Uncovering the spatial realm of cell metabolism: filament formation of CTP synthase in yeast

Abstract

Cell metabolism is comprised of a complex network of interactions. Regulating metabolic flux, especially in stress conditions, is essential to cell survival. An increasing number of studies suggest that the spatial organization of metabolic enzymes within the cell plays a critical role in regulating metabolic flux. In Saccharomyces cerevisiae, it is speculated that enzyme sequestration is a common mechanism of downregulating product synthesis rates in starvation conditions. Particularly, sequestration by filament formation is reported as a prevalent phenomenon. In this study, we investigate filament formation of CTP synthase in situ, using a cryo-CLEM tomography approach. We identify three individual instances of filament bundles and characterize them through filament averaging. To enable efficient implementation of rapid GPU-based template matching for locating CTP synthase in non-filamentous form, we develop a subvolume-based template matching approach. Altogether, we present a methodology that can be adapted for mapping out the spatial organization of metabolic pathways, to improve our understanding of how cells control their metabolism.