Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: coarse grained views of metabolic pathways.
Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: coarse grained views of metabolic pathways.
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稳定同位素标记为动植物系统中的代谢物混合物的系统NMR分析：代谢途径的粗粒粒度。
DOI：
10.1371/journal.pone.0003805
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发表时间：
2008
期刊：
影响因子：
3.7
通讯作者：
Kikuchi, Jun
中科院分区：
文献类型：
--
作者：
Chikayama, Eisuke;Suto, Michitaka;Nishihara, Takashi;Shinozaki, Kazuo;Hirayama, Takashi;Kikuchi, Jun
在后基因组学和蛋白质组学时代，代谢表型已经成为一种重要的鸟瞰技术，可以应用于高等生物，如模式植物和动物系统。尽管基因分型技术在过去十年中得到了极大的发展，但由于难以进行自上而下的化学分析，代谢表型分析一直萎靡不振。在这里，我们描述了一种系统的核磁共振方法，用于对植物和动物系统中的代谢物混合物进行稳定同位素标记和分析。该分析方法包括用于活体的稳定同位素标记技术；通过使用新开发的基于HSQC的代谢物化学位移数据库并结合异核多维核磁共振光谱同时识别大量代谢物的系统方法；主成分分析；以及使用代谢系统的粗粒度概述的可视化方法。该数据库包含超过1000个1H和13C化学位移，对应于142种在相同物理化学条件下测量的代谢物。利用稳定同位素标记技术，系统地检测了模式植物、拟南芥T87培养细胞和无脊椎动物模型家蚕的~(13)C-HSQC谱中的>；450个HSQC峰。此外，高效的13C标记首次允许使用分析分离技术，如高等生物提取物中的3D HCCH-COSY光谱，进行可靠的信号分配。通过粗粒度表示，可以检测到与家蚕关键发育阶段变化有关的总体生理变化并将其分类，其中，根据56种已鉴定代谢物的组成变化，可视化地显示了与特定发育阶段相关的代谢途径的组织。根据给定代谢物的13C原子在56个已鉴定的13C-HSQC信号中随发育而变化的观察强度，我们已经确定了与能量和氮代谢相关的代谢网络的变化。
Metabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of given metabolites on development-dependent changes in the 56 identified 13C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism.
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影响因子：
5.4
作者：
Bundy, Jacob G.;Sidhu, Jasmin K.;Rana, Faisal;Spurgeon, David J.;Svendsen, Claus;Wren, Jodie F.;Sturzenbaum, Stephen R.;Morgan, A. John;Kille, Peter
通讯作者：
Kille, Peter
影响因子：
3.7
作者：
Huang JT;Leweke FM;Tsang TM;Koethe D;Kranaster L;Gerth CW;Gross S;Schreiber D;Ruhrmann S;Schultze-Lutter F;Klosterkötter J;Holmes E;Bahn S
通讯作者：
Bahn S
DOI：
10.1073/pnas.0405065101
发表时间：
2004-08-24
影响因子：
11.1
作者：
de Graaf, RA;Mason, GF;Behar, KL
通讯作者：
Behar, KL
影响因子：
46.9
作者：
Cheng, Alan C.;Coleman, Ryan G.;Huang, Enoch S.
通讯作者：
Huang, Enoch S.
影响因子：
64.8
作者：
Jeong, H;Tombor, B;Barabási, AL
通讯作者：
Barabási, AL