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Fallon TR, Shende VV, Wierzbicki IH, Auber RP, Gonzalez DJ, Wisecaver JH, Moore BS. Giant polyketide synthase enzymes biosynthesize a giant marine polyether biotoxin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577497. [PMID: 38352448 PMCID: PMC10862718 DOI: 10.1101/2024.01.29.577497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Prymnesium parvum are harmful haptophyte algae that cause massive environmental fish-kills. Their polyketide polyether toxins, the prymnesins, are amongst the largest nonpolymeric compounds in nature, alongside structurally-related health-impacting "red-tide" polyether toxins whose biosynthetic origins have been an enigma for over 40 years. Here we report the 'PKZILLAs', massive P. parvum polyketide synthase (PKS) genes, whose existence and challenging genomic structure evaded prior detection. PKZILLA-1 and -2 encode giant protein products of 4.7 and 3.2 MDa with 140 and 99 enzyme domains, exceeding the largest known protein titin and all other known PKS systems. Their predicted polyene product matches the proposed pre-prymnesin precursor of the 90-carbon-backbone A-type prymnesins. This discovery establishes a model system for microalgal polyether biosynthesis and expands expectations of genetic and enzymatic size limits in biology.
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Affiliation(s)
- Timothy R. Fallon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego; 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
| | - Vikram V. Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego; 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
| | - Igor H. Wierzbicki
- Department of Pharmacology, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Robert P. Auber
- Department of Biochemistry, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jennifer H. Wisecaver
- Department of Biochemistry, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego; 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
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Ishida H, John U, Murray SA, Bhattacharya D, Chan CX. Developing model systems for dinoflagellates in the post-genomic era. JOURNAL OF PHYCOLOGY 2023; 59:799-808. [PMID: 37657822 DOI: 10.1111/jpy.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023]
Abstract
Dinoflagellates are a diverse group of eukaryotic microbes that are ubiquitous in aquatic environments. Largely photosynthetic, they encompass symbiotic, parasitic, and free-living lineages with a broad spectrum of trophism. Many free-living taxa can produce bioactive secondary metabolites such as biotoxins, some of which cause harmful algal blooms. In contrast, most symbiotic species are crucial for sustaining coral reef health. The year 2023 marked a decade since the first genome data of dinoflagellates became available. The growing genome-scale resources for these taxa are highlighting their remarkable evolutionary and genomic complexities. Here, we discuss the prospect of developing dinoflagellate models using the criteria of accessibility, tractability, resources, research support, and promise. Moving forward in the post-genomic era, we argue for the development of fit-to-purpose models that tailor to specific biological contexts, and that a one-size-fits-all model is inadequate for encapsulating the complex biology, ecology, and evolutionary history of dinoflagellates.
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Affiliation(s)
- Hisatake Ishida
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Shauna A Murray
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
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3
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Haq S, Oyler BL, Williams E, Khan MM, Goodlett DR, Bachvaroff T, Place AR. Investigating A Multi-Domain Polyketide Synthase in Amphidinium carterae. Mar Drugs 2023; 21:425. [PMID: 37623706 PMCID: PMC10455422 DOI: 10.3390/md21080425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Dinoflagellates are unicellular organisms that are implicated in harmful algal blooms (HABs) caused by potent toxins that are produced through polyketide synthase (PKS) pathways. However, the exact mechanisms of toxin synthesis are unknown due to a lack of genomic segregation of fat, toxins, and other PKS-based pathways. To better understand the underlying mechanisms, the actions and expression of the PKS proteins were investigated using the toxic dinoflagellate Amphidinium carterae as a model. Cerulenin, a known ketosynthase inhibitor, was shown to reduce acetate incorporation into all fat classes with the toxins amphidinol and sulpho-amphidinol. The mass spectrometry analysis of cerulenin-reacted synthetic peptides derived from ketosynthase domains of A. carterae multimodular PKS transcripts demonstrated a strong covalent bond that could be localized using collision-induced dissociation. One multi-modular PKS sequence present in all dinoflagellates surveyed to date was found to lack an AT domain in toxin-producing species, indicating trans-acting domains, and was shown by Western blotting to be post-transcriptionally processed. These results demonstrate how toxin synthesis in dinoflagellates can be differentiated from fat synthesis despite common underlying pathway.
