In today’s research materials, scientists investigating the aging of the brain report on their use short-lived killifish. The researchers show that a decline in proteasomal function precedes the destabilization of protein complexes and the formation of harmful protein aggregates, a feature of neurodegenerative conditions. The proteasome is a complex piece of protein machinery, an assembly of numerous distinct proteins into a functional whole. It is responsible for breaking down unwanted and damaged proteins, recycling their component parts to be reused in the synthesis of other proteins.

Increases in proteasomal activity have been shown to improve health and longevity in short-lived species. This has largely been achieved by providing increased amounts of rate-limiting protein components of a proteasome, thereby increasing the number of functional proteasomes present in cells. A lack of proteasomal activity should be damaging to cells in a number of ways, both by allowing broken proteins and other molecular waste to persist, but also by reducing the supply of recycled raw materials for protein synthesis. Indeed, it is well understood that proteasomal activity declines with age, and it is not surprising to see this decline implicated as a contributing cause of age-related degeneration.

Out of balance – Ability to eliminate spent proteins influences brain aging and individual life span

Researchers have used transcriptomic and proteomic methods to investigate the chain of molecular events that lead to loss of protein homeostasis during brain aging. The researchers used Nothobranchius furzeri (killifish) as a model of aging to study mechanisms triggering protein homeostasis dysfunction. They have a life span of only 3-12 months, and thus age-dependent processes are exacerbated in this species, making it easier to detect changes in the concentration of RNAs and proteins, as compared to other model organisms.

“When comparing the data for the different age groups, we found that almost half of the approximately 9000 proteins that we managed to quantify are affected by aging.” These age-related changes result in abnormal regulation of proteins (subunits) that compose macromolecular protein complexes, the types of machinery responsible for all cellular activities. Protein complexes are built by different proteins that need to be assembled in specific ratios. Our cells have mechanisms to guarantee the proper building of these complexes by regulating the precise (stoichiometric) number of specific subunits. This tightly regulated process, however, is impaired in aging.

There is a progressive loss of stoichiometry of protein complexes during aging, mainly affecting the ribosome, which is one of the most important protein complexes in the cell, responsible for producing all other proteins. The researchers demonstrated that ribosomes do not get adequately formed in old brains and aggregate, potentially influencing vital functions in the cell. Aggregation of ribosomes is not exclusive to killifish but also happens in mice, suggesting it is a conserved feature of brain aging.

Proteasomes are complexes of protein molecules that digest and recycle old or defective proteins and are an essential part of the protein homeostasis network (“garbage chipper” of the cell). The authors were able to show that proteasome activity is reduced early and progressively during the course of adult life and causes loss of protein complexes stoichiometry. They induced a reduction of proteasome activity during early adult life of the killifish using a specific drug for just four days and observed a premature aging signature including disrupted ratios of several protein complexes.  

The team also compared the gene expression data of more than 150 killifish with their lifespan. The analysis showed that the individuals’ lifespan could be predicted based on changes in the expression of genes encoding for proteasomal proteins: fish that showed a greater decrease in proteasome transcripts at the beginning of life lived considerably shorter than fish able to maintain or increase proteasome expression. This finding supports the hypothesis that the reduction of proteasome activity is an early driver of aging in vertebrates.

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

A progressive loss of protein homeostasis is characteristic of aging and a driver of neurodegeneration. To investigate this process quantitatively, we characterized proteome dynamics during brain aging in the short-lived vertebrate Nothobranchius furzeri combining transcriptomics and proteomics. We detected a progressive reduction in the correlation between protein and mRNA, mainly due to post-transcriptional mechanisms that account for over 40% of the age-regulated proteins. These changes cause a progressive loss of stoichiometry in several protein complexes, including ribosomes, which show impaired assembly/disassembly and are enriched in protein aggregates in old brains.

Mechanistically, we show that reduction of proteasome activity is an early event during brain aging and is sufficient to induce proteomic signatures of aging and loss of stoichiometry in vivo. Using longitudinal transcriptomic data, we show that the magnitude of early life decline in proteasome levels is a major risk factor for mortality. Our work defines causative events in the aging process that can be targeted to prevent loss of protein homeostasis and delay the onset of age-related neurodegeneration.