10 Jan 2023
by Richa

Summary- paper 1: Dynamic metabolome profiling uncovers potential TOR signaling genes

Stella Reichling, Peter F Doubleday, Tomas Germade, Ariane Bergmann, Robbie Loewith, Uwe Sauer, Duncan Holbrook-Smith

eLife, 2023

Questions/gaps addressed:

  • what is the metabolomic response of TOR related mutants when exposed to Rapamycin? Can these responses be used as signature to identify new genes in the pathway? Can this approach be more generalized for unknown pathways?

Major hypotheses:

  • Metabolomic signatures can be used to cluster and functional chracterization of unknown genes

Key methods:

  • High-throughput metabolomics by flow injection analysis chromatography free mass spectrometry (FIA-MS): provides broad coverage at < 1min/sample

  • Pearson correlation between metabolome profiles of TOR vs receptor collection. Manhattan distances between profiles of correlation followed by hierarchical clustering. False positive rate set to 0.2

  • Label free quantitative (LFQ) proteomics to compare proteomic changes.

Major takeaways:

  • Dynamic high-throughput metabolomics of 164 non-essential yeast deletion mutants (include 80 known TOR related, and 80 receptor related- supplement 1)- found 3 candidates as positive regulators of TOR signaling (YML079W/CFF1; Bck1; Cla4)

  • Cool and interesting approach with potential. Mechanistic insight or if the effects of the candidates are direct or indirect is unclear.

  • Data visualization web resource