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Affiliation(s)
- Saddef Haq
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
| | - Benjamin L. Oyler
- University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, MD 21201, USA; (B.L.O.); (M.M.K.)
| | - Ernest Williams
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
| | - Mohd M. Khan
- University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, MD 21201, USA; (B.L.O.); (M.M.K.)
| | - David R. Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8S 1P7, Canada;
| | - Tsvetan Bachvaroff
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
| | - Allen R. Place
- Institute for Marine and Environmental Technologies, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA; (S.H.); (E.W.); (T.B.)
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4
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Davison JR, Rajwani R, Zhao G, Bewley CA. The genome of antibiotic-producing colonies of the Pelagophyte alga Chrysophaeum taylorii reveals a diverse and non-canonical capacity for secondary metabolism. Sci Rep 2023; 13:11944. [PMID: 37488207 PMCID: PMC10366177 DOI: 10.1038/s41598-023-38042-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/01/2023] [Indexed: 07/26/2023] Open
Abstract
Chrysophaeum taylorii is a member of an understudied clade of marine algae that can be responsible for harmful coastal blooms and is known to accumulate bioactive natural products including antibiotics of the chrysophaentin class. Whole genome sequencing of laboratory-cultivated samples revealed an extensive and diverse complement of secondary metabolite biosynthetic genes in C. taylorii, alongside a small microbiome with a more limited biosynthetic potential. 16S microbiome analysis of laboratory cultured alongside wild-collected samples revealed several common taxa; however, analysis of biosynthetic genes suggested an algal origin for the chrysophaentins, possibly via one of several non-canonical polyketide synthase genes encoded within the genome.
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Affiliation(s)
- Jack R Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA.
- LifeMine Therapeutics, 30 Acorn Park Dr., Cambridge, MA, 02140, USA.
| | - Rahim Rajwani
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA.
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Wan X, Yao G, Wang K, Bao S, Han P, Wang F, Song T, Jiang H. Transcriptomic analysis of polyketide synthesis in dinoflagellate, Prorocentrum lima. HARMFUL ALGAE 2023; 123:102391. [PMID: 36894212 DOI: 10.1016/j.hal.2023.102391] [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: 08/30/2022] [Revised: 12/31/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
The benthic dinoflagellate Prorocentrum lima is among the most common toxic morphospecies with a cosmopolitan distribution. P. lima can produce polyketide compounds, such as okadaic acid (OA), dinophysistoxin (DTX) and their analogues, which are responsible for diarrhetic shellfish poisoning (DSP). Studying the molecular mechanism of DSP toxin biosynthesis is crucial for understanding the environmental driver influencing toxin biosynthesis as well as for better monitoring of marine ecosystems. Commonly, polyketides are produced by polyketide synthases (PKS). However, no gene has been confirmatively assigned to DSP toxin production. Here, we assembled a transcriptome from 94,730,858 Illumina RNAseq reads using Trinity, resulting in 147,527 unigenes with average sequence length of 1035 nt. Using bioinformatics analysis methods, we found 210 unigenes encoding single-domain PKS with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 15 transcripts encoding multi-domain PKS (forming typical type I PKSs modules) and 5 transcripts encoding hybrid nonribosomal peptide synthetase (NRPS)/PKS were found. Using comparative transcriptome and differential expression analysis, a total of 16 PKS genes were identified to be up-regulated in phosphorus-limited cultures, which was related to the up regulation of toxin expression. In concert with other recent transcriptome analyses, this study contributes to the building consensus that dinoflagellates may utilize a combination of Type I multi-domain and single-domain PKS proteins, in an as yet undefined manner, to synthesize polyketides. Our study provides valuable genomic resource for future research in order to understand the complex mechanism of toxin production in this dinoflagellate.
