One theory of aging is that the genome and other DNA of an organism accumulate increasing numbers of errors with age and that these errors are responsible for the macroscopic phenomenon we call “aging.” See the second theory of aging covered in my treatise, After a discussion of background I focus in this blog entry on a special topic related to very-recent research news, the role of the sirtuin SIRT6 in assuring genomic stability. I also touch on other possible roles of SIRT6 in assuring longevity.
Background on genomic stability, aging and DNA repair
The DNA in a healthy organism is hardly static. “In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day. (ref )” If there are on the order of 30 trillion cells in the body, it takes a calculator with a lot more decimal places than mine has to show the number of such daily molecular DNA damage events. “Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell’s ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell’s genome, which affect the survival of its daughter cells after it undergoes mitosis(ref ).” So, the health of the genome is driven by the dynamic interaction between an ongoing onslaught of DNA damage on the one hand and the body’s DNA repair and cell-policing machinery on the other hand. Damage can include:
* Double strand DNA breaks discussed in the blog entry DNA repair cleanup failure – a root cause for cancers. These are “breaks that can occur naturally in cell differentiation or that are created by radiation and certain chemicals.” The current view is that most spontaneous chromosomal rearrangements result from DSBs created mainly during DNA replication as a result of broken, stalled or collapsed replication forks(ref).”
* Aneuploidy– extra or missing chromosomes. Aneuploidy can occur during cell divisions
* Errors introduced inthe DNA repair process itself or in the process of repair cleanup. Some of these are discussed in the two aforementioned blog entries.
* Other types of DNA errors such as those listed here.
DNA damage can impede normal cell differentiation and division, can lead to cancers, Alzheimer’s Disease and numerous other diseases, and produce the phenotype of aging. Somatic mutation rate in Drosophila (fruit flies) correlates with aging(ref). Further, chromosomal and DNA damage is known in mice as well as Drosophila to increase with aging and vary by organ. For example, the amount of aneuploidy gain in chromosome 18 in mouse brains increases with age. (F. Faggioli, unpublished data). And, spontaneous mutation frequency in mouse intestines increases drastically with age but remains essentially flat with age in mouse spleen, testis and brains(ref).
The body has developed sophisticated mechanisms for detecting DNA damage and DNA repair. Discussion of some of the central DNA repair mechanisms are provided in the two aforementioned blog entries (ref)(ref). If the topic fascinates you, you could also look at these representative articles and their “related citations” lists: Dancing on damaged chromatin: functions of ATM and the RAD50/MRE11/NBS1 complex in cellular responses to DNA damage, Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template, DNA damage and repair in Alzheimer’s disease, and DNA repair, mitochondria, and neurodegeneration.
And of course, if a cell decides that DNA damage has occurred beyond that which can be repaired, if it has not already turned cancerous it brings its apoptotic mechanisms into play which is to say, commits suicide. See this blog entry on the P53 “guardian of the genome.”
In previous blog entries I have discussed how Sirtuins, SIRT1 in particular, might affect aging through their impact on the insulin/Igf1-like signaling pathway(ref)(ref)(ref)(ref), the pathway involved in calorie restriction life extension(ref). “Limited overexpression of the Sir2 gene (in humans known as SIRT1) results in a lifespan extension of about 30%, if the lifespan is measured as the number of cell divisions the mother cell can undergo before cell death(ref).” Other Sirtuins also affect aging through different pathways. Here, I will be concerned with the role of SIRT6 in a DNA repair pathway known as homologous recombination.
SIRT6 and DNA repair
As far back as 2006 it was recognized that SIRT6 plays a critical role in DNA repair. The 2006 publication Certainly can’t live without this: SIRT6 summarized the situation: “Cellular metabolic rates might regulate aging by impinging on genomic stability through the DNA repair pathways. A new study published in Cell (Mostoslavsky et al., 2006) reports that deficiency in one of the mammalian Sir2 homologs, SIRT6, results in genome instability through the DNA base excision repair pathway and leads to aging-associated degenerative phenotypes.” The Mostoslavsky paper Genomic instability and aging-like phenotype in the absence of mammalian SIRT6 reported “Here, we demonstrate that SIRT6 is a nuclear, chromatin-associated protein that promotes resistance to DNA damage and suppresses genomic instability in mouse cells, in association with a role in base excision repair (BER). SIRT6-deficient mice are small and at 2-3 weeks of age develop abnormalities that include profound lymphopenia, loss of subcutaneous fat, lordokyphosis, and severe metabolic defects, eventually dying at about 4 weeks. We conclude that one function of SIRT6 is to promote normal DNA repair, and that SIRT6 loss leads to abnormalities in mice that overlap with aging-associated degenerative processes.” Exactly how SIRT6 worked to support DNA damage repair was not known at that time.
