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ABSTRACT: Karenia brevis Wilson Transcriptome and Translatome

PROVIDER: PRJNA343279 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4253120_1.fastq.gz	Fastqsanger.gz
	SRR4253120_2.fastq.gz	Fastqsanger.gz
	SRR4253130_1.fastq.gz	Fastqsanger.gz
	SRR4253130_2.fastq.gz	Fastqsanger.gz
	SRR4253121_1.fastq.gz	Fastqsanger.gz

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Karenia brevis isolate:Wilson

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Karenia brevis strain:Wilson, SP1, and SP3

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Insights into brevetoxin biosynthesis and endogenous function by comparative quantitative proteomics of Karenia brevis strains

Project description:High toxin (HT) producing and a low toxin producing (LT) strains of Karenia brevis both derived from the Wilson strain. Samples were labeled with TMT11 plex, and fractionated into 8 fractions (ECL1_1191562 to 1191569). HT was labeled with 126, 127N, 127C, 128N, 129N. LT was labeled with 128C, 129C, 130C, 130N, 131N.

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Karenia brevis

Project description:Karenia brevis Transcriptome or Gene expression

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Project description:Karenia brevis microbial consortium

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Global Analysis of de novo Transcription Following Biosynthetic Labeling in a Dinoflagellate, Karenia brevis

Project description:Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into role of de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed RNA in Karenia brevis. These isolated fractions were then used for analysis of global de novo transcription by hybridization to a K. brevis microarray. As previous microarray studies indicated that transcripts for pentatricopeptide repeat (PPR) proteins rapidly increased in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of changes in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

2013-08-01 | GSE46175 | GEO

Global Analysis of mRNA Half-lives Following Biosynthetic Labeling in a Dinoflagellate, Karenia brevis

Project description:Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the role of differential mRNA stability in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed/pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 3 days, with a median of 33 hours. Thirteen percent of messages showed a half-life of 3 days, demonstrating their stability throughtout the course of the cell cycle and divison. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes.

2013-08-01 | GSE46174 | GEO

Karenia brevis

Project description:Transcriptional Responses of Karenia brevis to Acute Stresses

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Transcriptional Responses of Karenia brevis to Phosphorus Depletion and Addition

Project description:The role of coastal nutrient sources in the persistence of Karenia brevis red tides in coastal waters of Florida is currently a contentious issue that warrants investigation into the nutrient physiology of this dinoflagellate species. The molecular mechanisms by which dinoflagellates respond to nutrient availability are essentially unexplored. The current study sought to determine if the transcriptome of K. brevis is responsive to phosphorus and informative of nutrient status. Stationary phase P-limited cultures did not exhibit up-regulation of transcripts considered to be hallmark of P depletion relative to nutrient-replete stationary phase cultures, despite rapid growth upon addition of the limiting nutrient. To study transcriptome responses to nutrient addition, the limiting nutrient was added to depleted cells and changes in global gene expression were assessed over the first 48 hours following nutrient addition. P-addition resulted in significant changes in approximately 4% of genes on the microarray, using a significance cutoff of 1.7-fold and p<10-4. By far, the earliest responding genes were dominated by pentatricopeptide repeat (PPR) proteins, which increased in expression up to 3-fold by 1 h following nutrient addition. PPR proteins are nuclear encoded proteins involved in chloroplast and mitochondria RNA processing. Correspondingly, other functions enriched in response to both nutrients were photosystem and ribosomal genes. Transcriptomic responses to the addition of P reflected primarily chloroplast functions. Even the earliest responding transcripts, those encoding PPR proteins, possess a 5’ trans-spliced leader sequence, suggesting that the observed rapid response of the transcriptome may be achieved, in part, through post-transcriptional mechanisms.

2011-08-09 | GSE28419 | GEO

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