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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
| | - Kang Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Shaoheng Bao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Penggang Han
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Fuli Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Tianyu Song
- 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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Williams E, Bachvaroff T, Place A. A Comparison of Dinoflagellate Thiolation Domain Binding Proteins Using In Vitro and Molecular Methods. Mar Drugs 2022; 20:md20090581. [PMID: 36135770 PMCID: PMC9500876 DOI: 10.3390/md20090581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Dinoflagellates play important roles in ecosystems as primary producers and consumers making natural products that can benefit or harm environmental and human health but are also potential therapeutics with unique chemistries. Annotations of dinoflagellate genes have been hampered by large genomes with many gene copies that reduce the reliability of transcriptomics, quantitative PCR, and targeted knockouts. This study aimed to functionally characterize dinoflagellate proteins by testing their interactions through in vitro assays. Specifically, nine Amphidinium carterae thiolation domains that scaffold natural product synthesis were substituted into an indigoidine synthesizing gene from the bacterium Streptomyces lavendulae and exposed to three A. carterae phosphopantetheinyl transferases that activate synthesis. Unsurprisingly, several of the dinoflagellate versions inhibited the ability to synthesize indigoidine despite being successfully phosphopantetheinated. However, all the transferases were able to phosphopantetheinate all the thiolation domains nearly equally, defying the canon that transferases participate in segregated processes via binding specificity. Moreover, two of the transferases were expressed during growth in alternating patterns while the final transferase was only observed as a breakdown product common to all three. The broad substrate recognition and compensatory expression shown here help explain why phosphopantetheinyl transferases are lost throughout dinoflagellate evolution without a loss in a biochemical process.
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Dinoflagellate Phosphopantetheinyl Transferase (PPTase) and Thiolation Domain Interactions Characterized Using a Modified Indigoidine Synthesizing Reporter. Microorganisms 2022; 10:microorganisms10040687. [PMID: 35456738 PMCID: PMC9027781 DOI: 10.3390/microorganisms10040687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic dinoflagellates synthesize many toxic but also potential therapeutic compounds therapeutics via polyketide/non-ribosomal peptide synthesis, a common means of producing natural products in bacteria and fungi. Although canonical genes are identifiable in dinoflagellate transcriptomes, the biosynthetic pathways are obfuscated by high copy numbers and fractured synteny. This study focuses on the carrier domains that scaffold natural product synthesis (thiolation domains) and the phosphopantetheinyl transferases (PPTases) that thiolate these carriers. We replaced the thiolation domain of the indigoidine producing BpsA gene from Streptomyces lavendulae with those of three multidomain dinoflagellate transcripts and coexpressed these constructs with each of three dinoflagellate PPTases looking for specific pairings that would identify distinct pathways. Surprisingly, all three PPTases were able to activate all the thiolation domains from one transcript, although with differing levels of indigoidine produced, demonstrating an unusual lack of specificity. Unfortunately, constructs with the remaining thiolation domains produced almost no indigoidine and the thiolation domain for lipid synthesis could not be expressed in E. coli. These results combined with inconsistent protein expression for different PPTase/thiolation domain pairings present technical hurdles for future work. Despite these challenges, expression of catalytically active dinoflagellate proteins in E. coli is a novel and useful tool going forward.
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8
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Zhang J, Yang Q, Liu Q, Liu S, Zhu Y, Yao J, Wang H, Guan W. The responses of harmful dinoflagellate Karenia mikimotoi to simulated ocean acidification at the transcriptional level. HARMFUL ALGAE 2022; 111:102167. [PMID: 35016771 DOI: 10.1016/j.hal.2021.102167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 12/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
The HAB-forming, toxic dinoflagellate Karenia mikimotoi, previously found to benefit from ocean acidification (OA), was cultivated to investigate its transcriptional response to simulated OA for 30 generations. Batch cultures were grown under two CO2 concentrations, 450 (control) and 1100 (simulated OA) μatm, and physiological parameters [growth, pigments, catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD) activity], as well as transcriptomes (obtained via RNA-seq), were compared. Chlorophyll a (Chl a) and carotenoid (Caro) contents, as well as CAT and GR activities, were significantly increased under OA conditions. Transcriptomic analysis revealed 2,490 differentially expressed unigenes in response to OA, which comprised 1.54% of all unigenes. A total of 1,121 unigenes were upregulated, and 1,369 unigenes were downregulated in OA compared to control conditions. The downregulated expression of bicarbonate transporter and carbonic anhydrase genes was a landmark of OA acclimation. Key genes involved in energy metabolism, e.g., photosynthesis, tricarboxylic acid cycle, oxidative phosphorylation, and nitrogen metabolism, were highly upregulated under OA, contributing to increases in the Chl a (55.05%) and Caro (28.37%). The enhanced antioxidant enzyme activities (i.e. CAT, GR) and upregulated genes (i.e. glutathione peroxidase, ascorbate peroxidase, heat shock protein, 20S proteasome, aldehyde dehydrogenase, and apolipoprotein) benefit cells against the potential lower pH stress condition under OA. In addition, the downregulation of four genes associated with motility suggested that the preserved energy could further boost growth. In conclusion, the present study suggests that K. mikimotoi exhibits efficient gene expression regulation for the utilization of energy and resistance to OA-induced stress. Taken together, K. mikimotoi appeared as a tolerant species in response to OA. Thus, more extensive algal blooms that threaten marine organisms are likely in the future. These findings expand current knowledge on the gene expression of HAB-forming species in response to future OA.
