A genetically encoded metabolite sensor for malonyl-CoA

Malonyl-CoA is the rate-determining metabolite for long chain de novo fatty acid synthesis and allosterically inhibits the rate-setting step in long chain fatty acid β-oxidation. We developed a cell-based genetically encoded biosensor based on the malonyl-CoA responsive Bacillus subtilis transcriptional repressor, FapR, for living mammalian cells. Here, we show that fluctuations in malonyl-CoA, in mammalian cells, can regulate the transcription of a FapR-based malonyl-CoA biosensor. The biosensor reflects changes in malonyl-CoA flux regulated by malonyl-CoA decarboxylase and AMP-activated protein kinase in a concentration-dependent manner. To gain further insight into the regulatory mechanisms that affect fatty acid metabolism, we used the malonyl-CoA sensor to screen and identify several kinases. LIMK1 was identified and its expression was shown to alter both fatty acid synthesis and oxidation rates. This simple genetically encoded biosensor can be used to study the metabolic properties of live mammalian cells and enable screens for novel metabolic regulators.