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Zaheri B, Morse D. An overview of transcription in dinoflagellates. Gene 2022; 829:146505. [PMID: 35447242 DOI: 10.1016/j.gene.2022.146505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 02/18/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Dinoflagellates are a vital diverse family of unicellular algae widespread in various aquatic environments. Typically large genomes and permanently condensed chromosomes without histones make these organisms unique among eukaryotes in terms of chromatin structure and gene expression. Genomic and transcriptomic sequencing projects have provided new insight into the genetic foundation of dinoflagellate behaviors. Genes in tandem arrays, trans-splicing of mRNAs and lower levels of transcriptional regulation compared to other eukaryotes all contribute to the differences seen. Here we present a general overview of transcription in dinoflagellates based on previously described work.
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Affiliation(s)
- Bahareh Zaheri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada.
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2
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Wang H, Kim H, Ki JS. Transcriptome survey and toxin measurements reveal evolutionary modification and loss of saxitoxin biosynthesis genes in the dinoflagellates Amphidinium carterae and Prorocentrum micans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110474. [PMID: 32200147 DOI: 10.1016/j.ecoenv.2020.110474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
In the present study, we characterized the potential toxin genes for polyketide synthase (PKS) and saxitoxin (STX) biosynthesis using the transcriptomes of two non-STX producing dinoflagellates Amphidinium carterae and Prorocentrum micans. RNA sequencing revealed 94 and 166 PKS contigs in A. carterae and P. micans, respectively. We first detected type III PKS, which was closely related to bacteria. In addition, dozens of homologs of 20 STX biosynthesis genes were identified. Interestingly, the core STX-synthesizing genes sxtA and sxtB were only found in P. micans, whereas sxtD was detected in A. carterae alone. Bioinformatic analysis showed that the first two core genes (sxtA and sxtG) had a low sequence similarity (37.0-67.6%) and different domain organization compared to those of other toxigenic dinoflagellates, such as Alexandrium pacificum. These might result in the breakdown of the initial reactions in STX production and ultimately the loss of the ability to synthesize the toxins in both dinoflagellates. Our findings suggest that toxin-related PKS and sxt genes are commonly found in non-STX producing dinoflagellates. In addition to their involvement in the synthesis of toxins, our result indicates that genes may also have other molecular metabolic functions.
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Affiliation(s)
- Hui Wang
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Hansol Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea.
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3
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Wang H, Guo R, Lim WA, Allen AE, Ki JS. Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum. HARMFUL ALGAE 2020; 93:101777. [PMID: 32307068 DOI: 10.1016/j.hal.2020.101777] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 06/11/2023]
Abstract
In the present study, we extensively characterized potential toxin-related genes, including polyketide synthase (PKS), saxitoxin (STX) and fatty acid synthase (FAS) from the non-toxin producing marine dinoflagellate Cochlodinium polykrikoides, comparing to those of a toxigenic dinoflagellate Alexandrium pacificum. RNA sequencing revealed 50 and 271 PKS contigs from C. polykrikoides and A. pacificum, respectively. According to domain constitute and amino acid alteration, we further classified the dinoflagellate type I PKS genes into 4 sub-groups. Type III PKS was first identified in C. polykrikoides. Interestingly, we detected a large number (242 and 288) of homologs of 18 sxt genes from two studied dinoflagellates. Most of the eight key genes (sxtA, sxtB, sxtD, sxtG, sxtH/T, sxtI, sxtS and sxtU) for STX synthesis were detected in both dinoflatellates, whereas a core STX biosynthesis gene sxtG was not detected in C. polykrikoides. This may partially explain the absence of saxitoxin production in C. polykrikoides. In addition, we identified several type I and type II FAS genes, including FabD, FabF, FabG, FabH, FabI, and FabZ, whereas FabB was not found in C. polykrikoides. Overall, the numbers of the toxin-related genes in C. polykrikoides were less than that of A. pacificum. Phylogenetic analyses showed that type I PKS/FASs of dinoflagellates had close relationships with apicomplexans and bacteria. These suggest that the toxin-related PKS and sxt genes are commonly present in toxigenic and non-toxin producing dinoflagellates, and may be involved not only in the toxin synthesis, but also in other related molecular metabolic functions.
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Affiliation(s)
- Hui Wang
- Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea
| | - Ruoyu Guo
- Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea; Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, PR China
| | - Weol-Ae Lim
- Ocean Climate and Ecology Research Division, National Institute of Fisheries Science (NIFS), Busan 46083, South Korea
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA; Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea.