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Affiliation(s)
- Jiazhu Zhang
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qiongying Yang
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qianlou Liu
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shuqi Liu
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yue Zhu
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jiang Yao
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Hong Wang
- Department of Medical Laboratory Technology, Xinyang Vocational and Technical College, Xinyang, Henan 464000, China
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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Anestis K, Kohli GS, Wohlrab S, Varga E, Larsen TO, Hansen PJ, John U. Polyketide synthase genes and molecular trade-offs in the ichthyotoxic species Prymnesium parvum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148878. [PMID: 34252778 DOI: 10.1016/j.scitotenv.2021.148878] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Prymnesium parvum is a bloom forming haptophyte that has been responsible for numerous fish kill events across the world. The toxicity of P. parvum has been attributed to the production of large polyketide compounds, collectively called prymnesins, which based on their structure can be divided into A-, B- and C-type. The polyketide chemical nature of prymnesins indicates the potential involvement of polyketide synthases (PKSs) in their biosynthesis. However, little is known about the presence of PKSs in P. parvum as well as the potential molecular trade-offs of toxin biosynthesis. In the current study, we generated and analyzed the transcriptomes of nine P. parvum strains that produce different toxin types and have various cellular toxin contents. Numerous type I PKSs, ranging from 37 to 109, were found among the strains. Larger modular type I PKSs were mainly retrieved from strains with high cellular toxin levels and eight consensus transcripts were present in all nine strains. Gene expression variance analysis revealed potential molecular trade-offs associated with cellular toxin quantity, showing that basic metabolic processes seem to correlate negatively with cellular toxin content. These findings point towards the presence of metabolic costs for maintaining high cellular toxin quantity. The detailed analysis of PKSs in P. parvum is the first step towards better understanding the molecular basis of the biosynthesis of prymnesins and contributes to the development of molecular tools for efficient monitoring of future blooms.
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Affiliation(s)
- Konstantinos Anestis
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
| | - Gurjeet Singh Kohli
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
| | - Sylke Wohlrab
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity, Ammerländer Heerstraße 231, 26129 Oldenburg, Germany.
| | - Elisabeth Varga
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währinger Straße 40, 1090 Vienna, Austria.
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark.
| | - Per Juel Hansen
- Marine Biology Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark.
| | - Uwe John
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity, Ammerländer Heerstraße 231, 26129 Oldenburg, Germany.
