Nutrient signaling, stress response, and interorganelle communication are non-canonical determinants of cell fate

Abstract

Isogenic cells can manifest distinct cellular fates for a single stress, however the nongenetic mechanisms driving such fates remain poorly understood. Here, we implement a robust multi-channel live-cell imaging approach to uncover noncanonical factors governing cell fate. We show that in response to acute glucose removal (AGR), budding yeast undergo distinct fates becoming either quiescent or senescent. Senescent cells fail to resume mitotic cycles following glucose replenishment but remain responsive to nutrient stimuli. Whereas quiescent cells manifest starvation-induced adaptation, senescent cells display perturbed endomembrane trafficking and defective nucleus-vacuole junction (NVJ) expansion. Surprisingly, we also show senescence occurs in the absence of lipid droplets. Importantly, we identify the nutrient-sensing linked kinase Rim15 as a key biomarker that predicts cell fates before AGR stress. We propose that isogenic yeast challenged with acute nutrient shortage contain determinants that influence their post-stress fate, and demonstrate that specific nutrient signaling, stress-response, endomembrane trafficking, and inter-organelle tether biomarkers are early indicators for long-term fate outcomes.

Remodelling of Nucleus-Vacuole Junctions During Metabolic and Proteostatic Stress

“…This might be the case for other scenarios of cumulative cellular damage, for instance during cellular ageing (Chen et al, 2020(Chen et al, , 2021Li et al, 2020;Moreno and Aldea, 2020;Mouton et al, 2020). Though NVJs are not essential to drive entry into quiescence upon glucose starvation, prominent NVJ expansion seems to accompany this transition (Wood et al, 2020). Cells can persist in a quiescent state for a long time, awaiting re-entry into cell cycle upon more favourable conditions.…”

“…Accumulating studies on the dynamic remodelling and physiological relevance of NVJs highlight these contact sites as hubs to integrate metabolic cues and stress responses to determine cellular fate (Hariri et al, 2018;Lord and Wente, 2020;Wood et al, 2020;Tosal-Castano et al, 2021). While compromised NVJ formation remains without major effect on cellular viability in unperturbed cells (Wood et al, 2020), disruption of specific aspects of proteostasis, as shown for deficiencies in NPC assembly (Lord and Wente, 2020), necessitate efficient NVJ formation for survival. This might be the case for other scenarios of cumulative cellular damage, for instance during cellular ageing (Chen et al, 2020(Chen et al, , 2021Li et al, 2020;Moreno and Aldea, 2020;Mouton et al, 2020).…”

“…Cells within a clonal population that rapidly expanded NVJs during acute starvation were more likely to become quiescent, while senescent cells mostly lacked NVJ expansion. Still, the presence of Nvj1 was not required for entry into quiescence (Wood et al, 2020). Thus, even though NVJs seem to respond to signalling pathways coordinating the cellular path towards quiescence or senescence upon acute starvation, a distinct physiological role for Nvj1 in this process has not been identified yet.…”

“…Entry into quiescence has been shown to be accompanied by a drastic remodelling of distinct organelles and cellular structures (Sagot and Laporte, 2019). Recent work from Wood et al demonstrates that this organellar remodelling entails a prominent expansion of NVJs that serves as predictor of cell fate (Wood et al, 2020). Using abrupt restriction of glucose to force exit from cell cycle, the authors assessed biomarkers for nutrient signalling, interorganellar crosstalk, stress response and organelle homeostasis to predict quiescence versus senescence decisions of individual cells within an isogenic yeast population (Figure 2B) (Wood et al, 2020).…”

“…Recent work from Wood et al demonstrates that this organellar remodelling entails a prominent expansion of NVJs that serves as predictor of cell fate (Wood et al, 2020). Using abrupt restriction of glucose to force exit from cell cycle, the authors assessed biomarkers for nutrient signalling, interorganellar crosstalk, stress response and organelle homeostasis to predict quiescence versus senescence decisions of individual cells within an isogenic yeast population (Figure 2B) (Wood et al, 2020). In an elegant approach using multi-colour time-lapse imaging and automated singlecell analysis, they monitored protein-fluorophore chimeras, including Nvj1, throughout growth in high glucose, acute starvation for several hours and subsequent glucose replenishment.…”