Investigating the Biology of Toxin-Producing Karenia Species: A Transcriptomics Approach
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The dinoflagellate Karenia brevis is a prominent bloom-forming harmful algae species in the Gulf of Mexico. K. brevis produces two ladder-frame polyketide brevetoxins, PbTx-1 and PbTx-2. PbTx-1, PbTx-2, and their derivatives bind to neurotoxin receptor site 5 of voltage-gated Na+ channels and prevent channel deactivation. Through the depolarizing activity of brevetoxins, K. brevis blooms kill fish and may sicken humans who eat shellfish from the bloom region. Despite these risks, the biological function of brevetoxins is poorly characterized, including the genes that participate in PbTx synthesis. Large and repetitive, the K. brevis genome has not been sequenced. However, with de novo transcriptomics, genomic analyses of K. brevis are possible. During this dissertation study, the transcriptomes of multiple Karenia species, including three strains of K. brevis (SP1, SP3, and Wilson), cytotoxin-producing Karenia mikimotoi, and PbTx-2-producing Karenia papilionacea, were assembled and analyzed. Analyses included comparative transcriptomics among Karenia species and K. brevis strains, putative protein annotation, ortholog prediction, gene tree construction, and single nucleotide polymorphism (SNP) prediction. Through the comparison of multiple de novo transcriptome assembly methods, this study developed a pipeline to produce highly complete dinoflagellate reference transcriptomes. Thousands of Karenia transcripts were annotated with potential functions and gene ontology terms, including highly conserved putative voltage-gated cation channel genes. Because both Na^+ and Ca^2+ channels were identified, our work suggests that Karenia species are capable of selective transmembrane ion transport. It also highlights the need for biochemical research to investigate the interaction, if any, between brevetoxins and dinoflagellate voltage-gated Na^+ channels. The Karenia ortholog detection step identified 4799 genes that were expressed by brevetoxin-producing K. brevis and K. papilionacea, but not K. mikimotoi. Transcripts involved with “heterocycle production” were overrepresented in the 4799 “unique” orthologs, including five putative polyketide synthases. These genes represent interesting targets for further brevetoxin production research. Additionally, a novel transcript with high homology to multimodular type 1 PKSs was identified in the K. brevis transcriptome and RNA from field samples of K. brevis. The multimodular PKS, which has never been characterized before, indicates that K. brevis synthesizes polyketides and/or other secondary metabolites using both type I (multimodular) and type I-like (single domain) proteins.
Ryan, Darcie E (2016). Investigating the Biology of Toxin-Producing Karenia Species: A Transcriptomics Approach. Doctoral dissertation, Texas A & M University. Available electronically from