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4
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Wan X, Yao G, Liu Y, Chen J, Jiang H. Research Progress in the Biosynthetic Mechanisms of Marine Polyether Toxins. Mar Drugs 2019; 17:E594. [PMID: 31652489 PMCID: PMC6835853 DOI: 10.3390/md17100594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/28/2022] Open
Abstract
Marine polyether toxins, mainly produced by marine dinoflagellates, are novel, complex, and diverse natural products with extensive toxicological and pharmacological effects. Owing to their harmful effects during outbreaks of marine red tides, as well as their potential value for the development of new drugs, marine polyether toxins have been extensively studied, in terms of toxicology, pharmacology, detection, and analysis, structural identification, as well as their biosynthetic mechanisms. Although the biosynthetic mechanisms of marine polyether toxins are still unclear, certain progress has been made. In this review, research progress and current knowledge on the biosynthetic mechanisms of polyether toxins are summarized, including the mechanisms of carbon skeleton deletion, pendant alkylation, and polyether ring formation, along with providing a summary of mined biosynthesis-related genes. Finally, future research directions and applications of marine polyether toxins are discussed.
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Affiliation(s)
- Xiukun Wan
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Yanli Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Jisheng Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
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5
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Verma A, Kohli GS, Harwood DT, Ralph PJ, Murray SA. Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species. Environ Microbiol 2019; 21:4196-4211. [PMID: 31415128 DOI: 10.1111/1462-2920.14780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 12/01/2022]
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth. Their ecological success may be related to their production of complex toxic polyketide compounds. Ostreopsis species produce potent palytoxin-like compounds (PLTX), which are associated with human skin and eye irritations, and illnesses through the consumption of contaminated seafood. To investigate the genetic basis of PLTX-like compounds, we sequenced and annotated transcriptomes from two PLTX-producing Ostreopsis species; O. cf. ovata, O. cf. siamensis, one non-PLTX producing species, O. rhodesae and compared them to a close phylogenetic relative and non-PLTX producer, Coolia malayensis. We found no clear differences in the presence or diversity of ketosynthase and ketoreductase transcripts between PLTX producing and non-producing Ostreopsis and Coolia species, as both groups contained >90 and > 10 phylogenetically diverse ketosynthase and ketoreductase transcripts, respectively. We report for the first-time type I single-, multi-domain polyketide synthases (PKSs) and hybrid non-ribosomal peptide synthase/PKS transcripts from all species. The long multi-modular PKSs were insufficient by themselves to synthesize the large complex polyether backbone of PLTX-like compounds. This implies that numerous PKS domains, including both single and multi-, work together on the biosynthesis of PLTX-like and other related polyketide compounds.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Gurjeet S Kohli
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia.,Alfred-Wegener-Institute Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, 27515, Germany
| | - D Tim Harwood
- Cawthron Institute, 98, Halifax Street East, Nelson, 7010, New Zealand
| | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
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6
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Verma A, Barua A, Ruvindy R, Savela H, Ajani PA, Murray SA. The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms 2019; 7:E222. [PMID: 31362398 PMCID: PMC6722697 DOI: 10.3390/microorganisms7080222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023] Open
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia.
| | - Abanti Barua
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
- Department of Microbiology, Noakhali Science and Technology University, Chittagong 3814, Bangladesh
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, 00790 Helsinki, Finland
| | - Penelope A Ajani
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
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7
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Beedessee G, Hisata K, Roy MC, Van Dolah FM, Satoh N, Shoguchi E. Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates. Sci Rep 2019; 9:1204. [PMID: 30718591 PMCID: PMC6361889 DOI: 10.1038/s41598-018-37792-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/13/2018] [Indexed: 11/09/2022] Open
Abstract
Symbiodiniaceae dinoflagellates possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Till date, little is known about the evolution of secondary metabolism in dinoflagellates as comparative genomic approaches have been hampered by their large genome sizes. Here, we overcome this challenge by combining genomic and metabolomics approaches to investigate how chemical diversity arises in three decoded Symbiodiniaceae genomes (clades A3, B1 and C). Our analyses identify extensive diversification of polyketide synthase and non-ribosomal peptide synthetase genes from two newly decoded genomes of Symbiodinium tridacnidorum (A3) and Cladocopium sp. (C). Phylogenetic analyses indicate that almost all the gene families are derived from lineage-specific gene duplications in all three clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.
