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Reduce ERCs pathway

  1. 70% increase in maximal lifespan. hrm1-1 mutant had a 70% increase in life span, from around 25 replications to around 40, and the mechanism may be reduced ERCs (Defossez 1999). (How many cells were used in the experiment?)

  2. Increase in maximal lifespan. Fob1 mutants increased lifespan and also reduced ERCs (Defossez 1999).

Silencing chromatin pathway


Nutrient restriction pathway

Conserved hallmarks of aging between yeast and humans:

DNA integrity

Metabolic networks

Nutrient response

Chromatin dynamics

Proteostasis fidelity

Transcriptional signatures

Hallmarks of aging in yeast not in humans:

ERC accumulation

Hallmarks of aging in humans not in yeast:

Telomere attrition

Aging in yeast

Yeast Introduction

Yeasts are eukaryotic, single-celled microorganisms around 3–40 µm in diameter. They are classified as fungi. They are thought to have originated hundreds of millions of years ago. There are at least 1,500 known species, and are present in various environments throughout the world. Yeasts may have evolved from multicellular ancestors.


S. Cerevisiae Introduction

Saccharomyces cerevisiae (also called budding yeast) is round and around 5–10 μm in diameter. S. cerevisiae converts carbohydrates to carbon dioxide and alcohols through a process called fermentation. The products of this reaction have been used in baking and alcohol production for thousands of years, predating recorded history. The desire to cultivate wheat to ferment into bread may have motivated humans to adopt an agricultural lifestyle.


S. cerevisiae is not airborne, requiring a vector to spread. Ancient people used S. cerevisiae in things like the skin of grapes for fermentation without knowing what was performing the reaction. Anton van Leeuwenhoek, who discovered microorganisms in the 1670s, identified S. cerevisiae in 1680, although he thought it was not alive. Pasteur connected S. cerevisiae to fermentation in 1856. S. cerevisiae became a model organism for studying aging in the 1960s. S. cerevisiae has been found in the human gut microbiome as well as living on human skin. 


S. Cerevisiae Genome

S. cerevisiae cells can exist as both a diploid cell with 16 chromosome pairs or as a haploid cell with 16 chromosomes. These 16 chromosomes contain about 12 million base pairs, 6,275 genes, and 250 introns. Only about 5,800 of these genes correspond to open reading frames and are believed to be functional, and about 30% of these functional genes have homologs in humans.


S. Cerevisiae Mitosis and Meiosis

Chromosome III contains one of two alleles of a mating-type locus called MAT - a MATa or a MATα locus. This locus is only expressed in the haploid cells and determines their mating type - either a or α. Both haploid and diploid yeast cells reproduce by mitosis, referred to as budding. 


Diploid cells can additionally undergo meiosis to produce four haploid spores: two a spores and two α spores. Meiosis usually only occurs in response to adverse conditions, such as nutrient deprivation. Ideal conditions for a yeast cell include a temperature of about 30 °C. Yeast spores can exist in a dormant state for a long amount of time waiting for better conditions (how long?). 


Under suitable conditions, spores can become metabolically active haploid cells which can reproduce by budding and are capable of mating with other haploid cells of the opposite mating type to produce a stable diploid cell. 


Defining Yeast Aging

Budding in S. cerevisiae is asymmetric. The mother cell retains most of the misfolded proteins that have accumulated, while the bud daughter cell inherits mostly well-formed proteins, most of which are the proteins newly created during mitosis. One notable exception is the spindle pole body (SPB) of the budding yeast, which is its centrosome equivalent. The SPB duplicates in a conservative manner, producing an old and a new SPB. The old SPB is usually inherited by the bud (McMurray 2009).


The number of times an S. cerevisiae cell has budded is referred to as its replicative lifespan, which is counted in generations. Each budding generation increases the likelihood of the yeast cell’s death, which is referred to as replicative aging. Notable hallmarks of yeast replicative aging are an increased time between budding generations and a budding scar on the yeast cell wall. Budding usually does not happen at the same place twice, perhaps because of the previous generation’s budding scar. Yeast cells do not lose telomeres from budding. The mechanisms of asymmetric budding break down as the yeast cell ages replicatively and the division becomes more symmetric (K.A. Steinkraus 2009). After about twenty divisions (source needed), the S. cerevisiae cell exits the normal cell cycle and enters into a state of replicative senescence. 


S. cerevisiae replicative senescence was discovered in 1959 (Mortimer and Johnston ‘59) but was not commonly known until about a decade later (need evidence) and this is when they become a model organism for the study of aging. Yeast replicative senescence actually predates Haylick’s famous 1961 discovery that non-stem human somatic cells also do not divide indefinitely, and enter into a state of senescence. Hayflick’s 1961 paper does not cite Mortimer and Johnston’s paper. 


The chronological lifespan of a yeast cell is the length of time that the yeast cell survives without dividing. Nutrient exhaustion is one method of increasing chronological lifespan in yeast cells. There have been numerous interventions (discussed below) that have increased the maximal replicative lifespan of yeast cells. 



