Diurnal Transcriptional Regulation of Endosymbiotically Derived Genes in the Chlorarachniophyte Bigelowiella natans.
Diurnal Transcriptional Regulation of Endosymbiotically Derived Genes in the Chlorarachniophyte Bigelowiella natans.
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DOI：
10.1093/gbe/evw188
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发表时间：
2016-09-11
影响因子：
3.3
通讯作者：
Hirakawa Y
中科院分区：
文献类型：
--
作者：
Suzuki S;Ishida K;Hirakawa Y
绿蛛形藻具有由绿藻次生内共生获得的复杂质体，质体中含有内共生体的残核，即所谓的核形态。由于基因从内共生体向宿主的大量转移，许多涉及质体和核形态的蛋白质都由核基因组编码。基因组序列为内共生衍生基因的命运提供了蓝图；然而，这些基因的转录调控仍然知之甚少。为了深入了解内共生基因的进化，我们沿着光周期和暗周期同步的氯蛛形纲植物Bigelowiella natans的细胞周期进行了全基因组转录谱分析。我们的比较分析表明，7751个核基因（21706个基因中的35.7%）的转录水平在昼夜/细胞周期中显著振荡，其中包括780个和147个基因，分别用于推测的质体和核形靶向蛋白。这些基因的聚类分析揭示了与光合作用、碳代谢、翻译和DNA复制等特定生物过程相关的转录网络的存在。有趣的是，与其他光合作用生物不同的是，在黎明前诱导了许多叶绿体靶向蛋白的转录本。与核基因相比，99%的核形态基因在循环过程中组成性表达。我们还发现核形态DNA复制将由核编码的病毒样DNA聚合酶控制。本研究结果表明，核形态基因沿昼夜周期失去转录调控，核基因对包括核形态在内的复杂质体起调控作用。
Chlorarachniophyte algae possess complex plastids acquired by the secondary endosymbiosis of a green alga, and the plastids harbor a relict nucleus of the endosymbiont, the so-called nucleomorph. Due to massive gene transfer from the endosymbiont to the host, many proteins involved in plastid and nucleomorph are encoded by the nuclear genome. Genome sequences have provided a blueprint for the fate of endosymbiotically derived genes; however, transcriptional regulation of these genes remains poorly understood. To gain insight into the evolution of endosymbiotic genes, we performed genome-wide transcript profiling along the cell cycle of the chlorarachniophyte Bigelowiella natans, synchronized by light and dark cycles. Our comparative analyses demonstrated that transcript levels of 7,751 nuclear genes (35.7% of 21,706 genes) significantly oscillated along the diurnal/cell cycles, and those included 780 and 147 genes for putative plastid and nucleomorph-targeted proteins, respectively. Clustering analysis of those genes revealed the existence of transcriptional networks related to specific biological processes such as photosynthesis, carbon metabolism, translation, and DNA replication. Interestingly, transcripts of many plastid-targeted proteins in B. natans were induced before dawn, unlike other photosynthetic organisms. In contrast to nuclear genes, 99% nucleomorph genes were found to be constitutively expressed during the cycles. We also found that the nucleomorph DNA replication would be controlled by a nucleus-encoded viral-like DNA polymerase. The results of this study suggest that nucleomorph genes have lost transcriptional regulation along the diurnal cycles, and nuclear genes exert control over the complex plastid including the nucleomorph.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3.7
作者：
Idoine AD;Boulouis A;Rupprecht J;Bock R
通讯作者：
Bock R
DOI：
10.1073/pnas.1506469112
发表时间：
2015-09-22
影响因子：
11.1
作者：
Blanc, Guillaume;Gallot-Lavallee, Lucie;Maumus, Florian
通讯作者：
Maumus, Florian
影响因子：
5.1
作者：
Farinas, B;Mary, C;Moreau, H
通讯作者：
Moreau, H
影响因子：
10.7
作者：
Hirakawa, Yoshihisa;Suzuki, Shigekatsu;Ishida, Ken-ichiro
通讯作者：
Ishida, Ken-ichiro