Cho Kyuil, Evans Bradley S, Wood B McKay, Kumar Ritesh, Erb Tobias J, Warlick Benjamin P, Gerlt John A, Sweedler Jonathan V
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Institute for Microbiology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8093 Zurich, Switzerland.
Metabolomics. 2014 Sep 3;2014(August):503-17. doi: 10.1007/s11306-014-0713-3.
While recent advances in metabolomic measurement technologies have been dramatic, extracting biological insight from complex metabolite profiles remains a challenge. We present an analytical strategy that uses data obtained from high resolution liquid chromatography-mass spectrometry and a bioinformatics toolset for detecting actively changing metabolic pathways upon external perturbation. We begin with untargeted metabolite profiling to nominate altered metabolites and identify pathway candidates, followed by validation of those pathways with transcriptomics. Using the model organisms and , our results reveal metabolic pathways that are interconnected with methionine salvage. The rubrum-type methionine salvage pathway is interconnected with the active methyl cycle in which re-methylation, a key reaction for recycling methionine from homocysteine, is unexpectedly suppressed; instead, homocysteine is catabolized by the transsulfuration pathway. Notably, the non-mevalonate pathway is repressed, whereas the rubrum-type methionine salvage pathway contributes to isoprenoid biosynthesis upon 5'-methylthioadenosine feeding. In this process, glutathione functions as a coenzyme in vivo when 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) methylsulfurylase catalyzes dethiomethylation of MTXu 5-P. These results clearly show that our analytical approach enables unexpected metabolic pathways to be uncovered.
尽管代谢组学测量技术最近取得了显著进展，但从复杂的代谢物谱中提取生物学见解仍然是一项挑战。我们提出了一种分析策略，该策略使用从高分辨率液相色谱 - 质谱获得的数据以及一套生物信息学工具，用于检测外部扰动后活跃变化的代谢途径。我们首先进行非靶向代谢物谱分析，以提名改变的代谢物并识别途径候选物，然后用转录组学验证这些途径。使用模式生物 和 ，我们的结果揭示了与甲硫氨酸挽救相互关联的代谢途径。红螺菌型甲硫氨酸挽救途径与活性甲基循环相互关联，在活性甲基循环中，同型半胱氨酸再甲基化（从同型半胱氨酸回收甲硫氨酸的关键反应）意外受到抑制；相反，同型半胱氨酸通过转硫途径分解代谢。值得注意的是，非甲羟戊酸途径受到抑制，而在喂食5'-甲硫基腺苷时，红螺菌型甲硫氨酸挽救途径有助于类异戊二烯生物合成。在此过程中，当1-甲硫基-D-木酮糖5-磷酸（MTXu 5-P）甲基硫转移酶催化MTXu 5-P的脱硫甲基化时，谷胱甘肽在体内作为辅酶起作用。这些结果清楚地表明，我们的分析方法能够揭示意想不到的代谢途径。
