transferred from the bloom-forming cyanobacterium Microcystis. The Aer structural composition differed between evolutionary Planktothrix lineages, adapted to either shallow or deep waterbodies of the temperate climatic zone. Thus, for the first time among bloom-forming cyanobacteria, chemical diversification of a peptide family related to eco-evolutionary diversification has been described. It is concluded that various Aer peptides resulting from the recombination event act in chemical defense, possibly as a replacement for microcystins.
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Affiliation(s)
- Elisabeth Entfellner
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (E.E.); (K.B.L.B.)
| | - Kathrin B. L. Baumann
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (E.E.); (K.B.L.B.)
| | - Christine Edwards
- CyanoSol Research Group, Pharmacy & Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK;
| | - Rainer Kurmayer
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (E.E.); (K.B.L.B.)
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4
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Pawlik-Skowrońska B, Bownik A, Pogorzelec M, Kulczycka J, Sumińska A. First report on adverse effects of cyanobacterial anabaenopeptins, aeruginosins, microginin and their mixtures with microcystin and cylindrospermopsin on aquatic plant physiology: An experimental approach. Toxicon 2023; 236:107333. [PMID: 37951248 DOI: 10.1016/j.toxicon.2023.107333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/12/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023]
Abstract
Cyanobacteria produce a variety of oligopeptides beyond microcystins and other metabolites. Their biological activities are not fully recognized especially to aquatic plants. Acute toxicity tests on Spirodela polyrhiza and Lemna minor exposed to a range of concentrations of cyanobacterial metabolites: anabaenopeptins (ANA-A, ANA-B), aeruginosins 98 (Aer-A, Aer-B), microginin-FR1 (MG-FR1), microcystin-LR (MC-LR) and cylindrospermopsin (Cyl) were carried out to compare their influence on plant physiology. Effects of their binary mixtures were determined by isobole approach and calculation of the combination index (CI) that indicates a type of metabolites' interaction. Cyclic oligopeptides microcystin-LR and anabaenopeptin-A revealed the strongest inhibition of S. polyrhiza growth while other metabolites appeared less toxic. Oxygen evolution was inhibited by Cyl, MC-LR, ANA-A, ANA-B, while both variants of aeruginosins and MG-FR1 did not affect this process. Photosynthetic pigments' contents decreased in S. polyrhiza exposed to ANA-A and Cyl, while MC-LR and Aer-A caused their slight increase. 96 h-EC50 values showed that the growth of L. minor was more sensitive to MC-LR, ANA-A, MG-FR1 and Cyl than the growth of S. polyrhiza. In S. polyrhiza synergistic effects of all the binary mixtures of peptides with MC-LR on oxygen evolution were observed, while antagonistic one on the growth of S. polyrhiza exposed to the mixtures with aeruginosins and ANA-A. The mixtures of MC-LR and MG-FR1 with cylindrospermopsin revealed synergistic effects on the growth but antagonistic one to the O2 evolution. Quadruple mixtures (ANA-A + MC-LR + MG-FR1+Cyl) did not reveal any inhibitive effect on the plant growth and very slight on the oxygen evolution, irrespectively of their total concentrations. Various effects caused by ANA-A and ANA-B suggest the importance of molecule structures of metabolites for toxicity. Composition of the mixtures of cyanobacterial metabolites was essential for the observed effects.
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Affiliation(s)
- Barbara Pawlik-Skowrońska
- Department of Hydrobiology and Protection of Ecosystems, Faculty of Environmental Biology, University of Life Sciences in Lublin, Dobrzanskiego 37, 20-262, Lublin, Poland.
| | - Adam Bownik
- Department of Hydrobiology and Protection of Ecosystems, Faculty of Environmental Biology, University of Life Sciences in Lublin, Dobrzanskiego 37, 20-262, Lublin, Poland
| | - Magdalena Pogorzelec
- Department of Hydrobiology and Protection of Ecosystems, Faculty of Environmental Biology, University of Life Sciences in Lublin, Dobrzanskiego 37, 20-262, Lublin, Poland
| | - Justyna Kulczycka
- Department of Hydrobiology and Protection of Ecosystems, Faculty of Environmental Biology, University of Life Sciences in Lublin, Dobrzanskiego 37, 20-262, Lublin, Poland
| | - Aleksandra Sumińska
- Department of Hydrobiology and Protection of Ecosystems, Faculty of Environmental Biology, University of Life Sciences in Lublin, Dobrzanskiego 37, 20-262, Lublin, Poland
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5
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D'Agostino PM. Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria. Nat Prod Rep 2023; 40:1701-1717. [PMID: 37233731 DOI: 10.1039/d3np00011g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Covering: up to 2023Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.
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Affiliation(s)
- Paul M D'Agostino
- Technical University of Dresden, Chair of Technical Biochemistry, Bergstraβe 66, 01069 Dresden, Germany.
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6
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Yancey CE, Kiledal EA, Chaganti SR, Denef VJ, Errera RM, Evans JT, Hart LN, Isailovic D, James WS, Kharbush JJ, Kimbrel JA, Li W, Mayali X, Nitschky H, Polik CA, Powers MA, Premathilaka SH, Rappuhn NA, Reitz LA, Rivera SR, Zwiers CC, Dick GJ. The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. HARMFUL ALGAE 2023; 126:102440. [PMID: 37290887 DOI: 10.1016/j.hal.2023.102440] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.
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Affiliation(s)
- Colleen E Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - E Anders Kiledal
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Vincent J Denef
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Reagan M Errera
- National Oceanic and Atmospheric Administration (NOAA), Great Lakes Environmental Research Laboratory (GLERL), 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Jacob T Evans
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Lauren N Hart
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, United States of America; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - William S James
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jenan J Kharbush
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Helena Nitschky
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Catherine A Polik
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - McKenzie A Powers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - Nicole A Rappuhn
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Laura A Reitz
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sara R Rivera
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Claire C Zwiers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Gregory J Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America.
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7
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Yancey CE, Yu F, Tripathi A, Sherman DH, Dick GJ. Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie. Appl Environ Microbiol 2023; 89:e0209222. [PMID: 37070981 PMCID: PMC10231183 DOI: 10.1128/aem.02092-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/19/2023] Open
Abstract
Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCE Microcystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.
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Affiliation(s)
- Colleen E. Yancey
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Natural Products Discovery Core, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
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8
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Bownik A, Adamczuk M, Pawlik-Skowrońska B, Mieczan T. Cyanobacterial metabolites: aeruginosin 98A, microginin-FR1, anabaenopeptin-A, cylindrospermopsin and their mixtures affect behavioral and physiological responses of Daphnia magna. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023:104161. [PMID: 37245609 DOI: 10.1016/j.etap.2023.104161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
We determined the effects influence of cyanobacterial products metabolites: aeruginosin-A (AER-A), microginin-FR1 (MG-FR1), anabaenopeptin-A (ANA-A), cylindrospermopsin (CYL) and their binary and quadruple mixtures on swimming behavior, heart rate, thoracic limb activity, oxygen consumption and in vivo cell health of Daphnia magna. The study showed that CYL induced mortality of daphnids at the highest concentrations, however three oligopeptides had no lethal effect. All the tested Each single metabolites inhibited swimming speed. The mixtures AER+MG-FR1 and AER-A+ANA-A induced antagonistic and the quadruple mixture synergistic effects. Physiological endpoints were depressed by CYL, however they were simulated by the oligopeptides and their binary mixtures. The quadruple mixture inhibited the physiological parameters with antagonistic interactions between the components were antagonistic. Single CYL, MG-FR1 and ANA-A induced cytotoxicity with synergistic interactions and the metabolites in mixtures showed. The study suggests that swimming behavior and physiological parameters may be affected by single cyanobacterial oligopeptides, however their mixtures may induce different total effects.
