Aging and neurodegeneration compromise proteostasis, the cellular system that regulates protein synthesis, folding, degradation, and localization, ultimately leading to the accumulation of protein aggregates. This process is particularly critical in the brain, where postmitotic neurons are especially susceptible to proteostasis disruption, a key factor in age-related neurodegenerative disorders. To investigate this, the short-lived killifish Nothobranchius furzeri, is an attractive model due to its brief lifespan and conserved hallmarks of brain aging, including gliosis, neuroinflammation, senescence, and protein aggregation. Here, the authors conducted a comprehensive analysis of proteostasis in the aging killifish brain, integrating measurements of transcripts, proteins, and translational dynamics.

To dissect age-associated disruption of proteostasis in the Nothobranchius furzeri brain, the study integrated multiple omics approaches. RNA-seq and DIA mass spectrometry were used to quantify transcript and protein abundance, enabling calculation of a “decoupling score” that identified systematic transcript–protein mismatches. Cross-validation with TMT-based proteomics confirmed reproducibility. Multiple linear regression revealed that protein abundance, half-life (from mouse brain datasets), and amino acid composition significantly predicted decoupling, with lysine- and arginine-rich proteins—such as DNA repair and RNA-binding factors—most affected. Subcellular fractionation and detergent solubility profiling demonstrated that aging selectively altered ribosomal and respiratory chain complexes, with mitochondrial proteins showing increased aggregation and compositional remodelling, while cytosolic ribosomal proteins declined despite elevated transcript levels. Chronic in vivo proteasome inhibition (bortezomib) reproduced some proteostasis defects but induced distinct decoupling signatures, indicating non-equivalence with aging. Ribosome profiling (Ribo-Seq) further uncovered age-dependent translation elongation defects, including increased ribosome pausing and collisions at polybasic codons, mechanistically linking aberrant translation dynamics to reduced protein abundance and aggregation of ribosomal and nucleic acid–binding complexes.

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