1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Oliveira CYB, Abreu JL, Santos EP, Matos ÂP, Tribuzi G, Oliveira CDL, Veras BO, Bezerra RS, Müller MN, Gálvez AO. Light induces peridinin and docosahexaenoic acid accumulation in the dinoflagellate Durusdinium glynnii. Appl Microbiol Biotechnol 2022; 106:6263-6276. [PMID: 35972515 DOI: 10.1007/s00253-022-12131-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
Abstract
Peridinin is a light-harvesting carotenoid present in phototrophic dinoflagellates and has great potential for new drug applications and cosmetics development. Herein, the effects of irradiance mediated by light-emitting diodes on growth performance, carotenoid and fatty acid profiles, and antioxidant activity of the endosymbiotic dinoflagellate Durusdinium glynnii were investigated. The results demonstrate that D. glynnii is particularly well adapted to low-light conditions; however, it can be high-light-tolerant. In contrast to other light-harvesting carotenoids, the peridinin accumulation in D. glynnii occurred during high-light exposure. The peridinin to chlorophyll-a ratio varied as a function of irradiance, while the peridinin to total carotenoids ratio remained stable. Under optimal irradiance for growth, there was a peak in docosahexaenoic acid (DHA) bioaccumulation. This study contributes to the understanding of the photoprotective role of peridinin in endosymbiont dinoflagellates and highlights the antioxidant activity of peridinin-rich extracts. KEY POINTS: • Peridinin has a protective role against chlorophyll photo-oxidation • High light conditions induce cellular peridinin accumulation • D. glynnii accumulates high amounts of DHA under optimal light supply.
Collapse
Affiliation(s)
- Carlos Yure B Oliveira
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil.
| | - Jéssika L Abreu
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil
| | - Elizabeth P Santos
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil
| | - Ângelo P Matos
- Center of Agricultural Sciences, Federal University of Santa Catarina, Florianópolis, 88034-001, Brazil
| | - Giustino Tribuzi
- Department of Food Science and Technology, Federal University of Santa Catarina, Florianopolis, 88034-801, Brazil
| | - Cicero Diogo L Oliveira
- Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, 57072-900, Brazil
| | - Bruno O Veras
- Department of Biochemistry, Federal University of Pernambuco, Recife, 50740-550, Brazil
| | - Railson S Bezerra
- Department of Biochemistry, Federal University of Pernambuco, Recife, 50740-550, Brazil
| | - Marius N Müller
- Department of Oceanography, Federal University of Pernambuco, Recife, 50740-550, Brazil
| | - Alfredo O Gálvez
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Saati-Santamaría Z, Selem-Mojica N, Peral-Aranega E, Rivas R, García-Fraile P. Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products. Microb Genom 2022; 8:000758. [PMID: 35195510 PMCID: PMC8942027 DOI: 10.1099/mgen.0.000758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022] Open
Abstract
Microbes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus Pseudomonas. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in Pseudomonas type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select Pseudomonas strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 Pseudomonas species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in Pseudomonas. The types of metabolites encoded in Pseudomonas type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with Pseudomonas species diversification. Interestingly, only a few Pseudomonas species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by Pseudomonas type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of Pseudomonas and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.
Collapse
Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | | | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| |
Collapse
|
5
|
Sánchez-Suárez J, Garnica-Agudelo M, Villamil L, Díaz L, Coy-Barrera E. Bioactivity and Biotechnological Overview of Naturally Occurring Compounds from the Dinoflagellate Family Symbiodiniaceae: A Systematic Review. ScientificWorldJournal 2021; 2021:1983589. [PMID: 34955690 PMCID: PMC8709762 DOI: 10.1155/2021/1983589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/27/2021] [Indexed: 11/17/2022] Open
Abstract
Marine invertebrates are a significant source of biologically active compounds. Recent studies have highlighted the role of microbiota associated with marine invertebrates in the production of bioactive compounds. Corals and sponges are the main marine invertebrates producing bioactive substances, and Symbiodiniaceae dinoflagellates are well-recognized endosymbionts with corals and sponges playing vital functions. The biological properties of Symbiodiniaceae-derived compounds have garnered attention in the past decades owing to their ecological implications and potentiality for bioprospecting initiatives. This study aims to systematically review studies on bioactivities and potential biotechnological applications of Symbiodiniaceae-derived compounds. The PRISMA guidelines were followed. Our study showed that anti-inflammatory and vasoconstrictive activities of Symbiodiniaceae-derived compounds have been the most investigated. However, very few studies have been published, with in vitro culturing of Symbiodiniaceae being the most significant challenge. Therefore, we surveyed for the metabolites reported so far, analyzed their chemodiversity, and discussed approaches to overcome culturing-related limitations.