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Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Frances M Van Dolah
- College of Charleston, School of Sciences and Mathematics, 66 George St., Charleston, South Carolina, 29424, USA
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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8
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Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F, Bittner L. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol Ecol 2018; 27:2365-2380. [PMID: 29624751 DOI: 10.1111/mec.14579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/23/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023]
Abstract
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated with functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g., sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of, respectively, the toxic and symbiotic species represented in our analyses. Of these, 56% and 57%, respectively (i.e., 25,393 and 52,193 pCDs), completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
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Affiliation(s)
- Arnaud Meng
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique, Roscoff, France
| | - Ian Probert
- UPMC-CNRS, FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | | | - Raffaele Siano
- Ifremer - Centre de Brest, DYNECO PELAGOS, Plouzané, France
| | - Anita Annamale
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Adriana Alberti
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Corinne Da Silva
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
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9
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Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2018. [DOI: 10.3390/jmse6010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Van Dolah FM, Kohli GS, Morey JS, Murray SA. Both modular and single-domain Type I polyketide synthases are expressed in the brevetoxin-producing dinoflagellate, Karenia brevis (Dinophyceae). JOURNAL OF PHYCOLOGY 2017; 53:1325-1339. [PMID: 28949419 PMCID: PMC5725682 DOI: 10.1111/jpy.12586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/14/2017] [Indexed: 05/09/2023]
Abstract
Dinoflagellates are prolific producers of polyketide compounds, many of which are potent toxins with adverse impacts on human and marine animal health. To identify polyketide synthase (PKS) genes in the brevetoxin-producing dinoflagellate, Karenia brevis, we assembled a transcriptome from 595 million Illumina reads, sampled under different growth conditions. The assembly included 125,687 transcripts greater than 300 nt in length, with over half having >100× coverage. We found 121 transcripts encoding Type I ketosynthase (KS) domains, of which 99 encoded single KS domains, while 22 contained multiple KS domains arranged in 1-3 protein modules. Phylogenetic analysis placed all single domain and a majority of multidomain KSs within a monophyletic clade of protist PKSs. In contrast with the highly amplified single-domain KSs, only eight single-domain ketoreductase transcripts were found in the assembly, suggesting that they are more evolutionarily conserved. The multidomain PKSs were dominated by trans-acyltransferase architectures, which were recently shown to be prevalent in other algal protists. Karenia brevis also expressed several hybrid nonribosomal peptide synthetase (NRPS)/PKS sequences, including a burA-like sequence previously reported in a wide variety of dinoflagellates. This contrasts with a similarly deep transcriptome of Gambierdiscus polynesiensis, which lacked NRPS/PKS other than the burA-like transcript, and may reflect the presence of amide-containing polyketides in K. brevis and their absence from G. polynesiensis. In concert with other recent transcriptome analyses, this study provides evidence for both single domain and multidomain PKSs in the synthesis of polyketide compounds in dinoflagellates.
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Affiliation(s)
- Frances M. Van Dolah
- College of CharlestonSchool of Sciences and Mathematics66 George St.CharlestonSouth Carolina29424USA
- Hollings Marine Laboratory331 Fort Johnson Rd.CharlestonSouth Carolina29412USA
| | - Gurjeet S. Kohli
- Climate Change ClusterUniversity of Technology Sydney15 Broadway, UltimoSydneyNew South Wales2007Australia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingapore689528
| | - Jeanine S. Morey
- Hollings Marine Laboratory331 Fort Johnson Rd.CharlestonSouth Carolina29412USA
- JHT Incorporated2710 Discovery Dr.OrlandoFlorida32826USA
| | - Shauna A. Murray
- Climate Change ClusterUniversity of Technology Sydney15 Broadway, UltimoSydneyNew South Wales2007Australia
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11
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Zhang Y, Zhang SF, Lin L, Wang DZ. Whole Transcriptomic Analysis Provides Insights into Molecular Mechanisms for Toxin Biosynthesis in a Toxic Dinoflagellate Alexandrium catenella (ACHK-T). Toxins (Basel) 2017; 9:E213. [PMID: 28678186 PMCID: PMC5535160 DOI: 10.3390/toxins9070213] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 11/25/2022] Open
Abstract
