Quiescence is a conserved, reversible state of proliferative arrest, characterized by changes in cell physiology and metabolism. Many cells spend a considerable part of their lifetime in quiescence, including adult stem cells or microorganisms facing unfavorable environmental conditions. Cells can remain quiescent for long periods of time while retaining their viability and reproductive capacity, indicating a need to maintain protein homeostasis. Given the changes in intracellular organization, it has been unclear how protein quality control (PQC) functions in quiescent cells. In our recent study, we examined model misfolded proteins expressed in glucose-depleted quiescent yeast cells and found that quiescent cells maintain an active PQC that relies primarily on selective protein degradation, requiring the ubiquitin-proteasome system, intact nucleus-vacuole junctions and autophagy. Our results highlight the relevance of mitigating misfolded proteins in quiescence.

How protein quality control is maintained during acute metabolic stress remains poorly understood. In budding yeast, abrupt glucose depletion rapidly lowers ATP levels and leads to the formation of chaperone-containing inclusions, suggesting that ATP-dependent degradation of misfolded proteins may be compromised when energy becomes limiting. Here we find that selective degradation of misfolded proteins remains active during acute glucose starvation despite reduced cellular ATP levels. Using model misfolded substrates in yeast Saccharomyces cerevisiae , we show that misfolded proteins continue to be efficiently degraded throughout both early and late phases of acute glucose depletion. This degradation requires the proteasome and depends on its functional 19S regulatory particle, indicating that ATP-dependent proteasomal activity persists during metabolic stress. We further find that nucleus–vacuole junctions (NVJs) promote efficient degradation during prolonged glucose starvation, revealing a role for organelle contact sites in supporting proteostasis under energy limitation. Together, these findings indicate that cells preserve proteasome-mediated proteostasis during acute glucose starvation, while NVJ membrane contact sites help sustain degradation capacity when metabolic resources are scarce.

Processed meat products represent a major challenge for proteomic species identification due to extensive thermal treatment and protein structural changes. In this study, species-specific peptides in pork, chicken, and bovine meat products were identified using a directed fragmentation-assisted de novo sequencing workflow that combines 4-formylbenzene-1,3-disulfonic acid (FBDA) peptide derivatization, dual-polarity data-independent mass spectrometry (DIA-MS), and Protein Acrobat de novo sequencing software. Comparative analysis of non-fractionated and strong cation exchange (SCX)-fractionated pork luncheon samples improved peptide and protein identification after fractionation, with 312 peptides and 115 protein groups detected exclusively in fractionated samples. Species-specific peptides were predominantly assigned to conserved muscle-related proteins, including myosin, troponin, and tropomyosin, while sequence variability enabled reliable species discrimination despite protein conservation across species. To evaluate applicability for food fraud detection, mixed meat samples containing 10% chicken in pork or bovine matrices were analyzed, reflecting potential economically motivated adulteration through substitution with lower-cost meat components. Several chicken-specific peptides remained detectable in both mixtures, demonstrating robustness of the FBDA-assisted peptide sequencing combined with SCX fractionation and DIA-MS for detection of adulteration in complex processed food matrices. These findings establish a mass spectrometry-driven orthogonal method to ELISA testing for fast, reliable and accurate metaproteome analysis of highly processed food.