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10
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Williams EP, Bachvaroff TR, Place AR. A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates. Evol Bioinform Online 2021; 17:11769343211031871. [PMID: 34345159 PMCID: PMC8283056 DOI: 10.1177/11769343211031871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Many dinoflagellate species make toxins in a myriad of different molecular configurations but the underlying chemistry in all cases is presumably via modular synthases, primarily polyketide synthases. In many organisms modular synthases occur as discrete synthetic genes or domains within a gene that act in coordination thus forming a module that produces a particular fragment of a natural product. The modules usually occur in tandem as gene clusters with a syntenic arrangement that is often predictive of the resultant structure. Dinoflagellate genomes however are notoriously complex with individual genes present in many tandem repeats and very few synthetic modules occurring as gene clusters, unlike what has been seen in bacteria and fungi. However, modular synthesis in all organisms requires a free thiol group that acts as a carrier for sequential synthesis called a thiolation domain. We scanned 47 dinoflagellate transcriptomes for 23 modular synthase domain models and compared their abundance among 10 orders of dinoflagellates as well as their co-occurrence with thiolation domains. The total count of domain types was quite large with over thirty-thousand identified, 29 000 of which were in the core dinoflagellates. Although there were no specific trends in domain abundance associated with types of toxins, there were readily observable lineage specific differences. The Gymnodiniales, makers of long polyketide toxins such as brevetoxin and karlotoxin had a high relative abundance of thiolation domains as well as multiple thiolation domains within a single transcript. Orders such as the Gonyaulacales, makers of small polyketides such as spirolides, had fewer thiolation domains but a relative increase in the number of acyl transferases. Unique to the core dinoflagellates, however, were thiolation domains occurring alongside tetratricopeptide repeats that facilitate protein-protein interactions, especially hexa and hepta-repeats, that may explain the scaffolding required for synthetic complexes capable of making large toxins. Clustering analysis for each type of domain was also used to discern possible origins of duplication for the multitude of single domain transcripts. Single domain transcripts frequently clustered with synonymous domains from multi-domain transcripts such as the BurA and ZmaK like genes as well as the multi-ketosynthase genes, sometimes with a large degree of apparent gene duplication, while fatty acid synthesis genes formed distinct clusters. Surprisingly the acyl-transferases and ketoreductases involved in fatty acid synthesis (FabD and FabG, respectively) were found in very large clusters indicating an unprecedented degree of gene duplication for these genes. These results demonstrate a complex evolutionary history of core dinoflagellate modular synthases with domain specific duplications throughout the lineage as well as clues to how large protein complexes can be assembled to synthesize the largest natural products known.
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Affiliation(s)
- Ernest P Williams
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Allen R Place
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
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11
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Biosynthesis of marine toxins. Curr Opin Chem Biol 2020; 59:119-129. [DOI: 10.1016/j.cbpa.2020.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022]
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12
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Elleuch J, Barkallah M, Smith KF, Ben Neila I, Fendri I, Abdelkafi S. Quantitative PCR assay for the simultaneous identification and enumeration of multiple Karenia species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:36889-36899. [PMID: 32577959 DOI: 10.1007/s11356-020-09739-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Quantitative PCR (qPCR) is the method of choice for specific detection and quantification of harmful algal bloom (HAB) species. Development of qPCR assay for simultaneous enumeration of species that frequently co-exist in HABs is required. A high sensitivity TaqMan qPCR assay, using probe and primers, located at ITS1-5.8S-ITS2 rDNA region, detecting, specifically, Karenia selliformis, K. bidigitata, and K. mikimotoi, was designed. ITS1-5.8S-ITS2 rDNA region copy numbers per Karenia cell genome were estimated to 217.697 ± 67.904, allowing cell quantification. An application of the designed methodology in field samples has been conducted, and it showed high sensitivity (detection of around 10-1 cell/100 mg of bivalve mollusk tissue, equivalent to about 20 copies of the target sequence). We suggest that the optimized method could contribute to early detection of three closely related Karenia species in seafood cultivating areas to promote control quality, guarantee a fast and effective intervention, and improve public health prevention.
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Affiliation(s)
- Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia.
