Deep Proteome Analysis Identifies Age-Related Processes in C. elegans

Abstract

SummaryEffective network analysis of protein data requires high-quality proteomic datasets. Here, we report a near doubling in coverage of the C. elegans adult proteome, identifying >11,000 proteins in total with ∼9,400 proteins reproducibly detected in three biological replicates. Using quantitative mass spectrometry, we identify proteins whose abundances vary with age, revealing a concerted downregulation of proteins involved in specific metabolic pathways and upregulation of cellular stress responses with advancing age. Among these are ∼30 peroxisomal proteins, including the PRX-5/PEX5 import protein. Functional experiments confirm that protein import into the peroxisome is compromised in vivo in old animals. We also studied the behavior of the set of age-variant proteins in chronologically age-matched, long-lived daf-2 insulin/IGF-1-pathway mutants. Unexpectedly, the levels of many of these age-variant proteins did not scale with extended lifespan. This indicates that, despite their youthful appearance and extended lifespans, not all aspects of aging are reset in these long-lived mutants.

Dietary Restriction and AMPK Increase Lifespan via Mitochondrial Network and Peroxisome Remodeling

“…In addition, peroxisome import and protein expression decrease with age (Narayan et al, 2016). We therefore asked if peroxisomes have a role in drp-1;fzo-1 longevity.…”

“…To determine if peroxisomal function is required for drp-1;fzo-1 longevity we performed RNAi of prx-5 (ortholog of mammalian peroxisome biogenesis factor 5 (PEX5)). PRX-5/PEX5 is involved in the import of peroxisomal matrix enzymes (Narayan et al, 2016). Consistent with this and as previously reported (Narayan et al, 2016), prx-5 RNAi blocks import into peroxisomes, resulting in the mRFP-PTS1 fluorescence signal appearing diffuse, compared to punctate signal characteristic of peroxisomes in the control (Figure S5).…”

“…PRX-5/PEX5 is involved in the import of peroxisomal matrix enzymes (Narayan et al, 2016). Consistent with this and as previously reported (Narayan et al, 2016), prx-5 RNAi blocks import into peroxisomes, resulting in the mRFP-PTS1 fluorescence signal appearing diffuse, compared to punctate signal characteristic of peroxisomes in the control (Figure S5). Demonstrating that peroxisome function is required for drp-1;fzo-1 longevity, prx-5 RNAi blocks the increased lifespan of drp-1;fzo-1 double mutant animals (Figures 6H and 6I).…”

“…Mitochondria and peroxisomes function coordinately in several pathways, and share several components of the fission machinery including DRP1 (Rambold et al, 2015; Schrader, 2006; Sugiura et al, 2017). Peroxisome protein expression and import were recently shown to decrease with age in C. elegans (Narayan et al, 2016), however until now, it was unknown whether a longevity-associated role existed for interplay between these organelles. Our data reveal that AMPK and DR specifically modulate peroxisomes with age, suggesting the functional requirement - perhaps involving a metabolic shift towards increased FAO - may be of particular importance in later life.…”

Peroxisomal Dysfunction in Age-Related Diseases

“…Surprisingly, the number of peroxisomes is increased in older cells, suggesting accumulation of the defective organelles with aging [24]. Recently, a quantitative mass-spectrometry-based study in Caenorhadbditis elegans identified ~30 peroxisomal proteins whose abundance decreased with aging [32]. One such protein identified was Pex5, an import receptor for peroxisomal matrix proteins containing a conserved C-terminal tripeptide called peroxisomal targeting sequence 1 [33,34].…”