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Affiliation(s)
- Adam Bownik
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
| | - Małgorzata Adamczuk
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
| | - Barbara Pawlik-Skowrońska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
| | - Tomasz Mieczan
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
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9
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Liu J, Zhang M, Huang Z, Fang J, Wang Z, Zhou C, Qiu X. Diversity, Biosynthesis and Bioactivity of Aeruginosins, a Family of Cyanobacteria-Derived Nonribosomal Linear Tetrapeptides. Mar Drugs 2023; 21:md21040217. [PMID: 37103356 PMCID: PMC10143770 DOI: 10.3390/md21040217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Aeruginosins, a family of nonribosomal linear tetrapeptides discovered from cyanobacteria and sponges, exhibit in vitro inhibitory activity on various types of serine proteases. This family is characterized by the existence of the 2-carboxy-6-hydroxy-octahydroindole (Choi) moiety occupied at the central position of the tetrapeptide. Aeruginosins have attracted much attention due to their special structures and unique bioactivities. Although many studies on aeruginosins have been published, there has not yet been a comprehensive review that summarizes the diverse research ranging from biogenesis, structural characterization and biosynthesis to bioactivity. In this review, we provide an overview of the source, chemical structure as well as spectrum of bioactivities of aeruginosins. Furthermore, possible opportunities for future research and development of aeruginosins were discussed.
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Affiliation(s)
- Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Chengxu Zhou
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
- Correspondence:
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10
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McKindles KM, McKay RM, Bullerjahn GS. Genomic comparison of Planktothrix agardhii isolates from a Lake Erie embayment. PLoS One 2022; 17:e0273454. [PMID: 35998200 PMCID: PMC9398003 DOI: 10.1371/journal.pone.0273454] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/09/2022] [Indexed: 12/04/2022] Open
Abstract
Planktothrix agardhii is a filamentous cyanobacterial species that dominates harmful algal blooms in Sandusky Bay, Lake Erie and other freshwater basins across the world. P. agardhii isolates were obtained from early (June) blooms via single filament isolation; eight have been characterized from 2016, and 12 additional isolates have been characterized from 2018 for a total of 20 new cultures. These novel isolates were processed for genomic sequencing, where reads were used to generate scaffolds and contigs which were annotated with DIAMOND BLAST hit, Pfam, and GO. Analyses include whole genome alignment to generate phylogenetic trees and comparison of genetic rearrangements between isolates. Nitrogen acquisition and metabolism was compared across isolates. Secondary metabolite production was genetically explored including microcystins, two types of aeruginosin clusters, anabaenopeptins, cyanopeptolins, microviridins, and prenylagaramides. Two common and 4 unique CRISPR-cas islands were analyzed for similar sequences across all isolates and against the known Planktothrix-specific cyanophage, PaV-LD. Overall, the uniqueness of each genome from Planktothrix blooms sampled from the same site and at similar times belies the unexplored diversity of this genus.
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Affiliation(s)
- Katelyn M. McKindles
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - R. Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States of America
| | - George S. Bullerjahn
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States of America
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States of America
- * E-mail:
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11
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Heinilä LMP, Jokela J, Ahmed MN, Wahlsten M, Kumar S, Hrouzek P, Permi P, Koistinen H, Fewer DP, Sivonen K. Discovery of varlaxins, new aeruginosin-type inhibitors of human trypsins. Org Biomol Chem 2022; 20:2681-2692. [PMID: 35293909 DOI: 10.1039/d1ob02454j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-molecular weight natural products display vast structural diversity and have played a key role in the development of novel therapeutics. Here we report the discovery of novel members of the aeruginosin family of natural products, which we named varlaxins. The chemical structures of varlaxins 1046A and 1022A were determined using a combination of mass spectrometry, analysis of one- and two-dimensional NMR spectra, and HPLC analysis of Marfey's derivatives. These analyses revealed that varlaxins 1046A and 1022A are composed of the following moieties: 2-O-methylglyceric acid 3-O-sulfate, isoleucine, 2-carboxy-6-hydroxyoctahydroindole (Choi), and a terminal arginine derivative. Varlaxins 1046A and 1022A differ in the cyclization of this arginine moiety. Interestingly, an unusual α-D-glucopyranose moiety derivatized with two 4-hydroxyphenylacetic acid residues was bound to Choi, a structure not previously reported for other members of the aeruginosin family. We sequenced the complete genome of Nostoc sp. UHCC 0870 and identified the putative 36 kb varlaxin biosynthetic gene cluster. Bioinformatics analysis confirmed that varlaxins belong to the aeruginosin family of natural products. Varlaxins 1046A and 1022A strongly inhibited the three human trypsin isoenzymes with IC50 of 0.62-3.6 nM and 97-230 nM, respectively, including a prometastatic trypsin-3, which is a therapeutically relevant target in several types of cancer. These results substantially broaden the genetic and chemical diversity of the aeruginosin family and provide evidence that the aeruginosin family is a source of strong inhibitors of human serine proteases.
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Affiliation(s)
- L M P Heinilä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - J Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - M N Ahmed
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland. .,Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - M Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - S Kumar
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - P Hrouzek
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - P Permi
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - H Koistinen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - D P Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - K Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
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12
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Aldrich LN, Burdette JE, de Blanco EC, Coss CC, Eustaquio AS, Fuchs JR, Kinghorn AD, MacFarlane A, Mize B, Oberlies NH, Orjala J, Pearce CJ, Phelps MA, Rakotondraibe LH, Ren Y, Soejarto DD, Stockwell BR, Yalowich JC, Zhang X. Discovery of Anticancer Agents of Diverse Natural Origin. JOURNAL OF NATURAL PRODUCTS 2022; 85:702-719. [PMID: 35213158 PMCID: PMC9034850 DOI: 10.1021/acs.jnatprod.2c00036] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Research progress from mainly over the last five years is described for a multidisciplinary collaborative program project directed toward the discovery of potential anticancer agents from a broad range of taxonomically defined organisms. Selected lead compounds with potential as new antitumor agents that are representative of considerable structural diversity have continued to be obtained from each of tropical plants, terrestrial and aquatic cyanobacteria, and filamentous fungi. Recently, a new focus has been on the investigation of the constituents of U.S. lichens and their fungal mycobionts. A medicinal chemistry and pharmacokinetics component of the project has optimized structurally selected lead natural products, leading to enhanced cytotoxic potencies against selected cancer cell lines. Biological testing has shown several compounds to have in vivo activity, and relevant preliminary structure-activity relationship and mechanism of action studies have been performed. Several promising lead compounds worthy of further investigation have been identified from the most recent collaborative work performed.
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Affiliation(s)
- Leslie N. Aldrich
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Joanna E. Burdette
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | | | - Christopher C. Coss
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alessandra S. Eustaquio
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James R. Fuchs
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - A. Douglas Kinghorn
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda MacFarlane
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Brittney Mize
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 24702, United States
| | - Jimmy Orjala
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cedric J. Pearce
- Mycosynthetix, Inc., Hillsborough, North Carolina 27278, United States
| | - Mitch A. Phelps
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Yulin Ren
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Djaja Doel Soejarto
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Field Museum of Natural History, Chicago, Illinois 60605, United States
| | - Brent R. Stockwell
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jack C. Yalowich
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiaoli Zhang
- College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Ahmed MN, Wahlsten M, Jokela J, Nees M, Stenman UH, Alvarenga DO, Strandin T, Sivonen K, Poso A, Permi P, Metsä-Ketelä M, Koistinen H, Fewer DP. Potent Inhibitor of Human Trypsins from the Aeruginosin Family of Natural Products. ACS Chem Biol 2021; 16:2537-2546. [PMID: 34661384 PMCID: PMC8609519 DOI: 10.1021/acschembio.1c00611] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Serine proteases
regulate many physiological processes and play
a key role in a variety of cancers. Aeruginosins are a family of natural
products produced by cyanobacteria that exhibit pronounced structural
diversity and potent serine protease inhibition. Here, we sequenced
the complete genome of Nodularia sphaerocarpa UHCC 0038 and identified the 43.7 kb suomilide biosynthetic gene
cluster. Bioinformatic analysis demonstrated that suomilide belongs
to the aeruginosin family of natural products. We identified 103 complete
aeruginosin biosynthetic gene clusters from 12 cyanobacterial genera
and showed that they encode an unexpected chemical diversity. Surprisingly,
purified suomilide inhibited human trypsin-2 and -3, with IC50 values of 4.7 and 11.5 nM, respectively, while trypsin-1 was inhibited
with an IC50 of 104 nM. Molecular dynamics simulations
suggested that suomilide has a long residence time when bound to trypsins.
