The fate of lysine: Non-targeted stable isotope analysis reveals parallel ways for lysine catabolization in Phaeobacter inhibens

• Published in: PloS one Vol. 12; no. 10; p. e0186395
• Main Authors: Reimer, Lorenz C, Will, Sabine E, Schomburg, Dietmar
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.10.2017; Public Library of Science (PLoS)
• Subjects: Amino acids; Bacteria; Biochemistry; Bioinformatics; Biology and Life Sciences; Chromatography, High Pressure Liquid; Citric Acid Cycle; Degradation; Earth Sciences; Ecology and Environmental Sciences; Gas Chromatography-Mass Spectrometry; Genetic aspects; High-performance liquid chromatography; Identification; Intermediates; Internet; Isotopes; Isotopes - metabolism; Liquid chromatography; Lysine; Lysine - metabolism; Malate; Mass spectrometry; Metabolism; Metabolites; Physical Sciences; Physiological aspects; Plasmids; Proteomics; Pseudomonas putida; Research and Analysis Methods; Rhodobacteraceae - metabolism; Scientific imaging; Stable isotopes; Stem cells; Studies; Succinyl-CoA; Tricarboxylic acid cycle; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0186395

For a detailed investigation of the degradation of lysine in Phaeobacter inhibens DSM 17395, stable isotope experiments with uniformly 13C labeled L-lysine were carried out with lysine adapted cells and the metabolites were analyzed using GC/MS and HPLC/MS. A non-targeted stable isotope analysis was used which compares labeled and not labeled samples to determine the Mass Isotopomer Distribution not only for known metabolites but for all labeled compounds in our GC/MS analysis. We show that P. inhibens uses at least two parallel pathways for the first degradation steps of lysine. Further investigations identified L-pipecolate as an L-lysine degradation intermediate in P. inhibens. The analysis of HPLC/MS data as well as the labeling data of tricarboxylic acid (TCA) cycle intermediates show that L-lysine is not only catabolized directly to acetyl-CoA but also via the ethylmalonyl-CoA-pathway, leading to entry points into the TCA cycle via acetyl-CoA, succinyl-CoA, and malate. Altogether the presented data give a detailed insight into the catabolization of L-lysine following the fate of 13C labeled carbon via several ways into the TCA cycle.