A Two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways

Abstract

Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response to persistent transcription-blocking DNA damage, although the relevant lesions have not been identified. Here we show that loss of NTH-1, the only Base Excision Repair (BER) enzyme known to initiate repair of oxidative DNA damage inC. elegans, restores normal lifespan of the short-lived NER deficient xpa-1 mutant. Loss of NTH-1 leads to oxidative stress and global expression profile changes that involve upregulation of genes responding to endogenous stress and downregulation of ILS. A similar, but more extensive, transcriptomic shift is observed in the xpa-1 mutant whereas loss of both NTH-1 and XPA-1 elicits a different profile with downregulation of Aurora-B and Polo-like kinase 1 signaling networks as well as DNA repair and DNA damage response genes. The restoration of normal lifespan and absence oxidative stress responses in nth-1;xpa-1 indicate that BER contributes to generate transcription blocking lesions from oxidative DNA damage. Hence, our data strongly suggests that the DNA lesions relevant for aging are repair intermediates resulting from aberrant or attempted processing by BER of lesions normally repaired by NER.

Active transcriptomic and proteomic reprogramming in theC. elegansnucleotide excision repair mutant xpa-1

“…32,39 In our laboratory we have measured the mean lifespan of an unbiased population and found a 3-4 d reduced mean lifespan, but no reduction in maximum lifespan when the animals fed on OP50. 31 This result was independently confirmed in a collaborating laboratory which also showed that normal median lifespan was regained if we grow the same strain on E. coli HT115(DE3). 36 Hence, the lifespan of xpa-1 mutants is somewhat shorter than the isogenic wild-types, but it is influenced by external factors such as nutrition.…”

“…As expected from the near normal phenotype, xpa-1 mutants do not show the extensive transcriptomic modulation seen in segmental progeroid NER-defective mice. However, we, 31,36 and others, 51 identified a small yet informative set of genes differentially expressed in xpa-1 mutants. Gene set enrichment analyses (GSEA) revealed that the biological process (BP) "determination of adult lifespan" was the only overrepresented BP among the regulated genes.…”

“…We found that the steady-state levels of cdA and cdG were reduced in xpa-1 mutants, which argues against the notion that stochastic accumulation of these lesions is the cause of lifespan reduction. Although it is possible that accumulation of lesions in a few subsets of cells could be important, our observation that deletion of the BER enzyme NTH-1 restored normal lifespan in the xpa-1 mutants and suppressed the characteristic upregulation of oxidative stress response genes in xpa-1 mutants, 31 are difficult to reconcile with passive accumulation of DNA damage being the instigator of these complex phenotypes. Instead, this suggests that reprogramming of xpa-1 mutants is an active response.…”

“…However, nth-1-null mutants showed normal mean and maximum lifespan. 31 This suggests that extensive redundancy was not a reason for the lack of accelerated aging in DNA glycosylase-deficient mice. In fact, this would support the prevailing idea that BER substrates do not contribute to aging.…”

“…Overexpression and nuclear translocation of the SKN-1 target gene GST-4 confirmed that xpa-1 mutants experience oxidative stress. 31,36 We also used quantitative proteomics to assess whether the transcriptomic signatures were reflected at the level of the proteome. We used a newly developed technique called isobaric peptide terminal labeling (IPTL) technology, 52 which can be used to label proteins in freshly prepared extracts from whole worms 36 or from isolated tissues like the germline.…”