Researchers here look into protein synthesis rates in nematodes engineered to live twice as long via manipulation of the DAF-16 gene, analogous to FOXO in mammals. The goal is to reach for a better understanding of the relationship between various classes of molecular damage, quality assurance mechanisms, repair activities, and rate of aging. This is, needless to say, a very complex topic, full of counterintuitive results and baroque interactions between intricate evolved subsystems of the cell.
Cellular protein quality can be maintained by proteolytic elimination of damaged proteins and replacing them with newly synthesized copies, a process called protein turnover. Protein turnover rates have been estimated using SILAC (stable isotope labeling by amino acids in cell culture) in prokaryotes and eukaryotes. The last decade has witnessed a growing interest in the analysis of whole-organism proteome dynamics in metazoans using the same approach. Progressive decrease in protein synthesis and proteolytic clearance through the autophagosomal and proteasome systems with age results in a strong increase in protein half-life in many species, including nematodes. This finding led to the formulation of the protein turnover hypothesis, stating that the increase in protein dwell time with age results in the accumulation of damaged and misfolded proteins. The progressive decrease in general protein turnover might be responsible for the ultimate collapse of proteome homeostasis in aging cells, possibly also driving the aging process itself.
In this vein, it is expected that increased protein turnover rates would help to maintain a young undamaged proteome and extend the lifespan. However, in yeast and C. elegans, genetically induced attenuation of protein synthesis extends, rather than shortens, the lifespan. Moreover, proteomic studies suggest that low overall protein synthesis is a hallmark of long-lived C. elegans, either by dietary restriction or by mutation in the insulin signaling pathway. Similar findings have been reported for diet-restricted mice. Hence, why does reducing protein synthesis promotes lifespan extension? And how can this be reconciled with the protein turnover hypothesis, which predicts enhanced turnover rates in long-lived organisms? We hypothesized that DAF-16-dependent longevity in C. elegans is supported by differential protein turnover. Downregulating turnover of the majority of proteins could save much energy, which, in turn, could be spent at prioritized maintenance of specific proteins that are crucial to extend the lifespan. To test this hypothesis, we produced a dataset that reveals patterns of intracellular protein dynamics in the C. elegans model and shifts of these patterns that occur in the long-lived daf-2 mutant via DAF-16 activation.
Contrary to our hypothesis, we did not discover a delineated set of proteins with turnover priority in daf-2 mutants. The majority of the detected proteins (56%) exhibit prolonged half-lives in daf-2, whereas turnover of the remaining proteins is unchanged. Only three proteins (CPN-3, ASP-4, and VIT-6) display marginally significant higher turnover rates in daf-2, but they lack a clear biological relationship. One of our most notable observations is the drastic slowdown in turnover of the translation machinery in daf-2 mutants. This slowdown coincides with decreased levels of ribosomal proteins and enzymes with predicted function in ribosome assembly and biogenesis we and others observed earlier and probably relates to the decreased protein synthesis rates in this mutant. Our observation of decreased protein turnover in daf-2 mutants is not entirely surprising. In agreement with our observations, researchers demonstrated extended ribosomal and mitochondrial half-lives in long-lived, calorie-restricted mice. The insulin/IGF1 signaling pathway is a main activator of anabolic metabolism; hence, it is conceivable that mutants in this pathway show reduced protein turnover. This reduction allows the worm to save much energy, which may be diverted to other processes that support longevity, such as the synthesis of trehalose, a chemical chaperone that stabilizes membranes and proteins, for which a role in daf-2 longevity has already been shown.