Paralytic shellfish toxins (PSTs), a group of neurotoxic alkaloids, are the most potent biotoxins for aquatic ecosystems and human health. Marine dinoflagellates and freshwater cyanobacteria are two producers of PSTs. The biosynthesis mechanism of PSTs has been well elucidated in cyanobacteria; however, it remains ambiguous in dinoflagellates. Here, we compared the transcriptome profiles of a toxin-producing dinoflagellate Alexandrium catenella (ACHK-T) at different toxin biosynthesis stages within the cell cycle using RNA-seq. The intracellular toxin content increased gradually in the middle G1 phase and rapidly in the late G1 phase, and then remained relatively stable in other phases. Samples from four toxin biosynthesis stages were selected for sequencing, and finally yielded 110,370 unigenes, of which 66,141 were successfully annotated in the known databases. An analysis of differentially expressed genes revealed that 2866 genes altered significantly and 297 were co-expressed throughout the four stages. These genes participated mainly in protein metabolism, carbohydrate metabolism, and the oxidation-reduction process. A total of 138 homologues of toxin genes were identified, but they altered insignificantly among different stages, indicating that toxin biosynthesis might be regulated translationally or post-translationally. Our results will serve as an important transcriptomic resource to characterize key molecular processes underlying dinoflagellate toxin biosynthesis.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Shu-Fei Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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12
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Kohli GS, Campbell K, John U, Smith KF, Fraga S, Rhodes LL, Murray SA. Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae). J Eukaryot Microbiol 2017; 64:691-706. [PMID: 28211202 DOI: 10.1111/jeu.12405] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
Gambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s-malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I PKS and type II FAS genes were distinguished based on the arrangement of domains on the contigs and their sequence similarity and phylogenetic clustering with known PKS/FAS genes in other organisms. This differentiation of PKS and FAS pathways in Gambierdiscus is important, as it will facilitate approaches to investigating toxin biosynthesis pathways in dinoflagellates.
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Affiliation(s)
- Gurjeet S Kohli
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 689528, Singapore
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, United Kingdom
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, 27515, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, 26111, Germany
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Santiago Fraga
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Lesley L Rhodes
- Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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Kohli GS, John U, Van Dolah FM, Murray SA. Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes. ISME JOURNAL 2016; 10:1877-90. [PMID: 26784357 PMCID: PMC5029157 DOI: 10.1038/ismej.2015.263] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/18/2015] [Accepted: 12/07/2015] [Indexed: 11/09/2022]
Abstract
Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success.
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Affiliation(s)
- Gurjeet S Kohli
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia.,Sydney Institute of Marine Sciences, Mosman, New South Wales, Australia
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Frances M Van Dolah
- Marine Biotoxins Program, National Oceanic and Atmospheric Administration Center for Coastal and Environmental Health and Biomolecular Research, Charleston, SC, USA
| | - Shauna A Murray
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia.,Sydney Institute of Marine Sciences, Mosman, New South Wales, Australia
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Beedessee G, Hisata K, Roy MC, Satoh N, Shoguchi E. Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum. BMC Genomics 2015; 16:941. [PMID: 26573520 PMCID: PMC4647583 DOI: 10.1186/s12864-015-2195-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/05/2015] [Indexed: 11/17/2022] Open
Abstract
Background Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5–245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only recently have dinoflagellate polyketides been investigated. Transcriptomic analyses have characterized dinoflagellate polyketide synthase genes having single domains. The Genus Symbiodinium, with a comparatively small genome, is a group of major coral symbionts, and the S. minutum nuclear genome has been decoded. Results The present survey investigated the assembled S. minutum genome and identified 25 candidate polyketide synthase (PKS) genes that encode proteins with mono- and multifunctional domains. Predicted proteins retain functionally important amino acids in the catalytic ketosynthase (KS) domain. Molecular phylogenetic analyses of KS domains form a clade in which S. minutum domains cluster within the protist Type I PKS clade with those of other dinoflagellates and other eukaryotes. Single-domain PKS genes are likely expanded in dinoflagellate lineage. Two PKS genes of bacterial origin are found in the S. minutum genome. Interestingly, the largest enzyme is likely expressed as a hybrid non-ribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly of 10,601 amino acids, containing NRPS and PKS modules and a thioesterase (TE) domain. We also found intron-rich genes with the minimal set of catalytic domains needed to produce polyketides. Ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP) along with other optional domains are present. Mapping of transcripts to the genome with the dinoflagellate-specific spliced leader sequence, supports expression of multifunctional PKS genes. Metabolite profiling of cultured S. minutum confirmed production of zooxanthellamide D, a polyhydroxy amide polyketide and other unknown polyketide secondary metabolites. Conclusion This genomic survey demonstrates that S. minutum contains genes with the minimal set of catalytic domains needed to produce polyketides and provides evidence of the modular nature of Type I PKS, unlike monofunctional Type I PKS from other dinoflagellates. In addition, our study suggests that diversification of dinoflagellate PKS genes comprises dinoflagellate-specific PKS genes with single domains, multifunctional PKS genes with KS domains orthologous to those of other protists, and PKS genes of bacterial origin. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2195-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Michael C Roy