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
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13
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De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates. Mar Drugs 2020; 18:md18080386. [PMID: 32722301 PMCID: PMC7460133 DOI: 10.3390/md18080386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Many dinoflagellates species, especially of the Alexandrium genus, produce a series of toxins with tremendous impacts on human and environmental health, and tourism economies. Alexandrium tamutum was discovered for the first time in the Gulf of Naples, and it is not known to produce saxitoxins. However, a clone of A. tamutum from the same Gulf showed copepod reproduction impairment and antiproliferative activity. In this study, the full transcriptome of the dinoflagellate A. tamutum is presented in both control and phosphate starvation conditions. RNA-seq approach was used for in silico identification of transcripts that can be involved in the synthesis of toxic compounds. Phosphate starvation was selected because it is known to induce toxin production for other Alexandrium spp. Results showed the presence of three transcripts related to saxitoxin synthesis (sxtA, sxtG and sxtU), and others potentially related to the synthesis of additional toxic compounds (e.g., 44 transcripts annotated as "polyketide synthase"). These data suggest that even if this A. tamutum clone does not produce saxitoxins, it has the potential to produce toxic metabolites, in line with the previously observed activity. These data give new insights into toxic microalgae, toxin production and their potential applications for the treatment of human pathologies.
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Wu Z, Luo H, Yu L, Lee WH, Li L, Mak YL, Lin S, Lam PKS. Characterizing ciguatoxin (CTX)- and Non-CTX-producing strains of Gambierdiscus balechii using comparative transcriptomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137184. [PMID: 32084685 DOI: 10.1016/j.scitotenv.2020.137184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/28/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Gambierdiscus spp. can produce the polyketide compound, ciguatoxin (CTX), and are hence responsible for ciguatera fish poisoning (CFP). Studying the molecular mechanism that regulates CTX production is crucial for understanding the environmental trigger of CTX as well as for better informing fishery management. Commonly, polyketide synthases are important for polyketide synthesis; however, no gene has been confirmatively assigned to CTX production. Here, suppression subtractive hybridization (SSH) and transcriptome sequencing (RNA-Seq) were used to compare a CTX-producing strain with a non-CTX-producing strain. Using both methods, a total of 52 polyketide synthase (PKS) genes were identified to be up-regulated in the CTX-producing G. balechii, including transcripts encoding single-domain PKSs as well as transcripts encoding multi-domain PKSs. Using reverse transcription quantitative PCR, the expression of these genes in the CTX-producing strain and in nitrogen-limited cultures of the strain was further documented. These data suggest that PKSs are likely involved in polyketide synthesis and potentially in CTX synthesis in this dinoflagellate species. Our study provides the candidate biomarkers for the detection of CTXs or CFP in waters or any other organisms as well as a valuable genomic resource for the research on Gambierdiscus and other dinoflagellates.
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Affiliation(s)
- Zhen Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wai Hin Lee
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yim Ling Mak
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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15
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Van Dolah FM, Morey JS, Milne S, Ung A, Anderson PE, Chinain M. Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia. PLoS One 2020; 15:e0231400. [PMID: 32294110 PMCID: PMC7159223 DOI: 10.1371/journal.pone.0231400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/23/2020] [Indexed: 11/18/2022] Open
Abstract
Marine dinoflagellates produce a diversity of polyketide toxins that are accumulated in marine food webs and are responsible for a variety of seafood poisonings. Reef-associated dinoflagellates of the genus Gambierdiscus produce toxins responsible for ciguatera poisoning (CP), which causes over 50,000 cases of illness annually worldwide. The biosynthetic machinery for dinoflagellate polyketides remains poorly understood. Recent transcriptomic and genomic sequencing projects have revealed the presence of Type I modular polyketide synthases in dinoflagellates, as well as a plethora of single domain transcripts with Type I sequence homology. The current transcriptome analysis compares polyketide synthase (PKS) gene transcripts expressed in two species of Gambierdiscus from French Polynesia: a highly toxic ciguatoxin producer, G. polynesiensis, versus a non-ciguatoxic species G. pacificus, each assembled from approximately 180 million Illumina 125 nt reads using Trinity, and compares their PKS content with previously published data from other Gambierdiscus species and more distantly related dinoflagellates. Both modular and single-domain PKS transcripts were present. Single domain β-ketoacyl synthase (KS) transcripts were highly amplified in both species (98 in G. polynesiensis, 99 in G. pacificus), with smaller numbers of standalone acyl transferase (AT), ketoacyl reductase (KR), dehydratase (DH), enoyl reductase (ER), and thioesterase (TE) domains. G. polynesiensis expressed both a larger number of multidomain PKSs, and larger numbers of modules per transcript, than the non-ciguatoxic G. pacificus. The largest PKS transcript in G. polynesiensis encoded a 10,516 aa, 7 module protein, predicted to synthesize part of the polyether backbone. Transcripts and gene models representing portions of this PKS are present in other species, suggesting that its function may be performed in those species by multiple interacting proteins. This study contributes to the building consensus that dinoflagellates utilize a combination of Type I modular and single domain PKS proteins, in an as yet undefined manner, to synthesize polyketides.