This was confirmed experimentally for trypsin-1 and -3 (residence
times of 1.5 and 57 min, respectively). Suomilide also inhibited the
invasion of aggressive and metastatic PC-3M prostate cancer cells
without affecting cell proliferation. The potent inhibition of trypsin-3,
together with a long residence time and the ability to inhibit prostate
cancer cell invasion, makes suomilide an attractive drug lead for
targeting cancers that overexpress trypsin-3. These results substantially
broaden the genetic and chemical diversity of the aeruginosin family
and suggest that aeruginosins may be a source of selective inhibitors
of human serine proteases.
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Affiliation(s)
- Muhammad N. Ahmed
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Jouni Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Matthias Nees
- Department of Biochemistry and Molecular Biology, Medical University in Lublin, ul. Chodzki 1, Lublin 20-093, Poland
- Institute of Biomedicine and Western Cancer Centre FICAN West, University of Turku, Turku 20101, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - Danillo O. Alvarenga
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, Helsinki FIN-00014, Finland
| | - Kaarina Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, Kuopio FIN-70211, Finland
- Dept. of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, Tübingen DE-72076, Germany
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä FI-40014, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box
35, Jyväskylä FI-40014, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Turku FIN-20014, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - David P. Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
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14
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Chen M, Xu C, Wang X, Wu Y, Li L. Nonribosomal peptide synthetases and nonribosomal cyanopeptides synthesis in Microcystis: A comparative genomics study. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Baunach M, Chowdhury S, Stallforth P, Dittmann E. The Landscape of Recombination Events That Create Nonribosomal Peptide Diversity. Mol Biol Evol 2021; 38:2116-2130. [PMID: 33480992 PMCID: PMC8097286 DOI: 10.1093/molbev/msab015] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing and matching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the Acore domains, yet domain interfaces and the flexible Asub domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.
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Affiliation(s)
- Martin Baunach
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Elke Dittmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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16
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Lage S, Mazur-Marzec H, Gorokhova E. Competitive interactions as a mechanism for chemical diversity maintenance in Nodularia spumigena. Sci Rep 2021; 11:8970. [PMID: 33903638 PMCID: PMC8076297 DOI: 10.1038/s41598-021-88361-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/12/2021] [Indexed: 02/06/2023] Open
Abstract
Nodularia spumigena is a bloom-forming diazotrophic cyanobacterium inhabiting brackish waters worldwide. This species produces non-ribosomal peptides (NRPs), including the hepatotoxin nodularin, often referred to as cyanotoxin. Several known classes of NRPs have various biological activities, although their modes of action are poorly understood. In the Baltic N. spumigena, there is a high NRP chemodiversity among strains, allowing their grouping in specific chemotypes and subgroups. Therefore, it is relevant to ask whether the NRP production is affected by intraspecific interactions between the co-existing strains. Using a novel approach that combines culture technique and liquid chromatography-tandem mass spectrometry for the NRP analysis, we examined N. spumigena strains under mono- and co-culture conditions. The test strains were selected to represent N. spumigena belonging to the same or different chemotype subgroups. In this setup, we observed physiological and metabolic responses in the test strains grown without cell contact. The changes in NRP levels to co-culture conditions were conserved within a chemotype subgroup but different between the subgroups. Our results suggest that intraspecific interactions may promote a chemical diversity in N. spumigena population, with higher NRP production compared to a single-strain population. Studying allelochemical signalling in this cyanobacterium is crucial for understanding toxicity mechanisms and plankton community interactions in the Baltic Sea and other aquatic systems experiencing regular blooms.
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Affiliation(s)
- Sandra Lage
- grid.10548.380000 0004 1936 9377Department of Environmental Science, Stockholm University, Stockholm, Sweden ,grid.8585.00000 0001 2370 4076Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Gdynia, Poland
| | - Hanna Mazur-Marzec
- grid.8585.00000 0001 2370 4076Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Gdynia, Poland
| | - Elena Gorokhova
- grid.10548.380000 0004 1936 9377Department of Environmental Science, Stockholm University, Stockholm, Sweden
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17
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Dreher TW, Davis EW, Mueller RS, Otten TG. Comparative genomics of the ADA clade within the Nostocales. HARMFUL ALGAE 2021; 104:102037. [PMID: 34023075 DOI: 10.1016/j.hal.2021.102037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
The ADA clade of Nostocales cyanobacteria, a group that is prominent in current harmful algal bloom events, now includes over 40 genome sequences with the recent addition of sixteen novel sequenced genomes (Dreher et al., Harmful Algae, 2021). Fourteen genomes are complete (closed), enabling highly detailed assessments of gene content and genome architecture. ADA genomes contain 5 rRNA operons, genes expected to support a photoautotrophic and diazotrophic lifestyle, and a varied array of genes for the synthesis of bioactive secondary metabolites. Genes for the production of the taste-and-odor compound geosmin and the four major classes of cyanotoxins - anatoxin-a, cylindrospermopsin, microcystin and saxitoxin - are represented in members of the ADA clade. Notably, the gene array for the synthesis of cylindrospermopsin by Dolichospermum sp. DET69 was located on a plasmid, raising the possibility of facile horizontal transmission. However, genes supporting independent conjugative transfer of this plasmid are lacking. Further, analysis of genomic loci containing this and other cyanotoxin gene arrays shows evidence that these arrays have long-term stability and do not appear to be genomic islands easily capable of horizontal transmission to other cells. There is considerable diversity in the gene complements of individual ADA genomes, including the variable presence of physiologically important genes: genomes in three species-level subclades lack the gas vesicle genes that facilitate a planktonic lifestyle, and, surprisingly, the genome of Cuspidothrix issatschenkoi CHARLIE-1, a reported diazotroph, lacks the genes for nitrogen fixation. Notably, phylogenetically related genomes possess limited synteny, indicating a prominent role for chromosome rearrangements during ADA strain evolution. The genomes contain abundant insertion sequences and repetitive transposase genes, which could be the main drivers of genome rearrangement through active transposition and homologous recombination. No prophages were found, and no evidence of viral infection was observed in the bloom population samples from which the genomes discussed here were derived. Phages thus seem to have a limited influence on ADA evolution.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 USA.
| | - Edward W Davis
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA.
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18
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Shimura Y, Fujisawa T, Hirose Y, Misawa N, Kanesaki Y, Nakamura Y, Kawachi M. Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204 T and detailed analysis of secondary metabolite gene clusters. HARMFUL ALGAE 2021; 101:101942. [PMID: 33526179 DOI: 10.1016/j.hal.2020.101942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Planktothrix species are distributed worldwide, and these prevalent cyanobacteria occasionally form potentially devastating toxic blooms. Given the ecological and taxonomic importance of Planktothrix agardhii as a bloom species, we set out to determine the complete genome sequence of the type strain Planktothrix agardhii NIES-204. Remarkably, we found that the 5S ribosomal RNA genes are not adjacent to the 16S and 23S ribosomal RNA genes. The genomic structure of P. agardhii NIES-204 is highly similar to that of another P. agardhii strain isolated from a geographically distant site, although they differ distinctly by a large inversion. We identified numerous gene clusters that encode the components of the metabolic pathways that generate secondary metabolites. We found that the aeruginosin biosynthetic gene cluster was more similar to that of another toxic bloom-forming cyanobacterium Microcystis aeruginosa than to that of other strains of Planktothrix, suggesting horizontal gene transfer. Prenyltransferases encoded in the prenylagaramide gene cluster of Planktothrix strains were classified into two phylogenetically distinct types, suggesting a functional difference. In addition to the secondary metabolite gene clusters, we identified genes for inorganic nitrogen and phosphate uptake components and gas vesicles. Our findings contribute to further understanding of the ecologically important genus Planktothrix.
