Transcriptome Remodeling Associated with Chronological Aging in the Dinoflagellate, Karenia brevis. Karenia brevis

To gain an understanding of processes that underlie chronological aging in this dinoflagellate, a microarray study was carried out to identify changes in the global transcriptome that accompany the entry and maintenance of stationary phase up to the onset of cell death. The transcriptome of K. brevis was assayed using a custom 10,263 feature oligonucleotide microarray from mid-logarithmic growth to the onset of culture demise. A total of 2,958 (29%) features were differentially expressed, with the mid-stationary phase timepoint demonstrating peak changes in expression. Gene ontology enrichment analyses identified a significant shift in transcripts involved in energy acquisition, ribosome biogenesis, gene expression, stress adaptation, calcium signaling, and putative brevetoxin biosynthesis. The extensive remodeling of the transcriptome observed in the transition into a quiescent non-dividing phase appears to be indicative of a global shift in the metabolic and signaling requirements and provides the basis from which to understand the process of chronological aging in a dinoflagellate. Overall design: Twenty seven 900ml batch cultures of K. brevis were inoculated at a starting concentration of approximately 1000 cells/ml from mid-logarithmic stage starter cultures on day 0. Triplicate cultures were harvested every other day from day 2 to 18 and total RNA was extracted. One color arrays were then run on all biological replicates (n=3 at each timepoint) for days 4, 6, 10, 14 and 18.

为阐明该甲藻（dinoflagellate）时序衰老（chronological aging）背后的核心生物学过程，本研究开展微阵列（microarray）分析，以鉴定伴随静止期进入与维持直至细胞死亡发生时的全局转录组（transcriptome）表达变化。本研究针对短凯伦藻（K. brevis）的转录组进行检测，采用定制化10263探针的寡核苷酸微阵列（oligonucleotide microarray），覆盖从对数中期生长至培养物消亡的全周期。共计2958个探针（占总探针数的29%）呈现差异表达（differentially expressed），其中中期静止期时间点的表达变化幅度达到峰值。基因本体论（Gene Ontology, GO）富集分析显示，参与能量获取、核糖体生物发生、基因表达、应激适应、钙信号传导以及潜在短裸甲藻毒素（brevetoxin）生物合成的转录本发生了显著表达偏移。本研究观察到，细胞向静息非分裂期（quiescent non-dividing phase）转变过程中发生的大规模转录组重编程，似乎暗示代谢与信号传导需求发生了全局重塑，这为理解甲藻时序衰老过程提供了理论基础。实验设计：于第0日，以约1000个细胞/毫升的起始浓度，从对数中期种子培养物中接种27份900毫升批量培养的短凯伦藻。自第2日至第18日，每隔一日收集三份重复培养物并提取总RNA。针对第4、6、10、14和18日的所有生物学重复（每个时间点n=3），均进行单通道微阵列检测。