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Affiliation(s)
- Frances M. Van Dolah
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
- * E-mail:
| | - Jeanine S. Morey
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
| | - Shard Milne
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - André Ung
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
| | - Paul E. Anderson
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - Mireille Chinain
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
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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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Wang X, Niu X, Chen Y, Sun Z, Han A, Lou X, Ge J, Li X, Yang Y, Jian J, Gonçalves RJ, Guan W. Transcriptome sequencing of a toxic dinoflagellate, Karenia mikimotoi subjected to stress from solar ultraviolet radiation. HARMFUL ALGAE 2019; 88:101640. [PMID: 31582153 DOI: 10.1016/j.hal.2019.101640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Solar ultraviolet radiation (UVR) is a stress factor in aquatic environments and may act directly or indirectly on orgnisms in the upper layers of the water column. However, UVR effects are usually species-specific and difficult to extrapolate. Here we use the HAB-forming, toxic dinoflagellate Karenia mikimotoi (which was found to be relatively resistant in previous studies) to investigate its transcriptional responses to a one-week UVR exposure. For this, batch cultures of K. mikimotoi were grown with and without UVR, and their transcriptomes (generated via RNAseq technology) were compared. RNA-seq generated 45.31 million reads, which were further assembled to 202600 unigenes (>300bp). Among these, ca. 61% were annotated with NCBI, NR, GO, KOG, PFAM, Swiss-Prot, and KEGG database. Transcriptomic analysis revealed 722 differentially expressed unigenes (DEGs, defined as being within a |log2 fold change| ≥ 2 and padj < 0.05) responding to solar UVR, which were only 0.36% of all unigenes. 716 unigenes were down-regulated, and only 6 unigenes were up-regulated in the UVR compared to non-UVR treatment. KEGG pathway further analysis revealed DEGs were involved in the different pathway; genes involved in the ribosome, endocytosis and steroid biosynthesis pathways were highly down-regulated, but this was not the case for those involved in the energy metabolisms (including photosynthesis, oxidative phosphorylation) which may contribute to the sustainable growth observed in UVR treatment. The up-regulated expression of both zinc-finger proteins (ZFPs) and ribosomal protein L11 (RPL11) may be one of the acclimated mechanisms against UVR. In addition, this work identified down-regulated genes involved in fatty acid degradation and the hydrophobic branched chain amino acids (e.g., Valine, leucine, and isoleucine), which act as structural components of cell membranes modulating lipid homeostasis or turnover. In conclusion, the present study suggests that the toxic dinoflagellate K. mikimotoi has limited transcriptomic regulation but confirms that it appears as a tolerant species in response to solar UVR. These findings expand current knowledge of gene expression in HAB-forming species in response to natural environment factors such as solar radiation.
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Affiliation(s)
- Xinjie Wang
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China; Marine Biology Institute, Shantou University, Shantou, Guangdong 515063 China
| | - Xiaoqin Niu
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Yiji Chen
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Zhewei Sun
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Axiang Han
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Xiayuan Lou
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Jingke Ge
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Xuanwen Li
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Yuqian Yang
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063 China
| | - Rodrigo J Gonçalves
- Laboratorio de Oceanografía Biológica (LOBio), Centro para el Estudio de Sistemas Marinos (CESIMAR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). U9120ACD, Puerto Madryn, Argentina
| | - Wanchun Guan
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China.
