Integrative meta-analysis reveals that most yeast proteins are very stable

Abstract

Measurements for protein half-lives in yeast Saccharomyces cerevisiae reported large discrepancies, with median values between minutes to several hours. We present a unifying analysis that provides a consistent half-life estimate, based on our re-analysis of three published and one new dataset of cells grown under similar conditions. We found that degradation of many proteins can be approximated by exponential decay. Protein disappearance was primarily driven by dilution due to cell division, with cell doubling times ranging from ~2 to 3.5 hours across the four experiments. After adjusting for doubling time, protein half-lives increased to median values between ~7.5 to ~40 hours. Half-lives correlated with cell doubling time even after adjustment, implying that slow growth also slows protein degradation. All estimates were validated by multiple means and were robust to different analysis methods. Overall, protein stability correlated with abundance and showed weak enrichment for degradation signals such as degrons and disordered regions. Long-lived proteins often functioned in oxidation-reduction and amino acid synthesis. Short-lived proteins often functioned in ribosome biogenesis. Despite some overall differences in behavior, all methods were able to resolve subtle difference in half-lives of ribosomal proteins, e.g. the short lifespan of RPL10. Finally, our results help the design of future experiments: time series measurements need to cover at least two to three cell doubling times for accurate estimates, exponential decay provides a reasonable proxy for protein stability, and it can be sufficiently estimated with four measurement points. Words: 241All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery

“…Time to steady state will depend on the stability of the controlled protein. This is to hours for the stable protein Citrine, and the majority of yeast proteins have similar stability (Wiechecki et al, 2018). Those proteins with shorter halflives will reach steady state faster.…”

“…On the other hand, changes in the production rate a have no e↵ect on time to steady state, although both rates a↵ect the maximum level. Citrine is a remarkably stable protein (see Figure4-figure supplement 8), but recent data suggests that most (somewhere between 50-85% depending on the data set) of the yeast proteome is just as stable [13]. Therefore most other WTC 846 -controlled endogenous proteins will likely have a time to steady state around 7 hours, except those with a shorter half-life which will exhibit a shorter time to steady state.…”

Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instability

“…Protein half-lives in microorganisms are much longer than GTs, and take a similar value in human cells in culture. Thus most translation seems devoted to compensate the dilution caused more by growth rather than by degradation [29,30], except in cultured human cells in which the contributions of both are similar (Table 2). It should be noted that in nondividing cells, translation is quantitatively much less important because only protein degradation should be compensated [31].…”

Homeostasis in the Central Dogma of Molecular Biology: the importance of mRNA instability

“…Protein half-lives in microorganisms are much longer than GTs, and take a similar value in human cells in culture. Thus most translation seems devoted to compensate the dilution caused more by growth rather than by degradation (10,60), except in cultured human cells in which the contributions of both are similar (Table II). It should be noted that in nondividing cells, translation is quantitatively much less important because only protein degradation should be compensated (63).…”