Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana
Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana
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DOI：
10.1073/pnas.1300962110
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发表时间：
2013-04-30
影响因子：
11.1
通讯作者：
Baliga, Nitin S.
中科院分区：
文献类型：
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作者：
Ashworth, Justin;Coesel, Sacha;Baliga, Nitin S.
海洋硅藻是重要的初级生产者，在多样化和动态的环境中茁壮成长。从理论上讲，它们通过感知变化的环境并相应地调整它们的生理机能来做到这一点。使用模式物种海链藻，我们进行了详细的生理和转录组学调查，以衡量典型的硅藻生长在批量培养的特点，经常性的转录变化。大约40%的转录组变化显著且重复，反映了四种主要状态之间的大的、可再现的细胞状态转换：（i）“黎明”，12小时黑暗之后;（ii）“黄昏”，12小时光照之后;（iii）指数生长和营养补充;以及（iv）静止期和营养耗尽。在重复出现的黑暗期（黎明）结束时，数千个基因的表达增加，包括那些参与光合作用的基因（e.例如，在一个实施例中，核酮糖-1，5-二磷酸羧化酶加氧酶基因rbcS和rbcL），暗示了在基因调控水平上的大规模预期昼夜节律机制。伴随着四种细胞状态的转变，数百个编码感觉、信号和调节功能的基因的转录水平发生了重复的变化，提供了不同条件下高度协调的基因调控程序的初步图谱。几个假定的光传感和信号蛋白与周期性昼夜转换，这表明这些基因可能参与光敏感和昼夜调节细胞状态。这些结果开始解释，在全面的细节，硅藻基因调控程序如何在不同的环境条件下运作。这一动态分子过程的详细知识将是非常宝贵的新的假设生成和解释的遗传，环境和元转录组数据从现场研究。
Marine diatoms are important primary producers that thrive in diverse and dynamic environments. They do so, in theory, by sensing changing conditions and adapting their physiology accordingly. Using the model species Thalassiosira pseudonana, we conducted a detailed physiological and transcriptomic survey to measure the recurrent transcriptional changes that characterize typical diatom growth in batch culture. Roughly 40% of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-state transitions between four principal states: (i) "dawn," following 12 h of darkness; (ii) " dusk," following 12 h of light; (iii) exponential growth and nutrient repletion; and (iv) stationary phase and nutrient depletion. Increases in expression of thousands of genes at the end of the reoccurring dark periods (dawn), including those involved in photosynthesis (e. g., ribulose-1,5-bisphosphate carboxylase oxygenase genes rbcS and rbcL), imply large-scale anticipatory circadian mechanisms at the level of gene regulation. Repeated shifts in the transcript levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, providing a preliminary map of the highly coordinated gene regulatory program under varying conditions. Several putative light sensing and signaling proteins were associated with recurrent diel transitions, suggesting that these genes may be involved in light-sensitive and circadian regulation of cell state. These results begin to explain, in comprehensive detail, how the diatom gene regulatory program operates under varying environmental conditions. Detailed knowledge of this dynamic molecular process will be invaluable for new hypothesis generation and the interpretation of genetic, environmental, and metatranscriptomic data from field studies.