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18
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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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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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Lukowski AL, Narayan ARH. Natural Voltage-Gated Sodium Channel Ligands: Biosynthesis and Biology. Chembiochem 2019; 20:1231-1241. [PMID: 30605564 PMCID: PMC6579537 DOI: 10.1002/cbic.201800754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/18/2022]
Abstract
Natural product biosynthetic pathways are composed of enzymes that use powerful chemistry to assemble complex molecules. Small molecule neurotoxins are examples of natural products with intricate scaffolds which often have high affinities for their biological targets. The focus of this Minireview is small molecule neurotoxins targeting voltage-gated sodium channels (VGSCs) and the state of knowledge on their associated biosynthetic pathways. There are three small molecule neurotoxin receptor sites on VGSCs associated with three different classes of molecules: guanidinium toxins, alkaloid toxins, and ladder polyethers. Each of these types of toxins have unique structural features which are assembled by biosynthetic enzymes and the extent of information known about these enzymes varies among each class. The biosynthetic enzymes involved in the formation of these toxins have the potential to become useful tools in the efficient synthesis of VGSC probes.
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Affiliation(s)
- April L Lukowski
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
| | - Alison R H Narayan
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, 930 N University Ave., Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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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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Abstract
Covering: January to December 2017This review covers the literature published in 2017 for marine natural products (MNPs), with 740 citations (723 for the period January to December 2017) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1490 in 477 papers for 2017), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. Geographic distributions of MNPs at a phylogenetic level are reported.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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Kitchen SA, Bourdelais AJ, Taylor AR. Interaction of a dinoflagellate neurotoxin with voltage-activated ion channels in a marine diatom. PeerJ 2018; 6:e4533. [PMID: 29632739 PMCID: PMC5888156 DOI: 10.7717/peerj.4533] [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: 12/06/2017] [Accepted: 03/05/2018] [Indexed: 01/04/2023] Open
Abstract
Background The potent neurotoxins produced by the harmful algal bloom species Karenia brevis are activators of sodium voltage-gated channels (VGC) in animals, resulting in altered channel kinetics and membrane hyperexcitability. Recent biophysical and genomic evidence supports widespread presence of homologous sodium (Na+) and calcium (Ca2+) permeable VGCs in unicellular algae, including marine phytoplankton. We therefore hypothesized that VGCs of these phytoplankton may be an allelopathic target for waterborne neurotoxins produced by K. brevis blooms that could lead to ion channel dysfunction and disruption of signaling in a similar manner to animal Na+ VGCs. Methods We examined the interaction of brevetoxin-3 (PbTx-3), a K. brevis neurotoxin, with the Na+/Ca2+ VGC of the non-toxic diatom Odontella sinensis using electrophysiology. Single electrode current- and voltage- clamp recordings from O. sinensis in the presence of PbTx-3 were used to examine the toxin’s effect on voltage gated Na+/Ca2+ currents. In silico analysis was used to identify the putative PbTx binding site in the diatoms. We identified Na+/Ca2+ VCG homologs from the transcriptomes and genomes of 12 diatoms, including three transcripts from O. sinensis and aligned them with site-5 of Na+ VGCs, previously identified as the PbTx binding site in animals. Results Up to 1 µM PbTx had no effect on diatom resting membrane potential or membrane excitability. The kinetics of fast inward Na+/Ca2+ currents that underlie diatom action potentials were also unaffected. However, the peak inward current was inhibited by 33%, delayed outward current was inhibited by 25%, and reversal potential of the currents shifted positive, indicating a change in permeability of the underlying channels. Sequence analysis showed a lack of conservation of the PbTx binding site in diatom VGC homologs, many of which share molecular features more similar to single-domain bacterial Na+/Ca2+ VGCs than the 4-domain eukaryote channels. Discussion Although membrane excitability and the kinetics of action potential currents were unaffected, the permeation of the channels underlying the diatom action potential was significantly altered in the presence of PbTx-3. However, at environmentally relevant concentrations the effects of PbTx- on diatom voltage activated currents and interference of cell signaling through this pathway may be limited. The relative insensitivity of phytoplankton VGCs may be due to divergence of site-5 (the putative PbTx binding site), and in some cases, such as O. sinensis, resistance to toxin effects may be because of evolutionary loss of the 4-domain eukaryote channel, while retaining a single domain bacterial-like VGC that can substitute in the generation of fast action potentials.
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Affiliation(s)
- Sheila A Kitchen
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Andrea J Bourdelais
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Alison R Taylor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
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