OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants.
OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants.
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转录组，蛋白质组学和代谢组数据的ONPLS整合显示在转基因Hipi-超氧化物歧化酶Populus植物的形成中的多层氧化应激反应。
DOI：
10.1186/1471-2164-14-893
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发表时间：
2013-12-17
期刊：
影响因子：
4.4
通讯作者：
Wingsle G
中科院分区：
文献类型：
--
作者：
Srivastava V;Obudulu O;Bygdell J;Löfstedt T;Rydén P;Nilsson R;Ahnlund M;Johansson A;Jonsson P;Freyhult E;Qvarnström J;Karlsson J;Melzer M;Moritz T;Trygg J;Hvidsten TR;Wingsle G
活性氧参与了植物的多种生理过程，包括各种生物和非生物胁迫反应。因此，植物的氧化胁迫耐受机制是复杂的，为了理解它们，需要在多个水平上表征不同的反应。在这里，我们提出了系统的氧化应激反应，在杨树的形成层区域的野生型控制和植物表达高等电点超氧化物歧化酶（hipI-SOD）的转录反义方向的分析数据整合显示更高的生产超氧化物。形成层是一个薄的细胞层，产生分化形成韧皮部或木质部的细胞，并被假设为转基因植物中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），使用最新开发的正交投影到潜在结构（称为OnPLS）进行整合。OnPLS是一种对称的多块方法，当分析两个以上的块时，它不依赖于分析的顺序。然后在绘制的途径图中可视化显着影响的基因，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）。这些结果提供了ROS代谢和氧化应激反应的系统水平信息，并表明氧化应激的一些初始反应可能有共同的途径。所提出的数据评估策略显示了编译复杂的多平台数据集以获得重要生物信息的有效方法。
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.
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影响因子：
5.3
作者：
Caruso M;Merelo P;Distefano G;La Malfa S;Lo Piero AR;Tadeo FR;Talon M;Gentile A
通讯作者：
Gentile A
影响因子：
7.2
作者：
Hoelscher, Dirk;Shroff, Rohit;Svatos, Ales
通讯作者：
Svatos, Ales
影响因子：
2.9
作者：
Datta, Riddhi;Sinha, Ragini;Chattopadhyay, Sharmila
通讯作者：
Chattopadhyay, Sharmila
影响因子：
7.4
作者：
Baxter, Charles J.;Redestig, Henning;Sweetlove, Lee J.
通讯作者：
Sweetlove, Lee J.
影响因子：
7.2
作者：
Bylesjo, Max;Eriksson, Daniel;Trygg, Johan
通讯作者：
Trygg, Johan