Mechanisms of In Vivo Ribosome Maintenance Change in Response to Nutrient Signals

Abstract

Control of protein homeostasis is fundamental to the health and longevity of all organisms. Because the rate of protein synthesis by ribosomes is a central control point in this process, regulation, and maintenance of ribosome function could have amplified importance in the overall regulatory circuit. Indeed, ribosomal defects are commonly associated with loss of protein homeostasis, aging, and disease (1–4), whereas improved protein homeostasis, implying optimal ribosomal function, is associated with disease resistance and increased lifespan (5–7). To maintain a high-quality ribosome population within the cell, dysfunctional ribosomes are targeted for autophagic degradation. It is not known if complete degradation is the only mechanism for eukaryotic ribosome maintenance or if they might also be repaired by replacement of defective components. We used stable-isotope feeding and protein mass spectrometry to measure the kinetics of turnover of ribosomal RNA (rRNA) and 71 ribosomal proteins (r-proteins) in mice. The results indicate that exchange of individual proteins and whole ribosome degradation both contribute to ribosome maintenance in vivo. In general, peripheral r-proteins and those with more direct roles in peptide-bond formation are replaced multiple times during the lifespan of the assembled structure, presumably by exchange with a free cytoplasmic pool, whereas the majority of r-proteins are stably incorporated for the lifetime of the ribosome. Dietary signals impact the rates of both new ribosome assembly and component exchange. Signal-specific modulation of ribosomal repair and degradation could provide a mechanistic link in the frequently observed associations among diminished rates of protein synthesis, increased autophagy, and greater longevity (5, 6, 8, 9).

RACK1 on and off the ribosome

“…To overcome the intrinsic stability of the RACK1-ribosome interaction that we observed, however, regulatory control via RACK1 ribosome occupancy would require hours for its stochastic departure from the ribosome or active mechanisms to release RACK1. Indeed, our findings are consistent with the possibility that the ribosome-bound and small pool of free RACK1 can exchange stochastically over the lifetime of a ribosome (t1/2 ≈ 5-7 days) (Dice and Schimke 1972;Nikolov et al 1987;Defoiche et al 2009;Mathis et al 2017). Such exchange has been proposed for other RPs and may take place during viral infections in bacteria (Mizuno et al 2017) and neuronal functions of mammals (Shigeoka et al 2018).…”

Pronounced energy restriction with elevated protein intake results in no change in proteolysis and reductions in skeletal muscle protein synthesis that are mitigated by resistance exercise

“…Nonetheless, we acknowledge that there are data that show a reduction in the phosphorylation of Akt and 4EBP-1 after 10 d of ER (5), as well as a reduction in the MPS response to protein ingestion during ER (4, 7). Data from rodents suggest that ER results in the down-regulation of the phosphorylation of protein synthesis-related proteins (Akt, mammalian target of rapamycin, rps6, and p70S6K) (35) and a reduction in active ribosomes (36). Thus, strategies that target the mammalian target of rapamycin complex 1 pathway, such as resistance exercise and increased protein intake (3), are important for the preservation of MPS and LBM during ER.…”

On-site ribosome remodeling by locally synthesized ribosomal proteins in axons

“…A number of previous studies call into question the widely held view of the ribosome as a stable molecular machine whose components remain unchangeable during its lifetime. For example, several RPs in the ribosome have higher turnover rates than other RP components, suggesting the possibility that individual RPs in the ribosome are replaced by free cytoplasmic (extra-ribosomal) RPs (Lastick and McConkey, 1976;Mathis et al, 2017).…”