Regulation of Cellular Metabolism through Phase Separation of Enzymes

Abstract

Metabolism is the sum of the life-giving chemical processes that occur within a cell. Proper regulation of these processes is essential for all organisms to thrive and prosper. When external factors are too extreme, or if internal regulation is corrupted through genetic or epigenetic changes, metabolic homeostasis is no longer achievable and diseases such as metabolic syndrome or cancer, aging, and, ultimately, death ensue. Metabolic reactions are catalyzed by proteins, and the in vitro kinetic properties of these enzymes have been studied by biochemists for many decades. These efforts led to the appreciation that enzyme activities can be acutely regulated and that this regulation is critical to metabolic homeostasis. Regulation can be mediated through allosteric interactions with metabolites themselves or via post-translational modifications triggered by intracellular signal transduction pathways. More recently, enzyme regulation has attracted the attention of cell biologists who noticed that change in growth conditions often triggers the condensation of diffusely localized enzymes into one or more discrete foci, easily visible by light microscopy. This reorganization from a soluble to a condensed state is best described as a phase separation. As summarized in this review, stimulus-induced phase separation has now been observed for dozens of enzymes suggesting that this could represent a widespread mode of activity regulation, rather than, or in addition to, a storage form of temporarily superfluous enzymes. Building on our recent structure determination of TOROIDs (TORc1 Organized in Inhibited Domain), the condensate formed by the protein kinase Target Of Rapamycin Complex 1 (TORC1), we will highlight that the molecular organization of enzyme condensates can vary dramatically and that future work aimed at the structural characterization of enzyme condensates will be critical to understand how phase separation regulates enzyme activity and consequently metabolic homeostasis. This information may ultimately facilitate the design of strategies to target the assembly or disassembly of specific enzymes condensates as a therapeutic approach to restore metabolic homeostasis in certain diseases.

Widespread remodelling of proteome solubility in response to different protein homeostasis stresses

“…The clusters included proteins that increased and decreased solubility and suggests that the remodeling of the proteome solubility is functionally linked to core responses linked to the protein homeostasis stress induction. The key point here is that there is evidence that enzymes involved in metabolism pathways, including specifically those found in our study as hotspots for changes in solubility, form molecular condensates from phase separation in yeast and other cell models (84). This finding suggests a link between metabolic responses, stress granule formation and proteome solubility remodeling involving a quarter of the proteome.…”

Chaperone-Facilitated Aggregation of Thermo-Sensitive Proteins Shields Them from Degradation during Heat Stress

“…Even though they differ in their origin, the fate of 37 C and 42 C PACs is common: refolding during stress recovery in an Hsp104-dependent manner ( Figure 5). Reversible aggregation of specific proteins, such as Cdc19, may represent a strategy to allow metabolic re-programming during environmental changes, including growth at 42 C (Prouteau and Loewith, 2018;Saad et al, 2017); we propose that formation of Proteins enriched in these fractions were subjected to trypsin digestion and identified by label-free LC-MS/MS. (B) Venn diagram of the overlap between insoluble proteins identified at each growth condition.…”

Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis

“…Target-of-Rapamycin Complex 1 (TORC1) is the master regulator of protein homeostasis that controls the switch between anabolic protein synthesis and catabolic autophagy [38][39][40] . In yeast, TORC1 activity is regulated by glucose via increased pH/Gtr1-signalling, and indirectly by amino acid availability and energy charge via Gcn2 and Snf1/AMPK, respectively 22,27,40,41 . TORC1 activity is also sensitive to molecular crowding, pH and osmolality 31,39,42 .…”