Multilayered Control of Protein Turnover by TORC1 and Atg1

Abstract

Graphical Abstract Highlights d S. cerevisiae proteins harbor a minimum of 45,000 distinct phosphorylation sites d TORC1 and Atg1 regulate at least 26 protein and lipid kinases d Atg1 phosphorylates upstream regulators of TORC1 d TORC1 phosphorylates Atg29 to inhibit autophagy SUMMARYThe target of rapamycin complex 1 (TORC1) is a master regulator of cell homeostasis, which promotes anabolic reactions and synchronously inhibits catabolic processes such as autophagy-mediated protein degradation. Its prime autophagy target is Atg13, a subunit of the Atg1 kinase complex that acts as the gatekeeper of canonical autophagy. To study whether the activities of TORC1 and Atg1 are coupled through additional, more intricate control mechanisms than simply this linear pathway, we analyzed the epistatic relationship between TORC1 and Atg1 by using quantitative phosphoproteomics. Our in vivo data, combined with targeted in vitro TORC1 and Atg1 kinase assays, not only uncover numerous TORC1 and Atg1 effectors, but also suggest distinct bi-directional regulatory feedback loops and characterize Atg29 as a commonly regulated downstream target of both TORC1 and Atg1. Thus, an exquisitely multilayered regulatory network appears to coordinate TORC1 and Atg1 activities to robustly tune autophagy in response to nutritional cues.

Phosphoproteomic Analysis across the Yeast Life Cycle Reveals Control of Fatty Acyl Chain Length by Phosphorylation of the Fatty Acid Synthase Complex

“…The majority of the identified p-peptides (77%) feature a single p-site ( Figure 1D) and have a phosphorylation situated primarily on serine (S) (78%) and to a lesser extent on a threonine (T) (19%) or tyrosine (Y) residue (3%) ( Figure 1E). Overall, the obtained results and data metrics are congruent with previously published phosphoproteomics (Hu et al, 2019;Oliveira et al, 2015;Paulo and Gygi, 2015) and proteomics data (Figure S1) (Casanovas et al, 2015). Furthermore, by stringent statistical filtering, we found that the abundance of 7,922 p-peptides (55%) belonging to 1,792 phosphoproteins is significantly changed (q-value < 0.01) by >2-fold at least at one time point relative to the exponential phase (6 h) ( Figure 1C).…”

Sorting Nexins in Protein Homeostasis

“…Consistent with this, deletion of Snx4 results in insufficient PAS formation and a delayed autophagic response [138]. In a more recent phosphoproteomics study, Snx4 was identified as a direct substrate for Atg1 [139]. This phosphorylation event may direct Snx4 away from its physiological functions in endosomal sorting and selective autophagy and towards its role in starvation-induced autophagy.…”

Transcriptomic Analysis of Pichia pastoris (Komagataella phaffii) GS115 During Heterologous Protein Production Using a High-Cell-Density Fed-Batch Cultivation Strategy

“…Starvation induces autophagy in part through deactivation of the nutrient-sensing TORC1 kinase. Deactivation of TORC1 promotes the recruitment of the most upstream set of autophagy-regulating proteins, members of the ATG1 complex, to the phagophore assembly site (PAS) (Hu et al, 2019). ATG1 not only promotes autophagy induction, but may also facilitate late stages of auto-phagosome biogenesis (Kijanska and Peter, 2013).…”