Research Article: Proteomic analysis of age-dependent changes in protein solubility identifies genes that modulate lifespan

Date Published: February , 2012

Publisher: Blackwell Publishing Ltd

Author(s): Pedro Reis-Rodrigues, Gregg Czerwieniec, Theodore W Peters, Uday S Evani, Silvestre Alavez, Emily A Gaman, Maithili Vantipalli, Sean D Mooney, Bradford W Gibson, Gordon J Lithgow, Robert E Hughes.


While it is generally recognized that misfolding of specific proteins can cause late-onset disease, the contribution of protein aggregation to the normal aging process is less well understood. To address this issue, a mass spectrometry-based proteomic analysis was performed to identify proteins that adopt sodium dodecyl sulfate (SDS)-insoluble conformations during aging in Caenorhabditis elegans. SDS-insoluble proteins extracted from young and aged C. elegans were chemically labeled by isobaric tagging for relative and absolute quantification (iTRAQ) and identified by liquid chromatography and mass spectrometry. Two hundred and three proteins were identified as being significantly enriched in an SDS-insoluble fraction in aged nematodes and were largely absent from a similar protein fraction in young nematodes. The SDS-insoluble fraction in aged animals contains a diverse range of proteins including a large number of ribosomal proteins. Gene ontology analysis revealed highly significant enrichments for energy production and translation functions. Expression of genes encoding insoluble proteins observed in aged nematodes was knocked down using RNAi, and effects on lifespan were measured. 41% of genes tested were shown to extend lifespan after RNAi treatment, compared with 18% in a control group of genes. These data indicate that genes encoding proteins that become insoluble with age are enriched for modifiers of lifespan. This demonstrates that proteomic approaches can be used to identify genes that modify lifespan. Finally, these observations indicate that the accumulation of insoluble proteins with diverse functions may be a general feature of aging.

Partial Text

Longevity and aging phenotypes are under the influence of a large number of functionally diverse genes. Genes modulating lifespan are likely to affect multiple pathways and in many cases exert general effects on cellular homeostasis. Longevity of the nematode Caenorhabditis elegans is influenced by hundreds of genes encoding a range of signaling and metabolic processes including an insulin-like signaling pathway that regulates the FOXO transcription factor DAF-16 (Kenyon et al., 1993; Kimura et al., 1997; Ogg et al., 1997). Together with the stress response transcription factor, heat shock factor 1 (HSF-1), DAF-16 regulates the formation protein aggregates in C. elegans and also extend lifespan (Kenyon et al., 1993; Lin et al., 1997; Henderson & Johnson, 2001; Hsu et al., 2003; Cohen et al., 2006). Many of the targets of these transcription factors, such as the heat shock proteins, help maintain other proteins in functional states or target them for degradation. Over-expression of even one HSP-encoding gene was sufficient to confer stress resistance and lifespan extension in C. elegans and Drosophila melanogaster (Yokoyama et al., 2002; Walker & Lithgow, 2003; Morrow et al., 2004; Wang et al., 2004). This suggested that the maintenance of protein conformation is required for lifespan extension and that a loss of protein homeostasis could contribute to aging.

Aging is a major risk factor for a wide range of diseases including cancer, diabetes, and neurodegeneration. The accumulation of insoluble proteinaceous aggregates is a shared feature in the most common neurodegenerative diseases (Alzheimer’s, Parkinson’s, Huntington’s and amyotrophic lateral sclerosis), and these have been sometimes referred to as proteinopathies. We hypothesized that processes related to protein aggregation occurring during normal aging (in the absence of disease) may share features with pathologic processes underlying late-onset neurodegeneration. We thus considered a biochemical characterization of protein homeostasis and protein aggregation during normal aging important in understanding the cellular pathology of late-onset neurodegeneration.




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