- Imaging and Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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Kimura K, Okuda S, Nakayama K, Shikata T, Takahashi F, Yamaguchi H, Skamoto S, Yamaguchi M, Tomaru Y. RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi. PLoS One 2015; 10:e0142731. [PMID: 26561394 PMCID: PMC4641656 DOI: 10.1371/journal.pone.0142731] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 10/26/2015] [Indexed: 12/03/2022] Open
Abstract
The dinoflagellate Karenia mikimotoi forms blooms in the coastal waters of temperate regions and occasionally causes massive fish and invertebrate mortality. This study aimed to elucidate the toxic effect of K. mikimotoi on marine organisms by using the genomics approach; RNA-sequence libraries were constructed, and data were analyzed to identify toxin-related genes. Next-generation sequencing produced 153,406 transcript contigs from the axenic culture of K. mikimotoi. BLASTX analysis against all assembled contigs revealed that 208 contigs were polyketide synthase (PKS) sequences. Thus, K. mikimotoi was thought to have several genes encoding PKS metabolites and to likely produce toxin-like polyketide molecules. Of all the sequences, approximately 30 encoded eight PKS genes, which were remarkably similar to those of Karenia brevis. Our phylogenetic analyses showed that these genes belonged to a new group of PKS type-I genes. Phylogenetic and active domain analyses showed that the amino acid sequence of four among eight Karenia PKS genes was not similar to any of the reported PKS genes. These PKS genes might possibly be associated with the synthesis of polyketide toxins produced by Karenia species. Further, a homology search revealed 10 contigs that were similar to a toxin gene responsible for the synthesis of saxitoxin (sxtA) in the toxic dinoflagellate Alexandrium fundyense. These contigs encoded A1-A3 domains of sxtA genes. Thus, this study identified some transcripts in K. mikimotoi that might be associated with several putative toxin-related genes. The findings of this study might help understand the mechanism of toxicity of K. mikimotoi and other dinoflagellates.
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Affiliation(s)
- Kei Kimura
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, 1–757 Asahimachi-dori, Chuo-ku, Niigata, Japan
| | - Kei Nakayama
- Center for Marine Environmental Studies (CMES), Ehime University, 2–5 Bunkyo-cho, Matsuyama, Ehime, Japan
| | - Tomoyuki Shikata
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
| | - Fumio Takahashi
- Department of Biotechnology, College of Life Sciences, Rhitsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, Japan
| | - Haruo Yamaguchi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, 200, Monobe, Nankoku, Kochi, Japan
| | - Setsuko Skamoto
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
| | - Mineo Yamaguchi
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
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Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae). BMC Genomics 2015; 16:410. [PMID: 26016672 PMCID: PMC4445524 DOI: 10.1186/s12864-015-1625-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Marine microbial protists, in particular, dinoflagellates, produce polyketide toxins with ecosystem-wide and human health impacts. Species of Gambierdiscus produce the polyether ladder compounds ciguatoxins and maitotoxins, which can lead to ciguatera fish poisoning, a serious human illness associated with reef fish consumption. Genes associated with the biosynthesis of polyether ladder compounds are yet to be elucidated, however, stable isotope feeding studies of such compounds consistently support their polyketide origin indicating that polyketide synthases are involved in their biosynthesis. Results Here, we report the toxicity, genome size, gene content and transcriptome of Gambierdiscus australes and G. belizeanus. G. australes produced maitotoxin-1 and maitotoxin-3, while G. belizeanus produced maitotoxin-3, for which cell extracts were toxic to mice by IP injection (LD50 = 3.8 mg kg-1). The gene catalogues comprised 83,353 and 84,870 unique contigs, with genome sizes of 32.5 ± 3.7 Gbp and 35 ± 0.88 Gbp, respectively, and are amongst the most comprehensive yet reported from a dinoflagellate. We found three hundred and six genes involved in polyketide biosynthesis, including one hundred and ninty-two ketoacyl synthase transcripts, which formed five unique phylogenetic clusters. Conclusions Two clusters were unique to these maitotoxin-producing dinoflagellate species, suggesting that they may be associated with maitotoxin biosynthesis. This work represents a significant step forward in our understanding of the genetic basis of polyketide production in dinoflagellates, in particular, species responsible for ciguatera fish poisoning. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1625-y) contains supplementary material, which is available to authorized users.
