Aging disrupts the brain’s protein production machinery, study in killifish suggests

A recent study published in the journal Aging sheds light on how aging interferes with the brain’s ability to produce key proteins, potentially triggering a cascade of dysfunctions that contribute to age-related decline and neurodegenerative diseases. The researchers found that in aging killifish (a short-lived vertebrate used as a model for studying aging) the brain becomes less efficient at translating specific types of proteins. These disruptions appear to be driven by ribosomal stalling during protein synthesis, rather than changes in gene expression.

Aging affects nearly every aspect of brain function, but the molecular underpinnings of this decline remain complex and difficult to disentangle. One common feature of aging is the breakdown of proteostasis, the cellular process that manages the production, folding, and clearance of proteins. When proteostasis fails, damaged or misfolded proteins can accumulate and interfere with normal cellular function, a phenomenon that has been repeatedly linked to disorders such as Alzheimer’s and Parkinson’s disease.

Despite the centrality of proteostasis to aging, scientists still debate whether its decline is a cause or consequence of other age-related changes, such as DNA damage or mitochondrial dysfunction. Part of the challenge has been the lack of integrative studies that simultaneously examine multiple layers of gene expression—from transcription to translation to protein regulation—within the same tissue over time.

“Brain aging is characterized by a plethora of canonical molecular and cellular phenotypes (also known as aging hallmarks), such as DNA damage, splicing defects and proteostasis collapse, and by a generalized impairment of the entire RNA- and protein-biosynthetic chain on one hand and protein misfolding and inflammation on the other hand. It is widely recognized that these hallmark are interconnected, develop gradually and none can be singularly indicated as the initial driver,” said study author Alessandro Cellerino, an associate professor at Scuola Normale Superiore and Leibniz Chair at the Leibniz Institute on Aging – Fritz Lipmann Institute.

To address this gap, the researchers used the African turquoise killifish (Nothobranchius furzeri), which has a naturally short lifespan and develops many of the same brain aging features seen in mammals, including inflammation, gliosis, and spontaneous neurodegeneration. This allowed the researchers to capture a wide molecular snapshot of aging across multiple stages of life.

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The researchers used a combination of RNA sequencing and mass spectrometry to track mRNA and protein levels across the lifespan of the killifish. In theory, if a gene’s mRNA level remains stable, its protein product should also stay consistent.

But the study revealed a disconnect: while mRNA levels for many genes remained steady, the actual protein levels declined with age. This discrepancy, which the researchers refer to as “decoupling,” was especially pronounced in proteins enriched with basic amino acids like lysine and arginine—components commonly found in DNA- and RNA-binding proteins.

These proteins play essential roles in gene expression, DNA repair, and mitochondrial function. Their reduced presence in aging brains suggests that the protein synthesis machinery becomes less efficient at producing certain protein types. The authors linked this decline to a phenomenon called “ribosome pausing”—a disruption in the translation process where the ribosome stalls when decoding specific sequences, particularly those rich in basic amino acids.

To test the role of protein degradation, the team partially inhibited the proteasome—the cell’s protein recycling system—in adult fish. This manipulation mimicked some but not all of the protein changes seen in aging brains. It did not replicate the loss of basic amino acid-rich proteins, indicating that translation, rather than degradation, was the key bottleneck in older brains.

The study also employed ribosome profiling, a method that reveals which mRNA sequences are being actively translated. This analysis showed that ribosome stalling became more frequent with age, especially at sequences coding for basic amino acids. Notably, this stalling correlated with increased protein aggregation, providing a mechanistic link between impaired translation and the buildup of harmful protein clumps.

“Our recent multi-omics study in the aging killifish brain revealed increased translation pausing at transcripts encoding ribosomal proteins and proteins enriched in basic (positively charged) amino acids,” Cellerino told PsyPost. “Increased pausing at specific mRNAs correlates with reduced synthesis of their protein products, independently of changes in mRNA levels. The affected proteins include DNA repair enzymes, RNA polymerases, splicing factors, RNA transport proteins, ribosomal subunits, and the broader translational machinery. This pausing is also associated with misfolding of nascent proteins and the activation of an inflammatory stress response.”

“Our results naturally lead to the hypothesis that increased ribosome pausing plays a causal role in the impaired biogenesis of DNA- and RNA-binding proteins enriched in basic amino acids. This may represent a unifying upstream mechanism in brain aging, linking genome instability and reduced biosynthesis of RNA and protein to protein misfolding and inflammation.”

Additionally, the researchers observed that aging brains showed a marked reduction in the number of fully assembled ribosomes, which may limit the brain’s ability to meet its protein production needs. This unexpected shift in protein production could represent a compensatory adaptation, though the long-term effects remain unclear.

“The most surprising finding is that a reduction in the number of ribosomes paradoxically increased the translation of mRNAs with the highest affinity for ribosomes, such as those coding for mitochondrial respiration complexes,” Cellerino explained. “This is likely because an excessively high ribosome concentration on these transcripts normally impairs translational elongation.”

While the study presents compelling evidence that aging disrupts protein synthesis through ribosome pausing and selective translation failure, it stops short of establishing direct causation. The authors note that more work is needed to determine whether relieving ribosome pausing can delay or reverse signs of brain aging. Another open question is whether these mechanisms are conserved in mammals, including humans.

The findings suggest that targeted interventions—such as drugs that modulate translational efficiency or ribosome function—could eventually play a role in delaying age-associated brain disorders. However, the transferability of these results from killifish to humans remains to be demonstrated.

Going forward, the researchers plan to explore whether similar protein synthesis issues emerge in human brain tissue and to test whether restoring translational control can alter the trajectory of brain aging. They also emphasize that their dataset represents one of the most comprehensive molecular maps of brain aging to date, covering transcriptomics, proteomics, amino acid levels, tRNA profiles, and post-translational modifications.

“This study represents the most extensive molecular resource on brain aging to date, including profiling of free amino acids, total tRNAs, charged tRNAs, the transcriptome, translatome, proteome, three types of post-translational modifications, protein solubility, and subcellular localization,” Cellerino said. “It also validates the killifish as an innovative model organism for studying brain aging.”

The study, “Altered translation elongation contributes to key hallmarks of aging in the killifish brain,” was authored by Domenico Di Fraia, Antonio Marino, Jae Ho Lee, Erika Kelmer Sacramento, Mario Baumgart, Sara Bagnoli, Till Balla, Felix Schalk, Stephan Kamrad, Rui Guan, Cinzia Caterino, Chiara Giannuzzi, Pedro Tomaz da Silva, Amit Kumar Sahu, Hanna Gut, Giacomo Siano, Max Tiessen, Eva Terzibasi-Tozzini, Eugenio F. Fornasiero, Julien Gagneur, Christoph Englert, Kiran R. Patil, Clara Correia-Melo, Danny D. Nedialkova, Judith Frydman, Alessandro Cellerino, and Alessandro Ori.