Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
BMC Genomics. 2013 Dec 17;14:893. doi: 10.1186/1471-2164-14-893.
Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.
The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways.
The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
活性氧（ROS）参与植物中多种生理过程的调节，包括各种生物和非生物胁迫反应。因此，植物的氧化应激耐受机制很复杂，需要对多个层次的多种反应进行特征描述，以理解这些机制。在这里，我们通过整合对野生型对照和反义表达高等电点超氧化物歧化酶（hipI-SOD）转录物的形成导致超氧化物产生增加的拟南芥形成层区域分析数据，展示了杨树对氧化应激的系统反应。形成层是一层薄细胞，它产生分化为韧皮部或木质部的细胞，被假设是转基因植物表型扰动的主要原因。来自多个平台的数据，包括转录组学（微阵列分析）、蛋白质组学（UPLC/QTOF-MS）和代谢组学（GC-TOF/MS、UPLC/MS 和 UHPLC-LTQ/MS），使用最近开发的称为正交投影到潜在结构（OnPLS）的对称多块方法进行了整合。OnPLS 是一种对称的多块方法，当分析超过两个块时，不依赖于分析的顺序。然后在绘制的途径图中可视化受显著影响的基因、蛋白质和代谢物。
在转基因植物中似乎受到显著影响的主要类别是与氧化还原调节、碳代谢和蛋白质降解相关的途径，例如糖酵解和戊糖磷酸途径（PPP）。结果提供了 ROS 代谢和对氧化应激反应的系统水平信息，并表明一些对氧化应激的初始反应可能共享共同途径。
所提出的数据评估策略显示了一种编译复杂、多平台数据集以获取显著生物学信息的有效方法。