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Affiliation(s)
- Yohei Shimura
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Misawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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19
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Jeong Y, Cho SH, Lee H, Choi HK, Kim DM, Lee CG, Cho S, Cho BK. Current Status and Future Strategies to Increase Secondary Metabolite Production from Cyanobacteria. Microorganisms 2020; 8:E1849. [PMID: 33255283 PMCID: PMC7761380 DOI: 10.3390/microorganisms8121849] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
Cyanobacteria, given their ability to produce various secondary metabolites utilizing solar energy and carbon dioxide, are a potential platform for sustainable production of biochemicals. Until now, conventional metabolic engineering approaches have been applied to various cyanobacterial species for enhanced production of industrially valued compounds, including secondary metabolites and non-natural biochemicals. However, the shortage of understanding of cyanobacterial metabolic and regulatory networks for atmospheric carbon fixation to biochemical production and the lack of available engineering tools limit the potential of cyanobacteria for industrial applications. Recently, to overcome the limitations, synthetic biology tools and systems biology approaches such as genome-scale modeling based on diverse omics data have been applied to cyanobacteria. This review covers the synthetic and systems biology approaches for advanced metabolic engineering of cyanobacteria.
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Affiliation(s)
- Yujin Jeong
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Sang-Hyeok Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Hookeun Lee
- Institute of Pharmaceutical Research, College of Pharmacy, Gachon University, Incheon 21999, Korea;
| | | | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea;
| | - Choul-Gyun Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea;
| | - Suhyung Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Byung-Kwan Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
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20
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Calcott MJ, Owen JG, Ackerley DF. Efficient rational modification of non-ribosomal peptides by adenylation domain substitution. Nat Commun 2020; 11:4554. [PMID: 32917865 PMCID: PMC7486941 DOI: 10.1038/s41467-020-18365-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) enzymes form modular assembly-lines, wherein each module governs the incorporation of a specific monomer into a short peptide product. Modules are comprised of one or more key domains, including adenylation (A) domains, which recognise and activate the monomer substrate; condensation (C) domains, which catalyse amide bond formation; and thiolation (T) domains, which shuttle reaction intermediates between catalytic domains. This arrangement offers prospects for rational peptide modification via substitution of substrate-specifying domains. For over 20 years, it has been considered that C domains play key roles in proof-reading the substrate; a presumption that has greatly complicated rational NRPS redesign. Here we present evidence from both directed and natural evolution studies that any substrate-specifying role for C domains is likely to be the exception rather than the rule, and that novel non-ribosomal peptides can be generated by substitution of A domains alone. We identify permissive A domain recombination boundaries and show that these allow us to efficiently generate modified pyoverdine peptides at high yields. We further demonstrate the transferability of our approach in the PheATE-ProCAT model system originally used to infer C domain substrate specificity, generating modified dipeptide products at yields that are inconsistent with the prevailing dogma.
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Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
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21
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Draft Genome Sequences of Four Microcystis aeruginosa Strains (NIES-3787, NIES-3804, NIES-3806, and NIES-3807) Isolated from Lake Kasumigaura, Japan. Microbiol Resour Announc 2020; 9:9/14/e00052-20. [PMID: 32241856 PMCID: PMC7118182 DOI: 10.1128/mra.00052-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcystis aeruginosa is a bloom-forming cyanobacterium found in freshwater environments. The draft genomes of the M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, which were isolated from Lake Kasumigaura, Japan, were sequenced. The genome sizes of NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 4,524,637, 4,522,701, 4,370,004, and 4,378,226 bp, respectively. Microcystis aeruginosa is a bloom-forming cyanobacterium found in freshwater environments. The draft genomes of the M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, which were isolated from Lake Kasumigaura, Japan, were sequenced. The genome sizes of NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 4,524,637, 4,522,701, 4,370,004, and 4,378,226 bp, respectively.
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22
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Le TC, Katila N, Park S, Lee J, Yang I, Choi H, Choi DY, Nam SJ. Two new secondary metabolites, saccharochlorines A and B, from a marine bacterium Saccharomonospora sp. KCTC-19160. Bioorg Med Chem Lett 2020; 30:127145. [PMID: 32249119 DOI: 10.1016/j.bmcl.2020.127145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 11/15/2022]
Abstract
Two new chlorinated secondary metabolites, saccharochlorines A and B (1 and 2), were isolated from the saline cultivation of a marine-derived bacterium Saccharomonospora sp. (KCTC-19160). The chemical structures of the saccharochlorines were elucidated by 2D NMR and MS spectroscopic data. Saccharochlorines A and B (1 and 2) exhibit weak inhibition of β-secretase (BACE1) in biochemical inhibitory assay, but they induced the release of Aβ (1-40) and Aβ (1-42) in H4-APP neuroglial cells. This discrepancy might be derived from the differences between the cellular and sub-cellular environments or the epigenetic stimulation of BACE1 expression.
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Affiliation(s)
- Tu Cam Le
- Laboratory of Advanced Materials Chemistry, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Nikita Katila
- College of Pharmacy, Yeungnam University, Gyeongbuk 38541, Republic of Korea
| | - Songhee Park
- College of Pharmacy, Yeungnam University, Gyeongbuk 38541, Republic of Korea
| | - Jihye Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea; Laboratories of Marine New Drugs, REDONE Seoul, Seoul 08594, Republic of Korea
| | - Inho Yang
- Department of Convergence Study on the Ocean Science and Technology, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongbuk 38541, Republic of Korea.
| | - Dong-Young Choi
- College of Pharmacy, Yeungnam University, Gyeongbuk 38541, Republic of Korea.
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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23
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May DS, Crnkovic CM, Krunic A, Wilson TA, Fuchs JR, Orjala JE. 15N Stable Isotope Labeling and Comparative Metabolomics Facilitates Genome Mining in Cultured Cyanobacteria. ACS Chem Biol 2020; 15:758-765. [PMID: 32083834 DOI: 10.1021/acschembio.9b00993] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As genome mining becomes a more widely used approach to identify bacterial natural products, the challenge of matching biosynthetic gene clusters to their cognate secondary metabolites has become more apparent. Bioinformatic platforms such as AntiSMASH have made great progress in predicting chemical structures from genetic information, however the predicted structures are often incomplete. This complicates identifying the predicted compounds by mass spectrometry. Secondary metabolites produced by cyanobacteria represent a unique opportunity for bridging this gap. Cultured cyanobacteria incorporate inorganic nitrogen provided in chemically defined media into all nitrogen-containing secondary metabolites. Thus, stable isotope labeling with 15N labeled nitrate and subsequent comparative metabolomics can be used to match biosynthetic gene clusters to their cognate compounds in cell extracts. Analysis of the sequenced genome of Nostoc sp. UIC 10630 identified six biosynthetic gene clusters predicted to encode the production of a secondary metabolite with at least one nitrogen atom. Comparative metabolomic analysis of the 15N labeled and unlabeled cell extracts revealed four nitrogen containing compounds that contained the same number of nitrogen atoms as were predicted in the biosynthetic gene clusters. Two of the four compounds were new secondary metabolites, and their structures were elucidated by NMR, HRESIMS, and MS/MS.
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Affiliation(s)
- Daniel S. May
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Tyler A. Wilson
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jimmy E. Orjala
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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24
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Sieber S, Grendelmeier SM, Harris LA, Mitchell DA, Gademann K. Microviridin 1777: A Toxic Chymotrypsin Inhibitor Discovered by a Metabologenomic Approach. JOURNAL OF NATURAL PRODUCTS 2020; 83:438-446. [PMID: 31989826 PMCID: PMC7050427 DOI: 10.1021/acs.jnatprod.9b00986] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The toxicity of the cyanobacterium Microcystis aeruginosa EAWAG 127a was evaluated against the sensitive grazer Thamnocephalus platyurus, and the extract possessed strong activity. To investigate the compounds responsible for cytotoxicity, a series of peptides from this cyanobacterium were studied using a combined genomic and molecular networking approach. The results led to the isolation, structure elucidation, and biological evaluation of microviridin 1777, which represents the most potent chymotrypsin inhibitor characterized from this family of peptides to date. Furthermore, the biosynthetic gene clusters of microviridin, anabaenopeptin, aeruginosin, and piricyclamide were located in the producing organism, and six additional natural products were identified by tandem mass spectrometry analyses. These results highlight the potential of modern techniques for the identification of natural products, demonstrate the ecological role of protease inhibitors produced by cyanobacteria, and raise ramifications concerning the presence of novel, yet uncharacterized, toxin families in cyanobacteria beyond microcystin.
