title: Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways.
abstract: 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 organismsRhodospirillum rubrumandBacillus subtilis, 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.
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Kyuil
authors.initials: K
authors.lastname: Cho
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Evans
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: B McKay
authors.initials: BM
authors.lastname: Wood
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Ritesh
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Institute for Microbiology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Tobias J
authors.initials: TJ
authors.lastname: Erb
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Warlick
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Gerlt
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Jonathan V
authors.initials: JV
authors.lastname: Sweedler
keywords: Active pathway detection; Isoprenoid biosynthesis; Liquid chromatography–mass spectrometry; Metabolomics; Methionine salvage; Quantitative real time polymerase chain reaction; Transcriptomics