The complex processes and interactions that regulate aging and determine lifespan are not fully defined for any organism. Here, taking advantage of recent technological advances in studying aging in budding yeast, we discovered a previously unappreciated relationship between the number of copies of the ribosomal RNA gene present in its chromosomal array and replicative lifespan (RLS). Specifically, the chromosomal ribosomal DNA (rDNA) copy number (rDNA CN) positively correlated with RLS and this interaction explained over 70% of variability in RLS among a series of wild-type strains. In strains with low rDNA CN,
SIR2 expression was attenuated and extrachromosomal rDNA circle (ERC) accumulation was increased, leading to shorter lifespan. Suppressing ERC formation by deletion of
FOB1 eliminated the relationship between rDNA CN and RLS. These data suggest that previously identified rDNA CN regulatory mechanisms limit lifespan. Importantly, the RLSs of reported lifespan-enhancing mutations were significantly impacted by rDNA CN, suggesting that changes in rDNA CN might explain the magnitude of some of those reported effects. We propose that because rDNA CN is modulated by environmental, genetic, and stochastic factors, considering rDNA CN is a prerequisite for accurate interpretation of lifespan data.Budding yeast,
Saccharomyces cerevisiae, has been a foundational model organism for the study of cellular aging. Cells divide asymmetrically and the mother cell undergoes a limited number of divisions, which defines the cell’s replicative lifespan (RLS). Measuring RLS is technically challenging and only recent advances have enabled more efficient screening for lifespan-modulating factors (
1–
5).A number of processes, pathways, and mechanisms have been implicated in yeast aging (reviewed in ref.
6), with regulators of the ribosomal RNA gene array (rDNA) representing perhaps the best-characterized group of lifespan modulators. Proteins that act at the rDNA locus modify rDNA stability and the formation of extrachromosomal rDNA circles (ERCs), a known aging factor in
S. cerevisiae (
7). Sir2, the defining member of the Sirtuin family of histone deacetylases, silences the rDNA locus and suppresses formation of ERCs (
8). Conversely, the protein Fob1 binds to a replication fork barrier site in the rDNA locus, decreases rDNA stability, and thus promotes the production of ERCs (
9,
10). Since the accumulation of ERCs in the mother cell limits its RLS,
sir2Δ and
fob1Δ strains are short and long lived, respectively (
8,
11).The rDNA locus is highly repetitive and dynamic. While 150 repeats are considered a normal copy number (CN) for the strain background used in this study, the number of repeats commonly ranges from 100 to 250 copies (
12). And while the size of the rDNA array is relatively stable for a limited number of divisions, rDNA CN can change on a timescale faster than the estimated mutation rate (
13). Thus, it may be considered a type of “contingency locus,” which is characterized by environmentally responsive genetic variation that results in distinct phenotypic outcomes (
14–
16).The rDNA copy number varies significantly in strains found in the wild and those used in the laboratory (
12,
13,
17–
19). This variation can occur spontaneously, but can also be introduced by standard laboratory DNA transformation protocols or changes in growth environment (
12,
13,
20). In addition, there are Sir2- and Fob1-dependent feedback mechanisms in place by which a “normal” rDNA CN is maintained through modulation of Sir2 expression levels (
21). Interestingly, rDNA array size is anticorrelated with ERC abundance in young cells, suggesting that chromosomal and extrachromosomal rDNA are in an equilibrium (
13). Despite this known connection between rDNA array size and Sir2 and ERC levels, no evidence for array size impacting lifespan has been found (
12,
15,
18).Yet, significant variability exists within reported lifespans of
S. cerevisiae. A metastudy found that the RLS of the same wild-type strains varied between 20 and 40, depending on the study in which it was reported (
22). This variability was attributed to a reporting bias and small sample sizes. However, these findings are also consistent with uncontrolled genetic or environmental factors contributing to the variability. In addition, a genome-wide screen measuring the RLS of deleted nonessential genes found a significant discrepancy between strains with opposing mating types carrying the same gene deletion (
23). This discrepancy was mostly attributed to statistical error due to a low number of cells analyzed, but was not fully explored. Given this large degree of variability, which likely impacts the interpretation of any lifespan measurement, we wanted to address the underlying cause. Here we show that the chromosomal rDNA copy number is an important determinant of replicative lifespan in yeast and can explain a large part of the reported variability in lifespan.
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