title: A metabolomics-based method for studying the effect of yfcC gene in Escherichia coli on metabolism.
abstract: Metabolomics is a potent tool to assist in identifying the function of unknown genes through analysis of metabolite changes in the context of varied genetic backgrounds. However, the availability of a universal unbiased profiling analysis is still a big challenge. In this study, we report an optimized metabolic profiling method based on gas chromatography-mass spectrometry for Escherichia coli. It was found that physiological saline at -80°C could ensure satisfied metabolic quenching with less metabolite leakage. A solution of methanol/water (21:79, v/v) was proved to be efficient for intracellular metabolite extraction. This method was applied to investigate the metabolome difference among wild-type E. coli, its yfcC deletion, and overexpression mutants. Statistical and bioinformatic analysis of the metabolic profiling data indicated that the expression of yfcC potentially affected the metabolism of glyoxylate shunt. This finding was further validated by real-time quantitative polymerase chain reactions showing that expression of aceA and aceB, the key genes in glyoxylate shunt, was upregulated by yfcC. This study exemplifies the robustness of the proposed metabolic profiling analysis strategy and its potential roles in investigating unknown gene functions in view of metabolome difference.
authors: CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China.
authors: Xiyue
authors: X
authors: Wang
authors: School of Bioengineering, Dalian Polytechnic University, 116034 Dalian, China.
authors: Yuping
authors: Y
authors: Xie
authors: CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China. Electronic address: xuhe@medmail.com.cn.
authors: Peng
authors: P
authors: Gao
authors: Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
authors: Sufang
authors: S
authors: Zhang
authors: Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
authors: Haidong
authors: H
authors: Tan
authors: School of Bioengineering, Dalian Polytechnic University, 116034 Dalian, China.
authors: Fengxu
authors: F
authors: Yang
authors: School of Bioengineering, Dalian Polytechnic University, 116034 Dalian, China.
authors: Rongwei
authors: R
authors: Lian
authors: School of Bioengineering, Dalian Polytechnic University, 116034 Dalian, China. Electronic address: jingtian0306@hotmail.com.
authors: Jing
authors: J
authors: Tian
authors: CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China.
authors: Guowang
authors: G
authors: Xu
mesh_terms: D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D008401:Gas Chromatography-Mass Spectrometry; D006038:Glyoxylates / Q000378:metabolism; D055442:Metabolome; D055432:Metabolomics; D000432:Methanol / Q000737:chemistry; D060888:Real-Time Polymerase Chain Reaction; D015854:Up-Regulation; D014867:Water / Q000737:chemistry
chemical_list: D029968:Escherichia coli Proteins; D006038:Glyoxylates; D014867:Water; C031150:glyoxylic acid; D000432:Methanol
keywords: Escherichia coli; Gas chromatography–mass spectrometry; Metabolic profiling; Metabolomics; yfcC