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Perini F, Galluzzi L, Dell'Aversano C, Iacovo ED, Tartaglione L, Ricci F, Forino M, Ciminiello P, Penna A. SxtA and sxtG gene expression and toxin production in the Mediterranean Alexandrium minutum (Dinophyceae). Mar Drugs 2014; 12:5258-76. [PMID: 25341029 PMCID: PMC4210898 DOI: 10.3390/md12105258] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/23/2014] [Accepted: 10/15/2014] [Indexed: 01/18/2023] Open
Abstract
The dinoflagellate Alexandrium minutum is known for the production of potent neurotoxins affecting the health of human seafood consumers via paralytic shellfish poisoning (PSP). The aim of this study was to investigate the relationship between the toxin content and the expression level of the genes involved in paralytic shellfish toxin (PST) production. The algal cultures were grown both in standard f/2 medium and in phosphorus/nitrogen limitation. In our study, LC-HRMS analyses of PST profile and content in different Mediterranean A.minutum strains confirmed that this species was able to synthesize mainly the saxitoxin analogues Gonyautoxin-1 (GTX1) and Gonyautoxin-4 (GTX4). The average cellular toxin content varied among different strains, and between growth phases, highlighting a decreasing trend from exponential to stationary phase in all culture conditions tested. The absolute quantities of intracellular sxtA1 and sxtG mRNA were not correlated with the amount of intracellular toxins in the analysed A. minutum suggesting that the production of toxins may be regulated by post-transcriptional mechanisms and/or by the concerted actions of alternative genes belonging to the PST biosynthesis gene cluster. Therefore, it is likely that the sxtA1 and sxtG gene expression could not reflect the PST accumulation in the Mediterranean A. minutum populations under the examined standard and nutrient limiting conditions.
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Affiliation(s)
- Federico Perini
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro 61121, Italy.
| | - Luca Galluzzi
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro 61121, Italy.
| | - Carmela Dell'Aversano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy.
| | - Emma Dello Iacovo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy.
| | - Luciana Tartaglione
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy.
| | - Fabio Ricci
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro 61121, Italy.
| | - Martino Forino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy.
| | - Patrizia Ciminiello
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy.
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro 61121, Italy.
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18
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Comparative transcriptome analysis of four prymnesiophyte algae. PLoS One 2014; 9:e97801. [PMID: 24926657 PMCID: PMC4057078 DOI: 10.1371/journal.pone.0097801] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/23/2014] [Indexed: 11/25/2022] Open
Abstract
Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists.
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19
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Nett M. Genome mining: concept and strategies for natural product discovery. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2014; 99:199-245. [PMID: 25296440 DOI: 10.1007/978-3-319-04900-7_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Van Dolah FM, Zippay ML, Pezzolesi L, Rein KS, Johnson JG, Morey JS, Wang Z, Pistocchi R. Subcellular localization of dinoflagellate polyketide synthases and fatty acid synthase activity. JOURNAL OF PHYCOLOGY 2013; 49:1118-1127. [PMID: 27007632 DOI: 10.1111/jpy.12120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/25/2013] [Indexed: 06/05/2023]
Abstract
Dinoflagellates are prolific producers of polyketide secondary metabolites. Dinoflagellate polyketide synthases (PKSs) have sequence similarity to Type I PKSs, megasynthases that encode all catalytic domains on a single polypeptide. However, in dinoflagellate PKSs identified to date, each catalytic domain resides on a separate transcript, suggesting multiprotein complexes similar to Type II PKSs. Here, we provide evidence through coimmunoprecipitation that single-domain ketosynthase and ketoreductase proteins interact, suggesting a predicted multiprotein complex. In Karenia brevis (C.C. Davis) Gert Hansen & Ø. Moestrup, previously observed chloroplast localization of PKSs suggested that brevetoxin biosynthesis may take place in the chloroplast. Here, we report that PKSs are present in both cytosol and chloroplast. Furthermore, brevetoxin is not present in isolated chloroplasts, raising the question of what chloroplast-localized PKS enzymes might be doing. Antibodies to K. brevis PKSs recognize cytosolic and chloroplast proteins in Ostreopsis cf. ovata Fukuyo, and Coolia monotis Meunier, which produce different suites of polyketide toxins, suggesting that these PKSs may share common pathways. Since PKSs are closely related to fatty acid synthases (FAS), we sought to determine if fatty acid biosynthesis colocalizes with either chloroplast or cytosolic PKSs. [(3) H]acetate labeling showed fatty acids are synthesized in the cytosol, with little incorporation in chloroplasts, consistent with a Type I FAS system. However, although 29 sequences in a K. brevis expressed sequence tag database have similarity (BLASTx e-value <10(-10) ) to PKSs, no transcripts for either Type I (cytosolic) or Type II (chloroplast) FAS are present. Further characterization of the FAS complexes may help to elucidate the functions of the PKS enzymes identified in dinoflagellates.
