Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis

Abstract

Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of S. cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes.

iPAR: a new reporter for eukaryotic cytoplasmic protein aggregation

“…Deletion of the N-terminal signal peptide (Δss) of CPY inhibits entry to the secretory pathway and consequently the hydrolase mislocalizes to the cytoplasm (78). The ΔssCPY* mutant, which aggregates in the cytoplasm, serves as a useful marker for protein aggregation (50, 52, 79, 80). However, the endogenous PRC1 promotor (81) typically used to induce expression of this aggregate marker is metabolically regulated (55, 56); therefore, expression, and aggregation, often vary depending on the specific growth and stress conditions resulting in potential difficulties of interpretation.…”

Fabrication of Microfluidic Devices for Continuously Monitoring Yeast Aging

“…This work was supported by NIH R01 AG068112 (to NH), AG056440 (to NH, JH), GM144595 (to NH, JH), and GM111458 (to NH). This protocol was derived from the original work of Paxman et al (2022).…”

“…After this point, devices should be used for experiments within two weeks [see Paxman et al (2022) for details on experimental setup]. As a reference, yeast cells growing in the device can be seen in Figure 5E and 5F.Validation of protocolPaxman et al (2022). Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis.…”

Exploring the Molecular Tapestry: Organ-Specific Peptide and Protein Ultrafiltrates and Their Role in Therapeutics

“…For example, RNA-binding proteins (RBPs) have been known to play a key role in regulating a broad spectrum of cellular processes; however, recent studies on small RBPs have shed light on the therapeutic potential of RBPs for various indications. These findings suggest the possible involvement and mechanisms of RBPs in anti-aging [ 6 , 7 ] and anti-cellular senescence [ 8 ]. Similarly, spliceosome and small protein-regulated lipid metabolism also exhibit positive regulation in aging and cellular senescence [ 9 , 10 ].…”