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Affiliation(s)
- Simon Sieber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH 8057, Switzerland
| | - Simone M. Grendelmeier
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH 8057, Switzerland
| | - Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Karl Gademann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH 8057, Switzerland
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25
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Popin RV, Delbaje E, de Abreu VAC, Rigonato J, Dörr FA, Pinto E, Sivonen K, Fiore MF. Genomic and Metabolomic Analyses of Natural Products in Nodularia spumigena Isolated from a Shrimp Culture Pond. Toxins (Basel) 2020; 12:toxins12030141. [PMID: 32106513 PMCID: PMC7150779 DOI: 10.3390/toxins12030141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/13/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
The bloom-forming cyanobacterium Nodularia spumigena CENA596 encodes the biosynthetic gene clusters (BGCs) of the known natural products nodularins, spumigins, anabaenopeptins/namalides, aeruginosins, mycosporin-like amino acids, and scytonemin, along with the terpenoid geosmin. Targeted metabolomics confirmed the production of these metabolic compounds, except for the alkaloid scytonemin. Genome mining of N. spumigena CENA596 and its three closely related Nodularia strains—two planktonic strains from the Baltic Sea and one benthic strain from Japanese marine sediment—revealed that the number of BGCs in planktonic strains was higher than in benthic one. Geosmin—a volatile compound with unpleasant taste and odor—was unique to the Brazilian strain CENA596. Automatic annotation of the genomes using subsystems technology revealed a related number of coding sequences and functional roles. Orthologs from the Nodularia genomes are involved in the primary and secondary metabolisms. Phylogenomic analysis of N. spumigena CENA596 based on 120 conserved protein sequences positioned this strain close to the Baltic Nodularia. Phylogeny of the 16S rRNA genes separated the Brazilian CENA596 strain from those of the Baltic Sea, despite their high sequence identities (99% identity, 100% coverage). The comparative analysis among planktic Nodularia strains showed that their genomes were considerably similar despite their geographically distant origin.
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Affiliation(s)
- Rafael Vicentini Popin
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Vinicius Augusto Carvalho de Abreu
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Institute of Exact and Natural Sciences, Federal University of Pará, Rua Augusto Corrêa 1, Belém 66075-10, Pará, Brazil
| | - Janaina Rigonato
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Felipe Augusto Dörr
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Marli Fatima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Correspondence:
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26
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Yamaguchi H, Suzuki S, Osana Y, Kawachi M. Genomic Characteristics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa NIES-102. J Genomics 2020; 8:1-6. [PMID: 31892993 PMCID: PMC6930136 DOI: 10.7150/jgen.40978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/20/2019] [Indexed: 01/10/2023] Open
Abstract
Microcystis aeruginosa, a bloom-forming cyanobacterium distributed mainly in freshwater environments, can be divided into at least 12 groups (A-K and X) based on multi-locus phylogenetic analyses. In this study, we characterized the genome of microcystin-producing M. aeruginosa NIES-102, assigned to group A, isolated from Lake Kasumigaura, Japan. The complete genome sequence of M. aeruginosa NIES-102 comprised a 5.87-Mbp circular chromosome containing 5,330 coding sequences. The genome was the largest among all sequenced genomes for the species. In a comparison with the genome of M. aeruginosa NIES-843, which belongs to the same group, the microcystin biosynthetic gene cluster and CRISPR-Cas locus were highly similar. A synteny analysis revealed small-scale rearrangements between the two genomes. Genes encoding transposases were more abundant in these two genomes than in other Microcystis genomes. Our results improve our understanding of structural genomic changes and adaptation to a changing environment in the species.
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Affiliation(s)
- Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Yasunori Osana
- Department of Electrical and Electronics Engineering, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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27
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Götze S, Arp J, Lackner G, Zhang S, Kries H, Klapper M, García-Altares M, Willing K, Günther M, Stallforth P. Structure elucidation of the syringafactin lipopeptides provides insight in the evolution of nonribosomal peptide synthetases. Chem Sci 2019; 10:10979-10990. [PMID: 32953002 PMCID: PMC7472662 DOI: 10.1039/c9sc03633d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Modular biosynthetic machineries such as polyketide synthases (PKSs) or nonribosomal peptide synthetases (NRPSs) give rise to a vast structural diversity of bioactive metabolites indispensable in the treatment of cancer or infectious diseases. Here, we provide evidence for different evolutionary processes leading to the diversification of modular NRPSs and thus, their respective products. Discovery of a novel lipo-octapeptide family from Pseudomonas, the virginiafactins, and detailed structure elucidation of closely related peptides, the cichofactins and syringafactins, allowed retracing recombinational diversification of the respective NRPS genes. Bioinformatics analyses allowed us to spot an evolutionary snapshot of these processes, where recombination occurred both within the same and between different biosynthetic gene clusters. Our systems feature a recent diversification process, which may represent a typical paradigm to variations in modular biosynthetic machineries.
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Affiliation(s)
- Sebastian Götze
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Johannes Arp
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Gerald Lackner
- Independent Junior Research Group Synthetic Microbiology , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Shuaibing Zhang
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Hajo Kries
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Martin Klapper
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - María García-Altares
- Department Biomolecular Chemistry , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Karsten Willing
- Department Bio Pilot Plant , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Markus Günther
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Pierre Stallforth
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
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28
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Nivina A, Yuet KP, Hsu J, Khosla C. Evolution and Diversity of Assembly-Line Polyketide Synthases. Chem Rev 2019; 119:12524-12547. [PMID: 31838842 PMCID: PMC6935866 DOI: 10.1021/acs.chemrev.9b00525] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Assembly-line polyketide synthases (PKSs) are among the most complex protein machineries known in nature, responsible for the biosynthesis of numerous compounds used in the clinic. Their present-day diversity is the result of an evolutionary path that has involved the emergence of a multimodular architecture and further diversification of assembly-line PKSs. In this review, we provide an overview of previous studies that investigated PKS evolution and propose a model that challenges the currently prevailing view that gene duplication has played a major role in the emergence of multimodularity. We also analyze the ensemble of orphan PKS clusters sequenced so far to evaluate how large the entire diversity of assembly-line PKS clusters and their chemical products could be. Finally, we examine the existing techniques to access the natural PKS diversity in natural and heterologous hosts and describe approaches to further expand this diversity through engineering.
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Affiliation(s)
- Aleksandra Nivina
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Kai P. Yuet
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Jake Hsu
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
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29
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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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30
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Structural and functional investigation of AerF, a NADPH-dependent alkenal double bond reductase participating in the biosynthesis of Choi moiety of aeruginosin. J Struct Biol 2019; 209:107415. [PMID: 31726097 DOI: 10.1016/j.jsb.2019.107415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 10/27/2019] [Accepted: 11/08/2019] [Indexed: 01/16/2023]
Abstract
The 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety is an essential residue for the antithrombotic activities of aeruginosins, which are a class of cyanobacterial derived bioactive linear tetrapeptides. Biosynthetic pathway of Choi is still elusive. AerF was suggested to be involved in the biosynthesis of Choi, and can be assigned to the short-chain dehydrogenase/reductase (SDR) superfamily. However, both the exact role and the catalytic mechanism of AerF have not been elucidated. In this study, functional and mechanistic analyses of AerF from Microcystis aeruginosa were performed. Observation of enzymatic assay demonstrates that AerF is a NADPH-dependent alkenal double bond reductase that catalyzes the reduction of dihydro-4-hydroxyphenylpyruvate (H2HPP) to generate tetrahydro-4-hydroxyphenylpyruvate (H4HPP), which is the third step of the biosynthetic pathway from prephenate to Choi. Comparative structural analysis indicates that ligand binding-induced conformational change of AerF is different from that of the other SDR superfamily reductase using H2HPP as a substrate. Analyses of NADPH and substrate analogue binding sites combined with the results of mutagenesis analyses suggest that a particular serine residue mainly involves in the initiation of the proton transfer between the substrate and the residues of AerF, which is an uncommon feature in SDR superfamily reductase. Furthermore, based on the observations of structural and mutagenesis analyses, the catalytic mechanism of AerF is proposed and a proton transfer pathway in AerF is deduced.