As S. cerevisiae cells age, rDNA circles arise independently of the chromatin rDNA. These extrachromosomal rDNA circles (ERCs) replicate with each subsequent division and in general accumulate in the mother cell and are not inherited by the daughter cell. Hence, old and especially senescent yeast cells are characterized by enlarged and fragmented nuclei (Sinclair 1997 ). 


Yeast Nucleolus

The nucleolus of S. cerevisiae is composed mainly of 100–200 copies of rDNA in tandem on chromosome XII. Unlike DNA replication in general, rDNA is unique in yeast in that replication is unidirectional. Yeast have cellular machinery to block the replication machinery in one direction in the nucleolus. The FOB1 protein is required for this blocking, as FOB1 negative mutants have bidirectional rDNA replication. HRM is a class of mutations in yeast that affect recombination in the rDNA and not other DNA. Hrm1 mutants enjoy a much longer life span. The cloning of HRM1 reveals that it is identical to FOB1. Induction of ERCs reduces the lifespan of yeast.


Life span of individual yeast cells

1959 - Robert Mortimer and John Johnston. The paper that originally discovered yeast cell senescence. 


The serial cultivation of human diploid cell strains

1961 - Hayflick and Moorhead. A famous paper that first documented senescence in a human fibroblast cell. 


Elimination of Replication Block Protein Fob1 Extends the Life Span of Yeast Mother Cells

1999 - Pierre-Antoine Defossez. This study showed that mutation of FOB1 reduces the formation of ERCs and extends yeast replicative life span. hrm1-1 mutant had a 70% increase in life span, from around 25 replications to around 40, and the mechanism may be reduced ERCs. 


Replicative Aging in Yeast

2009 - K.A. Steinkraus and M. Kaeberlein. In this review article, I learned that mammals have many nucleoli. There are mechanisms to ensure mitosis is asymmetric with the aberrant proteins staying with the mother, with the notable exception of the spindle body. These mechanisms break down as the yeast cell ages replicatively and the division becomes more symmetric. The chronological time between divisions increases. Budding leaves scars on the cell wall of the yeast, and budding usually does not happen at the same place twice. Yeast do not lose telomeres from mitosis.


Histone H4 lysine-16 acetylation regulates cellular lifespan

2009 - Weiwei Dang. Yeast Sir2 upregulates chromatin silencing by removing H4K16ac and recruiting other silencing proteins. This study shows an age-associated decrease in Sir2 protein abundance accompanied by an increase in H4K16ac and loss of histones at specific subtelomeric regions in replicatively old yeast cells, which results in compromised transcriptional silencing at these loci.


Septins: molecular partitioning and the generation of cellular asymmetry

2009 - Michael McMurray and Jeremy Thorner. Septins are proteins that are expressed in all eukaryotes except higher plants. They form octamer complexes similar to histones, and these complexes form larger rods. These rods function as scaffolds and contribute to the asymmetric division when mitosis when mitosis is asymmetric. Septins are long-lived, lasting multiple cell cycles. Duplication and distribution of septins are semiconservative. However, the spindle pole body (SPB) of the budding yeast, which is its centrosome equivalent, duplicates in a conservative manner, producing an old and a new SPB. The old SPB is usually inherited by the bud.


Elevated histone expression promotes lifespan extension

2010 - Jason Feser, Jessica Tyler. This study shows that aging is accompanied by a loss of histone proteins in yeast, and significant lifespan extension was achieved by genetically modifying the yeast to have more histones. They also provided evidence of a decrease of H3 in mice with age. 


The SAGA histone deubiquitinase module controls yeast replicative lifespan via Sir2 interaction

2014 - Mark A. McCormick, Weiwei Dang, et al. Yeast strains lacking genes SGF73, SGF11, and UBP8 - which encode SAGA/SLIK complex histone deubiquitinase module (DUBm) components - are exceptionally long-lived. In particular, the sgf73 deletion strain extended the maximum replicative lifespan of yeast by 53%. SGF73 and UBP8 deletions have identical lifespan increases and deleting multiple of these genes has no enhanced effect, suggesting that all these deletions work by altering the same pathway. SIR2 is required for this life extension, suggesting that these deletions enhance the function of Sir2. Sir2 has many functions, but the authors suggest that it is the telomere-proximal gene and rDNA silencing functions of Sir2 that are being enhanced. This leads to a decrease in the accumulation of ERCs. Replicative lifespan of either sgf73Δ or ubp8Δ far surpasses the extension observed by overexpression of SIR2 or deletion of FOB1. Ataxin-7 is the human Sgf73 ortholog and the cause of spinocerebellar ataxia type 7.


Yeast replicative aging: a paradigm for defining conserved longevity interventions

2014 - 


Insights into the Conserved Regulatory Mechanisms of Human and Yeast Aging

2020 - Rashmi Dahiya. Review article.