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Affiliation(s)
- Frances M Van Dolah
- Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, South Carolina, 29412, USA
- Marine Biomedical and Environmental Sciences, Medical University of South Carolina, Charleston, South Carolina, 29412, USA
| | - Mackenzie L Zippay
- Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, South Carolina, 29412, USA
- Marine Biomedical and Environmental Sciences, Medical University of South Carolina, Charleston, South Carolina, 29412, USA
| | - Laura Pezzolesi
- Interdepartmental Research Centre for Environmental Science (CIRSA), University of Bologna, Ravenna, 48123, Italy
| | - Kathleen S Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, USA
| | - Jillian G Johnson
- Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, South Carolina, 29412, USA
- Marine Biomedical and Environmental Sciences, Medical University of South Carolina, Charleston, South Carolina, 29412, USA
| | - Jeanine S Morey
- Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, South Carolina, 29412, USA
| | - Zhihong Wang
- Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, South Carolina, 29412, USA
| | - Rossella Pistocchi
- Interdepartmental Research Centre for Environmental Science (CIRSA), University of Bologna, Ravenna, 48123, Italy
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21
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Transcription and Maturation of mRNA in Dinoflagellates. Microorganisms 2013; 1:71-99. [PMID: 27694765 PMCID: PMC5029490 DOI: 10.3390/microorganisms1010071] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/10/2013] [Accepted: 10/14/2013] [Indexed: 01/17/2023] Open
Abstract
Dinoflagellates are of great importance to the marine ecosystem, yet scant details of how gene expression is regulated at the transcriptional level are available. Transcription is of interest in the context of the chromatin structure in the dinoflagellates as it shows many differences from more typical eukaryotic cells. Here we canvas recent transcriptome profiles to identify the molecular building blocks available for the construction of the transcriptional machinery and contrast these with those used by other systems. Dinoflagellates display a clear paucity of specific transcription factors, although surprisingly, the rest of the basic transcriptional machinery is not markedly different from what is found in the close relatives to the dinoflagellates.
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Orr RJS, Stüken A, Murray SA, Jakobsen KS. Evolution and distribution of saxitoxin biosynthesis in dinoflagellates. Mar Drugs 2013; 11:2814-28. [PMID: 23966031 PMCID: PMC3766867 DOI: 10.3390/md11082814] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/16/2022] Open
Abstract
Numerous species of marine dinoflagellates synthesize the potent environmental neurotoxic alkaloid, saxitoxin, the agent of the human illness, paralytic shellfish poisoning. In addition, certain freshwater species of cyanobacteria also synthesize the same toxic compound, with the biosynthetic pathway and genes responsible being recently reported. Three theories have been postulated to explain the origin of saxitoxin in dinoflagellates: The production of saxitoxin by co-cultured bacteria rather than the dinoflagellates themselves, convergent evolution within both dinoflagellates and bacteria and horizontal gene transfer between dinoflagellates and bacteria. The discovery of cyanobacterial saxitoxin homologs in dinoflagellates has enabled us for the first time to evaluate these theories. Here, we review the distribution of saxitoxin within the dinoflagellates and our knowledge of its genetic basis to determine the likely evolutionary origins of this potent neurotoxin.