Collapse
Affiliation(s)
- Jeysson Sánchez-Suárez
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
| | - Mariana Garnica-Agudelo
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Luisa Villamil
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
| | - Luis Díaz
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá, Colombia
| |
Collapse
|
6
|
Jean-Louis Kraus. Natural Products as Potential Antiviral Drugs: The Specific Case of Marine Biotoxins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1127-1132. [PMID: 34931111 PMCID: PMC8675108 DOI: 10.1134/s1068162021060133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/04/2022]
Abstract
To fight against various viral infections researchers turned to new chemical structures resulting from natural medicinal plants and more recently from "marine origin" as sources of active molecules against viral infections. The present manuscript describes complex marine origin drugs, their chemical complex structure, their therapeutic use, and their antiviral properties. Emphasis is placed more particularly on the properties of ionic channels (Na+, K+, Ca2+) blockers compounds from marine origin, named Dinotoxins, derived from "dinoflagellates microalgae". These compounds are of particular pharmaceutical interest since ionic channels blockers could be used to fight against a wide diversity of viruses, including SARS-CoV2 virus.
Collapse
Affiliation(s)
- Jean-Louis Kraus
- Institut de Biologie du Développement de Marseille (IBDM), UMR-7288 CNRS Aix-Marseille University, 13288 Marseille Cedex, France
| |
Collapse
|
7
|
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: 12] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
8
|
Chen YH, Chiang PW, Rogozin DY, Degermendzhy AG, Chiu HH, Tang SL. Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach. Commun Biol 2021; 4:996. [PMID: 34426638 PMCID: PMC8382752 DOI: 10.1038/s42003-021-02510-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/01/2021] [Indexed: 11/08/2022] Open
Abstract
Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.
Collapse
Affiliation(s)
- Yu-Hsiang Chen
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Denis Yu Rogozin
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
- Siberian Federal University, Krasnoyarsk, Russia
| | - Andrey G Degermendzhy
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Lin Tang
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Ripken C, Khalturin K, Shoguchi E. Response of Coral Reef Dinoflagellates to Nanoplastics under Experimental Conditions Suggests Downregulation of Cellular Metabolism. Microorganisms 2020; 8:microorganisms8111759. [PMID: 33182359 PMCID: PMC7695302 DOI: 10.3390/microorganisms8111759] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
Plastic products contribute heavily to anthropogenic pollution of the oceans. Small plastic particles in the microscale and nanoscale ranges have been found in all marine ecosystems, but little is known about their effects upon marine organisms. In this study, we examine changes in cell growth, aggregation, and gene expression of two symbiotic dinoflagellates of the family Symbiodiniaceae, Symbiodinium tridacnidorum (clade A3), and Cladocopium sp. (clade C) under exposure to 42-nm polystyrene beads. In laboratory experiments, the cell number and aggregation were reduced after 10 days of nanoplastic exposure at 0.01, 0.1, and 10 mg/L concentrations, but no clear correlation with plastic concentration was observed. Genes involved in dynein motor function were upregulated when compared to control conditions, while genes related to photosynthesis, mitosis, and intracellular degradation were downregulated. Overall, nanoplastic exposure led to more genes being downregulated than upregulated and the number of genes with altered expression was larger in Cladocopium sp. than in S. tridacnidorum, suggesting different sensitivity to nano-plastics between species. Our data show that nano-plastic inhibits growth and alters aggregation properties of microalgae, which may negatively affect the uptake of these indispensable symbionts by coral reef organisms.