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31
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Kim Tiam S, Gugger M, Demay J, Le Manach S, Duval C, Bernard C, Marie B. Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics. Toxins (Basel) 2019; 11:E498. [PMID: 31461939 PMCID: PMC6784222 DOI: 10.3390/toxins11090498] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with diverse chemical structures and potent biological activities and toxicities. The chemical identification of these compounds remains a major bottleneck. Strategies that can prioritize the most prolific strains and novel compounds are of great interest. Here, we combine chemical analysis and genomics to investigate the chemodiversity of secondary metabolites based on their pattern of distribution within some cyanobacteria. Planktothrix being a cyanobacterial genus known to form blooms worldwide and to produce a broad spectrum of toxins and other bioactive compounds, we applied this combined approach on four closely related strains of Planktothrix. The chemical diversity of the metabolites produced by the four strains was evaluated using an untargeted metabolomics strategy with high-resolution LC-MS. Metabolite profiles were correlated with the potential of metabolite production identified by genomics for the different strains. Although, the Planktothrix strains present a global similarity in terms of a biosynthetic cluster gene for microcystin, aeruginosin, and prenylagaramide for example, we found remarkable strain-specific chemodiversity. Only few of the chemical features were common to the four studied strains. Additionally, the MS/MS data were analyzed using Global Natural Products Social Molecular Networking (GNPS) to identify molecular families of the same biosynthetic origin. In conclusion, we depict an efficient, integrative strategy for elucidating the chemical diversity of a given genus and link the data obtained from analytical chemistry to biosynthetic genes of cyanobacteria.
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Affiliation(s)
- Sandra Kim Tiam
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, 28 rue du Dr Roux, 75724 Paris Cedex 05, France
| | - Justine Demay
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Séverine Le Manach
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France.
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Tanabe Y, Yamaguchi H, Sano T, Kawachi M. A novel salt-tolerant genotype illuminates the sucrose gene evolution in freshwater bloom-forming cyanobacterium Microcystis aeruginosa. FEMS Microbiol Lett 2019; 366:5561441. [PMID: 31504438 DOI: 10.1093/femsle/fnz190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022] Open
Abstract
Microcystis aeruginosa is a water bloom-forming cyanobacterium found in fresh and brackish water ecosystems worldwide. Previously, we showed that several instances of M. aeruginosa bloom in brackish water can be explained by the proliferation of salt-tolerant M. aeruginosa strains harboring genes for a compatible solute sucrose. However, evolutionary history of sucrose genes in M. aeruginosa remains unclear because salt-tolerant strains have been poorly described. Here, we characterized a novel salt-tolerant strain of M. aeruginosa (NIES-4325) isolated from the brackish water of Lake Abashiri, Japan. A whole-genome analysis of M. aeruginosa NIES-4325 identified genes for sucrose synthesis (sppA, spsA and susA). Quantitative sucrose and gene expression analyses suggested that sucrose is implicated in acclimation to high salt in NIES-4325. Notably, the sucrose genes of M. aeruginosa are monophyletic, yet sucrose genes of NIES-4325 are highly divergent from those of other salt-tolerant M. aeruginosa strains. This suggests an early sucrose gene import into M. aeruginosa from other cyanobacteria, followed by multiple losses during intraspecific diversification. One of a few survivors of salt-tolerant strains is a likely donor of recent horizontal spreads of sucrose genes across M. aeruginosa lineages.
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Affiliation(s)
- Yuuhiko Tanabe
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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33
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Huang IS, Zimba PV. Cyanobacterial bioactive metabolites-A review of their chemistry and biology. HARMFUL ALGAE 2019; 86:139-209. [PMID: 31358273 DOI: 10.1016/j.hal.2019.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 11/16/2018] [Indexed: 06/10/2023]
Abstract
Cyanobacterial blooms occur when algal densities exceed baseline population concentrations. Cyanobacteria can produce a large number of secondary metabolites. Odorous metabolites affect the smell and flavor of aquatic animals, whereas bioactive metabolites cause a range of lethal and sub-lethal effects in plants, invertebrates, and vertebrates, including humans. Herein, the bioactivity, chemistry, origin, and biosynthesis of these cyanobacterial secondary metabolites were reviewed. With recent revision of cyanobacterial taxonomy by Anagnostidis and Komárek as part of the Süβwasserflora von Mitteleuropa volumes 19(1-3), names of many cyanobacteria that produce bioactive compounds have changed, thereby confusing readers. The original and new nomenclature are included in this review to clarify the origins of cyanobacterial bioactive compounds. Due to structural similarity, the 157 known bioactive classes produced by cyanobacteria have been condensed to 55 classes. This review will provide a basis for more formal procedures to adopt a logical naming system. This review is needed for efficient management of water resources to understand, identify, and manage cyanobacterial harmful algal bloom impacts.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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34
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Qiu X, Zhu W, Wang W, Jin H, Zhu P, Zhuang R, Yan X. Structural and functional insights into the role of a cupin superfamily isomerase in the biosynthesis of Choi moiety of aeruginosin. J Struct Biol 2019; 205:44-52. [DOI: 10.1016/j.jsb.2019.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/12/2019] [Accepted: 01/26/2019] [Indexed: 01/12/2023]
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35
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Huang IS, Zimba PV. Cyanobacterial bioactive metabolites-A review of their chemistry and biology. HARMFUL ALGAE 2019; 83:42-94. [PMID: 31097255 DOI: 10.1016/j.hal.2018.11.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Cyanobacterial blooms occur when algal densities exceed baseline population concentrations. Cyanobacteria can produce a large number of secondary metabolites. Odorous metabolites affect the smell and flavor of aquatic animals, whereas bioactive metabolites cause a range of lethal and sub-lethal effects in plants, invertebrates, and vertebrates, including humans. Herein, the bioactivity, chemistry, origin, and biosynthesis of these cyanobacterial secondary metabolites were reviewed. With recent revision of cyanobacterial taxonomy by Anagnostidis and Komárek as part of the Süβwasserflora von Mitteleuropa volumes 19(1-3), names of many cyanobacteria that produce bioactive compounds have changed, thereby confusing readers. The original and new nomenclature are included in this review to clarify the origins of cyanobacterial bioactive compounds. Due to structural similarity, the 157 known bioactive classes produced by cyanobacteria have been condensed to 55 classes. This review will provide a basis for more formal procedures to adopt a logical naming system. This review is needed for efficient management of water resources to understand, identify, and manage cyanobacterial harmful algal bloom impacts.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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36
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Draft Genome Sequence of Microcystis aeruginosa NIES-4285, Isolated from Brackish Water (Lake Abashiri, Japan). Microbiol Resour Announc 2019; 8:MRA00001-19. [PMID: 30746511 PMCID: PMC6368646 DOI: 10.1128/mra.00001-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 01/18/2019] [Indexed: 01/25/2023] Open
Abstract
Microcystis aeruginosa is a bloom-forming cyanobacterium found in fresh and brackish waters worldwide. We sequenced the whole genome of M. aeruginosa NIES-4285, isolated from Lake Abashiri, Japan. Microcystis aeruginosa is a bloom-forming cyanobacterium found in fresh and brackish waters worldwide. We sequenced the whole genome of M. aeruginosa NIES-4285, isolated from Lake Abashiri, Japan. Its genome contains approximately 5.2 Mbp with an average G+C content of 42.60% and is predicted to have 4,980 protein-coding genes.