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Affiliation(s)
- Russell J. S. Orr
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Anke Stüken
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
| | - Shauna A. Murray
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, PO Box 123 Broadway, NSW 2007, Australia; E-Mail:
- Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Kjetill S. Jakobsen
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +47-22854602; Fax: +47-22854001
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Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans. Prog Lipid Res 2013; 52:488-512. [PMID: 23827884 DOI: 10.1016/j.plipres.2013.06.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 06/16/2013] [Accepted: 06/17/2013] [Indexed: 12/22/2022]
Abstract
Lipid metabolism is of crucial importance for pathogens. Lipids serve as cellular building blocks, signalling molecules, energy stores, posttranslational modifiers, and pathogenesis factors. Parasites rely on a complex system of uptake and synthesis mechanisms to satisfy their lipid needs. The parameters of this system change dramatically as the parasite transits through the various stages of its life cycle. Here we discuss the tremendous recent advances that have been made in the understanding of the synthesis and uptake pathways for fatty acids and phospholipids in apicomplexan and kinetoplastid parasites, including Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania. Lipid synthesis differs in significant ways between parasites from both phyla and the human host. Parasites have acquired novel pathways through endosymbiosis, as in the case of the apicoplast, have dramatically reshaped substrate and product profiles, and have evolved specialized lipids to interact with or manipulate the host. These differences potentially provide opportunities for drug development. We outline the lipid pathways for key species in detail as they progress through the developmental cycle and highlight those that are of particular importance to the biology of the pathogens and/or are the most promising targets for parasite-specific treatment.
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An overview on the marine neurotoxin, saxitoxin: genetics, molecular targets, methods of detection and ecological functions. Mar Drugs 2013; 11:991-1018. [PMID: 23535394 PMCID: PMC3705384 DOI: 10.3390/md11040991] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/17/2013] [Accepted: 02/19/2013] [Indexed: 11/17/2022] Open
Abstract
Marine neurotoxins are natural products produced by phytoplankton and select species of invertebrates and fish. These compounds interact with voltage-gated sodium, potassium and calcium channels and modulate the flux of these ions into various cell types. This review provides a summary of marine neurotoxins, including their structures, molecular targets and pharmacologies. Saxitoxin and its derivatives, collectively referred to as paralytic shellfish toxins (PSTs), are unique among neurotoxins in that they are found in both marine and freshwater environments by organisms inhabiting two kingdoms of life. Prokaryotic cyanobacteria are responsible for PST production in freshwater systems, while eukaryotic dinoflagellates are the main producers in marine waters. Bioaccumulation by filter-feeding bivalves and fish and subsequent transfer through the food web results in the potentially fatal human illnesses, paralytic shellfish poisoning and saxitoxin pufferfish poisoning. These illnesses are a result of saxitoxin’s ability to bind to the voltage-gated sodium channel, blocking the passage of nerve impulses and leading to death via respiratory paralysis. Recent advances in saxitoxin research are discussed, including the molecular biology of toxin synthesis, new protein targets, association with metal-binding motifs and methods of detection. The eco-evolutionary role(s) PSTs may serve for phytoplankton species that produce them are also discussed.
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25
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Eichholz K, Beszteri B, John U. Putative monofunctional type I polyketide synthase units: a dinoflagellate-specific feature? PLoS One 2012; 7:e48624. [PMID: 23139807 PMCID: PMC3489724 DOI: 10.1371/journal.pone.0048624] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/02/2012] [Indexed: 11/19/2022] Open
Abstract
Marine dinoflagellates (alveolata) are microalgae of which some cause harmful algal blooms and produce a broad variety of most likely polyketide synthesis derived phycotoxins. Recently, novel polyketide synthesase (PKS) transcripts have been described from the Florida red tide dinoflagellate Karenia brevis (gymnodiniales) which are evolutionarily related to Type I PKS but were apparently expressed as monofunctional proteins, a feature typical of Type II PKS. Here, we investigated expression units of PKS I-like sequences in Alexandrium ostenfeldii (gonyaulacales) and Heterocapsa triquetra (peridiniales) at the transcript and protein level. The five full length transcripts we obtained were all characterized by polyadenylation, a 3′ UTR and the dinoflagellate specific spliced leader sequence at the 5′end. Each of the five transcripts encoded a single ketoacylsynthase (KS) domain showing high similarity to K. brevis KS sequences. The monofunctional structure was also confirmed using dinoflagellate specific KS antibodies in Western Blots. In a maximum likelihood phylogenetic analysis of KS domains from diverse PKSs, dinoflagellate KSs formed a clade placed well within the protist Type I PKS clade between apicomplexa, haptophytes and chlorophytes. These findings indicate that the atypical PKS I structure, i.e., expression as putative monofunctional units, might be a dinoflagellate specific feature. In addition, the sequenced transcripts harbored a previously unknown, apparently dinoflagellate specific conserved N-terminal domain. We discuss the implications of this novel region with regard to the putative monofunctional organization of Type I PKS in dinoflagellates.
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Affiliation(s)
- Karsten Eichholz
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Bánk Beszteri
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Uwe John
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- * E-mail:
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