Collapse
Affiliation(s)
- Christina Ripken
- Light-Matter Interactions for Quantum Technologies Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.K.); (E.S.)
- Correspondence:
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.K.); (E.S.)
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.K.); (E.S.)
| |
Collapse
|
11
|
Shoguchi E, Beedessee G, Hisata K, Tada I, Narisoko H, Satoh N, Kawachi M, Shinzato C. A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. Genome Biol Evol 2020; 13:5955767. [PMID: 33146374 PMCID: PMC7875005 DOI: 10.1093/gbe/evaa235] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose-methanol-choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.
Collapse
Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Haruhi Narisoko
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| |
Collapse
|
12
|
Beedessee G, Kubota T, Arimoto A, Nishitsuji K, Waller RF, Hisata K, Yamasaki S, Satoh N, Kobayashi J, Shoguchi E. Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. BMC Biol 2020; 18:139. [PMID: 33050904 PMCID: PMC7557087 DOI: 10.1186/s12915-020-00873-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Our understanding of dinoflagellate toxin biosynthesis has been hampered by their unusually large genomes. To overcome this challenge, for the first time, we sequenced the genome, microRNAs, and mRNA isoforms of a basal dinoflagellate, Amphidinium gibbosum, and employed an integrated omics approach to understand its secondary metabolite biosynthesis. RESULTS We assembled the ~ 6.4-Gb A. gibbosum genome, and by probing decoded dinoflagellate genomes and transcriptomes, we identified the non-ribosomal peptide synthetase adenylation domain as essential for generation of specialized metabolites. Upon starving the cells of phosphate and nitrogen, we observed pronounced shifts in metabolite biosynthesis, suggestive of post-transcriptional regulation by microRNAs. Using Iso-Seq and RNA-seq data, we found that alternative splicing and polycistronic expression generate different transcripts for secondary metabolism. CONCLUSIONS Our genomic findings suggest intricate integration of various metabolic enzymes that function iteratively to synthesize metabolites, providing mechanistic insights into how dinoflagellates synthesize secondary metabolites, depending upon nutrient availability. This study provides insights into toxin production associated with dinoflagellate blooms. The genome of this basal dinoflagellate provides important clues about dinoflagellate evolution and overcomes the large genome size, which has been a challenge previously.
Collapse
Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
- Present address: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Takaaki Kubota
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima, 722-0073, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing 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
| | - Jun'ichi Kobayashi
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| |
Collapse
|
13
|
Scanlan JL, Gledhill-Smith RS, Battlay P, Robin C. Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the 'detoxification-by-phosphorylation' enzymes of insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103429. [PMID: 32540344 DOI: 10.1016/j.ibmb.2020.103429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/25/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a phase II detoxification reaction that, among animals, occurs near exclusively in insects, but the enzymes responsible have never been cloned or otherwise identified. We propose the hypothesis that members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene family in 12 species of Drosophila and explored their evolution within the genus. Many ancestral EcKL clades are evolutionarily unstable and have experienced repeated gene gain and loss events, while others are conserved as single-copy orthologs. Leveraging multiple published gene expression datasets from D. melanogaster, and using the cytochrome P450s-a classical detoxification family-as a test case, we demonstrate relationships between xenobiotic induction, detoxification tissue-enriched expression and evolutionary instability in the EcKLs and the P450s. We devised a systematic method for identifying candidate detoxification genes in large gene families that is concordant with experimentally determined functions of P450 genes in D. melanogaster. Applying this method to the EcKLs suggested a significant proportion of these genes play roles in detoxification, and that the EcKLs may constitute a detoxification gene family in insects. Additionally, we estimate that between 11 and 16 uncharacterised D. melanogaster P450s are strong detoxification candidates. Lastly, we also found previously unreported genomic and transcriptomic variation in a number of EcKLs and P450s associated with toxic stress phenotypes using a targeted phenome-wide association study (PheWAS) approach in D. melanogaster, presenting multiple future avenues of research for detoxification genetics in this species.
Collapse
Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Rebecca S Gledhill-Smith
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Paul Battlay
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| |
Collapse
|
14
|
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: 15] [Impact Index Per Article: 3.8] [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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|