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37
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Lezcano MÁ, Agha R, Cirés S, Quesada A. Spatial-temporal survey of Microcystis oligopeptide chemotypes in reservoirs with dissimilar waterbody features and their relation to genetic variation. HARMFUL ALGAE 2019; 81:77-85. [PMID: 30638501 DOI: 10.1016/j.hal.2018.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
The ability of cyanobacteria to produce toxins and other secondary metabolites is patchily distributed in natural populations, enabling the use of cellular oligopeptide compositions as markers to classify strains into ecologically-relevant chemotypical subpopulations. The composition and spatiotemporal distribution of Microcystis chemotypes within and among waterbodies was studied at different time scales by analyzing (i) Microcystis strains isolated between 1998 and 2007 from different Spanish reservoirs and (ii) individual Microcystis aeruginosa colonies collected from pelagic and littoral habitats in Valmayor reservoir (Spain) during a bloom. No agreement between chemotypes and both morphotypes and genotypes (based on cpcBA-IGS, 16S-23S rRNA ITS and mcyB genes) was found, suggesting that oligopeptide profiles in individual strains evolve independently across morphospecies and phylogenetic genotypes, and that the diversity of microcystin variants produced cannot be explained by mcyB gene variations alone. The presence of identical chemotypes in spatially-distant reservoirs with dissimilar trophic state, lithology or depth indicate that waterbody characteristics and geographical boundaries weakly affect chemotype composition and distribution. At smaller spatiotemporal scales (i.e. during bloom), M. aeruginosa populations showed high number of chemotypes, as well as marked differences in chemotype composition and relative abundance among the littoral and pelagic habitats. This indicates that the factors influencing chemotype composition, relative abundance and dynamics operate at short spatial and temporal scales, and supports emerging hypotheses about interactions with antagonistic microorganisms as possible drivers for widespread chemical polymorphisms in cyanobacteria.
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Affiliation(s)
- M Á Lezcano
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
| | - R Agha
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, 12587, Germany.
| | - S Cirés
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
| | - A Quesada
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
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38
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Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW. A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales. HARMFUL ALGAE 2018; 77:93-107. [PMID: 30005805 DOI: 10.1016/j.hal.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.
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Affiliation(s)
- Connor B Driscoll
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Kevin A Meyer
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Akademijos Str. 2, LT-08412, Vilnius, Lithuania
| | - Nathan M Brown
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Gregory J Dick
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Huansheng Cao
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Giedrius Gasiūnas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Albertas Timinskas
- Department of Bioinformatics, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Zachary C Landry
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
| | - Susan B Watson
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, ON L7S 1A1, Canada
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
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Yamaguchi H, Suzuki S, Osana Y, Kawachi M. Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of Group G M. aeruginosa. J Genomics 2018; 6:30-33. [PMID: 29576807 PMCID: PMC5865083 DOI: 10.7150/jgen.24935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/21/2018] [Indexed: 11/05/2022] Open
Abstract
Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium that is distributed worldwide. M. aeruginosa can be divided into at least 8 phylogenetic groups (A-G and X) at the intraspecific level. Here, we report the complete genome sequence of M. aeruginosa NIES-2481, which was isolated from Lake Kasumigaura, Japan, and is assigned to group G. The complete genome sequence of M. aeruginosa NIES-2481 comprises a 4.29-Mbp circular chromosome and a 147,539-bp plasmid; the circular chromosome and the plasmid contain 4,332 and 167 protein-coding genes, respectively. Comparative analysis with the complete genome of M. aeruginosa NIES-2549, which belongs to the same group with NIES-2481, showed that the genome size is the smallest level in previously sequenced M. aeruginosa strains, and the genomes do not contain a microcystin biosynthetic gene cluster in common. Synteny analysis revealed only small-scale rearrangements between the two genomes.
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Affiliation(s)
- Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Yasunori Osana
- Department of Electrical and Electronics Engineering, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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40
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Veselá I, Kolísková PC, Kuchařová V, Tomenendálová J, Kováčová V, Pikula J, Repková B, Rapekta P, Hrouzek P, Cheel J, Doubek J. Cytotoxic Effect of Aeruginosin-865, Resveratrol and Capsaicin on Mouse Fibroblasts and Cells Derived from Fallow Deer. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Natural substances offer interesting bioactivity patterns including antiproliferative, antioxidant or cytotoxic effects. However, the safety profile of many of them has not been extensively determined. In this study, the cytotoxic effect of Aeruginosin-865, resveratrol and capsaicin at different concentrations was tested on normal mouse cells (NIH/3T3) and tumour fibroblasts (WEHI-13VAR) as well as on liver- and kidney-derived cells from fallow deer. A lactate dehydrogenase cytotoxicity assay kit was used to measure cell death in response to treatment with the test substances. It was found that NIH/3T3 cells tolerated Aeruginosin-865 (10-200 μM) and resveratrol (5-100 μM) treatment without any cytotoxic effect, while capsaicin exerted a cytotoxic effect only at the highest tested concentration (200 μ M). Mouse fibrosarcoma cells were more sensitive to the cytotoxic effect of all three compounds where Aeruginosin-865 (100-200 μM) and resveratrol (50–100 μM) showed high-dose cytotoxicity and capsaicin showed low- and high-dose cytotoxicity (25 μM and 200 μ M). The three tested compounds at the highest concentrations were found to be cytotoxic to both liver- and kidney-derived cells from fallow deer. Overall, the results indicate that the cytotoxic effects of the three tested natural substances on cells derived from fallow deer and mouse tumour fibroblasts differ significantly from those exerted on normal fibroblasts. The results demonstrate the potential of these natural compounds as therapeutic agents and pave the way for future in vivo toxicological investigations.
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Affiliation(s)
- Ivana Veselá
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Petra Celá Kolísková
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Vendula Kuchařová
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Jaroslava Tomenendálová
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Veronika Kováčová
- Department of Ecology and Diseases of Game, Fish and Bees, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jiří Pikula
- Department of Ecology and Diseases of Game, Fish and Bees, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Barbora Repková
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Polina Rapekta
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Pavel Hrouzek
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Trebon, Czech Republic
| | - José Cheel
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Trebon, Czech Republic
| | - Jaroslav Doubek
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
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41
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Evolution-guided adaptation of an adenylation domain substrate specificity to an unusual amino acid. PLoS One 2017; 12:e0189684. [PMID: 29240815 PMCID: PMC5730197 DOI: 10.1371/journal.pone.0189684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022] Open
Abstract
Adenylation domains CcbC and LmbC control the specific incorporation of amino acid precursors in the biosynthesis of lincosamide antibiotics celesticetin and lincomycin. Both proteins originate from a common L-proline-specific ancestor, but LmbC was evolutionary adapted to use an unusual substrate, (2S,4R)-4-propyl-proline (PPL). Using site-directed mutagenesis of the LmbC substrate binding pocket and an ATP-[32P]PPi exchange assay, three residues, G308, A207 and L246, were identified as crucial for the PPL activation, presumably forming together a channel of a proper size, shape and hydrophobicity to accommodate the propyl side chain of PPL. Subsequently, we experimentally simulated the molecular evolution leading from L-proline-specific substrate binding pocket to the PPL-specific LmbC. The mere change of three amino acid residues in originally strictly L-proline-specific CcbC switched its substrate specificity to prefer PPL and even synthetic alkyl-L-proline derivatives with prolonged side chain. This is the first time that such a comparative study provided an evidence of the evolutionary relevant adaptation of the adenylation domain substrate binding pocket to a new sterically different substrate by a few point mutations. The herein experimentally simulated rearrangement of the substrate binding pocket seems to be the general principle of the de novo genesis of adenylation domains' unusual substrate specificities. However, to keep the overall natural catalytic efficiency of the enzyme, a more comprehensive rearrangement of the whole protein would probably be employed within natural evolution process.
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Inhibitors of Serine Proteases from a Microcystis sp. Bloom Material Collected from Timurim Reservoir, Israel. Mar Drugs 2017; 15:md15120371. [PMID: 29194403 PMCID: PMC5742831 DOI: 10.3390/md15120371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 01/13/2023] Open
Abstract
Two new natural products, micropeptin TR1058 (1) and aeruginosin TR642 (2), were isolated from the hydrophilic extract of bloom material of Microcystis sp. collected from the Timurim water reservoir in Israel. The structures of compounds 1 and 2 were determined using 1D and 2D NMR spectroscopy and HR ESI MS and MS/MS techniques. Micropeptin TR1058 (1) was extremely unstable under the isolation conditions, and several degradation products were identified. NMR analysis of aeruginosin TR642 (2) revealed a mixture of eight isomers, and elucidation of its structure was challenging. Aeruginosin TR642 contains a 4,5-didehydroaraginal subunit that has not been described before. Micropeptin TR1058 (1) inhibited chymotrypsin with an IC50 of 6.78 µM, and aeruginosin TR642 (2) inhibited trypsin and thrombin with inhibition concentration (IC50) values of 3.80 and 0.85 µM, respectively. The structures and biological activities of the new compounds are discussed.
