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Guo, Ruoyu,Youn, Seok Hyun,Ki, Jang-Seu Hindawi Publishing Corporation 2015 International journal of genomics Vol.2015 No.-
<P>The marine dinoflagellate <I>Cochlodinium polykrikoides</I> is responsible for harmful algal blooms in aquatic environments and has spread into the world's oceans. As a microeukaryote, it seems to have distinct genomic characteristics, like gene structure and regulation. In the present study, we characterized heat shock protein (HSP) 70/90 of <I>C. polykrikoides</I> and evaluated their transcriptional responses to environmental stresses. Both HSPs contained the conserved motif patterns, showing the highest homology with those of other dinoflagellates. Genomic analysis showed that the <I>CpHSP70</I> had no intron but was encoded by tandem arrangement manner with separation of intergenic spacers. However, <I>CpHSP90</I> had one intron in the coding genomic regions, and no intergenic region was found. Phylogenetic analyses of separate HSPs showed that CpHSP70 was closely related with the dinoflagellate <I>Crypthecodinium cohnii</I> and CpHSP90 with other Gymnodiniales in dinoflagellates. Gene expression analyses showed that both <I>HSP</I> genes were upregulated by the treatments of separate algicides CuSO<SUB>4</SUB> and NaOCl; however, they displayed downregulation pattern with PCB treatment. The transcription of <I>CpHSP90</I> and <I>CpHSP70</I> showed similar expression patterns under the same toxicant treatment, suggesting that both genes might have cooperative functions for the toxicant induced gene regulation in the dinoflagellate.</P>
Ruoyu Guo,기장서 한국조류학회I 2011 ALGAE Vol.26 No.3
Spliced leader (SL) trans-splicing is a mRNA processing mechanism in dinoflagellate nuclear genes. Although studies have identified a short, conserved dinoflagellate SL (dinoSL) sequence (22-nt) in their nuclear-encoded transcripts,whether the majority of nuclear-coded transcripts in dinoflagellates have the dinoSL sequence remains doubtful. In this study, we investigated dinoSL-containing gene transcripts using 454 pyrosequencing data (Cochlodinium polykrikoides,93 K sequence reads, 31 Mb; Prorocentrum minimum, 773 K sequence reads, 291 Mb). After making comparisons and performing local BLAST searches, we identified dinoSL for one C. polykrikoides gene transcript and eight P. minimum gene transcripts. This showed transcripts containing the dinoSL sequence were markedly fewer in number than the total expressed sequence tag (EST) transcripts. In addition, we found no direct evidence to prove that most dinoflagellate nuclear-coded transcripts have this dinoSL sequence.
Guo, Ruoyu,Ki, Jang-Seu The Korean Society of Phycology 2011 ALGAE Vol.26 No.3
Spliced leader (SL) trans-splicing is a mRNA processing mechanism in dinoflagellate nuclear genes. Although studies have identified a short, conserved dinoflagellate SL (dinoSL) sequence (22-nt) in their nuclear-encoded transcripts, whether the majority of nuclear-coded transcripts in dinoflagellates have the dinoSL sequence remains doubtful. In this study, we investigated dinoSL-containing gene transcripts using 454 pyrosequencing data (Cochlodinium polykrikoides, 93 K sequence reads, 31 Mb; Prorocentrum minimum, 773 K sequence reads, 291 Mb). After making comparisons and performing local BLAST searches, we identified dinoSL for one C. polykrikoides gene transcript and eight P. minimum gene transcripts. This showed transcripts containing the dinoSL sequence were markedly fewer in number than the total expressed sequence tag (EST) transcripts. In addition, we found no direct evidence to prove that most dinoflagellate nuclear-coded transcripts have this dinoSL sequence.
Guo, Ruoyu,Ki, Jang-Seu Chapman Hall ; Kluwer Academic Publishers 2012 Ecotoxicology Vol.21 No.5
<P>The dinoflagellate algae survive variations in water temperature as well as sudden exposures to toxic substances; heat shock proteins (HSPs) seem to function as part of their cell survival strategy. In the present study, we determined the complete open reading frame (ORF) of HSP90 gene in the dinoflagellate Prorocentrum minimum (PmHSP90), and examined the expression levels of the gene after exposure to thermal stressors, copper metal, and endocrine-disrupting chemicals, including bisphenol A (BPA) and polychlorinated biphenyl (PCB). The complete ORF of PmHSP90 was 2,130-bp long, encoding a 709-amino acid-long polypeptide (81.62?kDa), and bearing characteristics of the HSP90 family and conserved domains. Real-time (RT)-PCR analyses revealed different expression patterns after exposure to heat, metals, and chemicals. The expression of PmHSP90 was significantly upregulated by increased thermal stresses, with the highest changes of 2.4-fold and 1.9-fold occurring after 24?h at 25?C and 30?C, respectively. The gene expression dramatically increased (2.1 to 8.9-fold changes) with increasing concentrations of copper (one-way ANOVA, P?<?0.01). Treatment with BPA or PCB, however, did not induce significant changes in PmHSP90 expression. These data suggest that the dinoflagellate HSP90 responds to thermal stressors, but may differentially respond to toxic substances such as metals and endocrine-disrupting chemicals.</P>
Guo, Ruoyu,Lim, Weol-Ae,Ki, Jang-Seu Elsevier 2016 Harmful algae Vol.57 No.1
<P><B>Abstract</B></P> <P>Copper is an essential trace metal for organisms; however, excess copper may damage cellular processes. Their efficiency and physiological effects of biocides have been well documented; however, molecular transcriptome responses to biocides are insufficiently studied. In the present study, a 6.0K oligonucleotide chip was developed to investigate the molecular responses of the harmful dinoflagellate <I>Prorocentrum minimum</I> to copper sulfate (CuSO<SUB>4</SUB>) treatment. The results revealed that 515 genes (approximately 8.6%) responded to CuSO<SUB>4</SUB>, defined as being within a 2-fold change. Further, KEGG pathway analysis showed that differentially expressed genes (DEGs) were involved in ribosomal function, RNA transport, carbon metabolism, biosynthesis of amino acids, photosystem maintenance, and other cellular processes. Among the DEGs, 49 genes were related to chloroplasts and mitochondria. Furthermore, the genes involved in the RAS signaling pathway, MAPK signaling pathway, and transport pathways were identified. An additional experiment showed that the photosynthesis efficiency decreased considerably, and reactive oxygen species (ROS) production increased in <I>P. minimum</I> after CuSO<SUB>4</SUB> exposure. These results suggest that CuSO<SUB>4</SUB> caused cellular oxidative stress in <I>P. minimum</I>, affecting the ribosome and mitochondria, and severely damaged the photosystem. These effects may potentially lead to cell death, although the dinoflagellate has developed a complex signal transduction process to combat copper toxicity.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microarray analysis revealed 515 genes responded to CuSO<SUB>4</SUB> in <I>P. minimum</I>. </LI> <LI> Among differentially expressed genes, 49 genes (9.5%) are related to chloroplast and mitochondria. </LI> <LI> Genes for ribosome, transport, and signal transduction pathways were significantly involved. </LI> <LI> Photosynthesis of <I>P. minimum</I> was considerably inhibited by copper sulfate. </LI> </UL> </P>