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43
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Pancrace C, Jokela J, Sassoon N, Ganneau C, Desnos-Ollivier M, Wahlsten M, Humisto A, Calteau A, Bay S, Fewer DP, Sivonen K, Gugger M. Rearranged Biosynthetic Gene Cluster and Synthesis of Hassallidin E in Planktothrix serta PCC 8927. ACS Chem Biol 2017; 12:1796-1804. [PMID: 28489343 DOI: 10.1021/acschembio.7b00093] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria produce a wide range of natural products with antifungal bioactivity. The cyclic glycosylated lipopeptides of the hassallidin family have potent antifungal activity and display a great degree of chemical diversity. Here, we report the discovery of a hassallidin biosynthetic gene cluster from the filamentous cyanobacterium Planktothrix serta PCC 8927. The hassallidin gene cluster showed heavy rearrangement and marks of genomic plasticity. Nucleotide bias, differences in GC content, and phylogenetic incongruence suggested the acquisition of the hassallidin biosynthetic gene cluster in Planktothrix serta PCC 8927 by horizontal gene transfer. Chemical analyses by liquid chromatography and mass spectrometry demonstrated that this strain produced hassallidin E, a new glycosylated hassallidin variant. Hassallidin E was the only structural variant produced by Planktothrix serta PCC 8927 in all tested conditions. Further evaluated on human pathogenic fungi, hassallidin E showed an antifungal bioactivity. Hassallidin production levels correlated with nitrogen availability, in the only nitrogen-fixing Planktothrix described so far. Our results provide insights into the distribution and chemical diversity of cyanobacterial antifungal compounds as well as raise questions on their ecological relevance.
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Affiliation(s)
- Claire Pancrace
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06,
UPEC, UDD, CNRS, INRA, IRD, IEES-Paris, Paris, France
| | - Jouni Jokela
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | | | - Christelle Ganneau
- Institut Pasteur, Unit Chemistry of Biomolecules, Paris, France
- CNRS UMR 3523, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur/CNRS URA3012, National Refence Center
for Invasive Mycoses and Antifungals, Molecular Mycology Unit, Paris, France
| | - Matti Wahlsten
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Anu Humisto
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Alexandra Calteau
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Genoscope/CNRS,
UMR 8030, Laboratoire d’Analyse Bioinformatique en Génomique
et Métabolisme, Evry, France
| | - Sylvie Bay
- Institut Pasteur, Unit Chemistry of Biomolecules, Paris, France
- CNRS UMR 3523, Paris, France
| | - David P. Fewer
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Kaarina Sivonen
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Muriel Gugger
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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Haruštiaková D, Welker M. Chemotype diversity in Planktothrix rubescens (cyanobacteria) populations is correlated to lake depth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:158-168. [PMID: 28085220 DOI: 10.1111/1758-2229.12519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
The cyanobacterial species Planktothrix rubescens is known to preferably inhabit deep, stratified, oligo- to mesotrophic lakes. It is also known for the production of diverse bioactive peptides, including the hepatotoxic microcystins. A number of studies showed that P. rubescens populations generally consist of multiple distinct genotypes or chemotypes, respectively. In the present study, variability of chemotype diversity was analysed. Filaments of P. rubescens were isolated from water samples originating from 10 European lakes and analysed by MALDI-TOF mass spectrometry. In most of the analysed filaments multiple peptides belonging to multiple peptide classes could be detected. A resulting data matrix of 964 filaments and 37 individual peptides was subjected to correspondence analysis and K-means clustering. From the latter analysis the distribution of chemotypes among the lakes was established and diversity estimated by computing Shannon-Indices. Diversity varied strongly among lakes with the lowest diversity found in non-alpine lakes. Further, chemotype diversity was strongly correlated to the maximum depth of the sampled lakes in alpine and non-alpine lakes. The possible influence of both factors, geographic isolation and water column depth, on the observed patterns of chemotype diversity of P. rubescens populations is discussed.
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Affiliation(s)
- Danka Haruštiaková
- Institute of Biostatistics and Analysis, Masaryk University, Kamenice 126/3, Brno, 625 00, Czech Republic
| | - Martin Welker
- Institute of Chemistry, Technische Universität Berlin, Franklinstr 29, Berlin, 12587, Germany
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Liaimer A, Jensen JB, Dittmann E. A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L. Front Microbiol 2016; 7:1693. [PMID: 27847500 PMCID: PMC5088731 DOI: 10.3389/fmicb.2016.01693] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/10/2016] [Indexed: 12/04/2022] Open
Abstract
Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
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Affiliation(s)
- Anton Liaimer
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of NorwayTromsø, Norway
| | - John B. Jensen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of NorwayTromsø, Norway
| | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of PotsdamPotsdam, Germany
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Nakashima Y, Egami Y, Kimura M, Wakimoto T, Abe I. Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'. PLoS One 2016; 11:e0164468. [PMID: 27732651 PMCID: PMC5061366 DOI: 10.1371/journal.pone.0164468] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an ‘Entotheonella’ sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.
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Affiliation(s)
- Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoko Egami
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Miki Kimura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
- * E-mail: (TW); (IA)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (TW); (IA)
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48
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Dittmann E, Gugger M, Sivonen K, Fewer DP. Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria. Trends Microbiol 2016; 23:642-652. [PMID: 26433696 DOI: 10.1016/j.tim.2015.07.008] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/07/2015] [Accepted: 07/17/2015] [Indexed: 10/23/2022]
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms.
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Affiliation(s)
- Elke Dittmann
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, Golm, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - David P Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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D'Agostino PM, Woodhouse JN, Makower AK, Yeung ACY, Ongley SE, Micallef ML, Moffitt MC, Neilan BA. Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:3-13. [PMID: 26663762 DOI: 10.1111/1758-2229.12366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/10/2015] [Accepted: 12/05/2015] [Indexed: 06/05/2023]
Abstract
A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist.
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Affiliation(s)
- Paul M D'Agostino
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - Jason N Woodhouse
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - A Katharina Makower
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, 14476, Germany
| | - Anna C Y Yeung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - Sarah E Ongley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - Melinda L Micallef
- School of Science and Health, University of Western Sydney, Sydney, NSW, 2571, Australia
| | - Michelle C Moffitt
- School of Science and Health, University of Western Sydney, Sydney, NSW, 2571, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
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50
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Qiu X, Xu C, Chen X. Crystallographic analysis of a cupin superfamily enzyme from Microcystis aeruginosa involved in aeruginosin biosynthesis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1511-5. [PMID: 26625293 DOI: 10.1107/s2053230x15021937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 11/17/2015] [Indexed: 11/11/2022]
Abstract
Aeruginosins are a class of cyanobacteria-derived bioactive linear tetrapeptides composed of nonproteinogenic amino-acid residues, such as the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety, which is the hallmark of aeruginosin. The biosynthetic pathway of the Choi moiety remains elusive. Previous studies have suggested that AerE, a protein that possesses two cupin domains, participates in the biosynthesis of the Choi moiety. In this study, recombinant AerE from Microcystis aeruginosa, which was overexpressed in Escherichia coli and purified by Ni(2+)-chelating affinity and gel-filtration chromatography, was successfully crystallized and X-ray diffraction analysis was performed. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 34.770, b = 62.133, c = 87.401 Å. The diffraction data from the crystal were scaled to a maximum resolution of 1.60 Å. The calculated Matthews coefficient of the crystal is 1.93 Å(3) Da(-1), suggesting that there is one molecule in the asymmetric unit.
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Affiliation(s)
- Xiaoting Qiu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Cui Xu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Xu Chen
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
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