A 2008 publication SIRT6 in DNA repair, metabolism and ageing looked more carefully at the role of SIRT6 as well as the other sirtuins in DNA repair and promoting longevity. “Overexpression or hyperactivity of sirtuins in many organisms – including yeast, worms, flies, and potentially fish and mammals – promotes longevity . Mammals possess at least seven sirtuins, termed SIRT1–SIRT7 [3, 4]. Sirtuins exert their effects via NAD+-dependent enzymatic modification of other proteins: — SIRT6 deficiency causes a degenerative syndrome with progeroid features — From the standpoint of ageing research, SIRT6 deficiency causes the most striking phenotype among all the sirtuin knockouts. At the cellular level, SIRT6 deficiency leads to slow growth and increased sensitivity to certain forms of genotoxic damage. In addition, SIRT6-deficient cells show increased spontaneous genomic instability, characterized by numerous non-clonal chromosomal aberrations . These findings suggest a defect in the ability of SIRT6-deficient cells to cope with DNA damage.” This paper goes on to speculate how SIRT6 may affect DNA damage repair, but more clarity on this subject is provided by very-recent publications cited here directly below.
Exactly how SIRT6 impacts on DNA repair is characterised in a September 2010 publication Human SIRT6 Promotes DNA End Resection Through CtIP Deacetylation. “We found that human SIRT6 has a role in promoting DNA end resection, a crucial step in DNA double-strand break (DSB) repair by homologous recombination. SIRT6 depletion impaired the accumulation of replication protein A and single-stranded DNA at DNA damage sites, reduced rates of homologous recombination, and sensitized cells to DSB-inducing agents. We identified the DSB resection protein CtIP [C-terminal binding protein (CtBP) interacting protein] as a SIRT6 interaction partner and showed that SIRT6-dependent CtIP deacetylation promotes resection. A nonacetylatable CtIP mutant alleviated the effect of SIRT6 depletion on resection, thus identifying CtIP as a key substrate by which SIRT6 facilitates DSB processing and homologous recombination. These findings further clarify how SIRT6 promotes genome stability.” Double-strand breaks (DSBs)and DNA repair via homologous recombination are simply described in the blog entry DNA repair cleanup failure – a root cause for cancers. DNA resection is a critical step in the repair process for DSBs . “DNA-end resection, the first step in recombination, is a key step that contributes to the choice of DSB repair. Resection, an evolutionarily conserved process that generates single-stranded DNA, is linked to checkpoint activation and is critical for survival. Failure to regulate and execute this process results in defective recombination and can contribute to human disease(ref).”
An editor of Science summarized the important finding in the September 2010 Editor’s Choice article under the caption UnSIRT6ain Repair. He wrote “Efficient and accurate repair of double-strand DNA breaks is critical for genome stability and involves a process known as homologous recombination. During repair of the sheared ends, the DNA must be resected by trimming one of the two strands on either side of the break. For the repair to be accurate, the remaining single-stranded DNA (ssDNA) has to be bound by the ssDNA-binding protein, RPA, after which the ssDNA can then bind homologous sequences. Kaidi et al. found that the mammalian deacetylase, SIRT6 (which has been implicated in maintaining genome stability), was critical for resection. At sites of DNA damage, SIRT6 deacetylated and activated CtIP (a protein important for resection), ensuring that resection occurred at the appropriate place and time.”
Other longevity-related roles of SIRT6
I have previously pointed out that SIRT6 appears to also have other important health and possibly longevity-producing effects, particularly the inhibition of NF-kappaB signaling. See the 2009 article SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span.
Also, SIRT6 appears to exercise control over critical glucose-metabolic pathways which could affect lifespan regulation. SIRT6 may also play an important role in repressing cancers. The Massachusetts General Hospital 2010 news release Lack of cellular enzyme triggers switch in glucose processing discusses SIRT6. “In a series of experiments in mouse cells, the researchers showed that SIRT6-deficiency hypoglycemia is caused by increased cellular uptake of glucose and not by elevated insulin levels or defects in the absorption of glucose from food. They then found increased levels of glycolysis and reduced mitochondrial respiration in SIRT6-knockout cells, something usually seen when cells are starved for oxygen or glucose, and showed that activation of the switch from cellular respiration to glycolysis is controlled through SIRT6’s regulation of a protein called HIF1alpha. Normally, SIRT6 represses glycolytic genes through its role as a compactor of chromatin – the tightly wound combination of DNA and a protein backbone that makes up chromosomes. In the absence of SIRT6, this structure is opened, causing activation of these glycolytic genes. — Elevated glycolysis also is commonly found in tumor cells, suggesting that a lack of SIRT6 could contribute to tumor growth.” The same Raul Mostoslavsky is still studying sirtuins and DNA repair. “The Mostoslavsky Laboratory at Massachusetts General Hospital is interested in understanding the influence of chromatin on DNA repair, and the relationship between the DNA damage response and the metabolic adaptation of cells. We focus on the study of a group of proteins called SIRTs, the mammalian homologues of the yeast Sir2. Sir2 is a chromatin silencer that functions as an NAD-dependent histone deacetylase to inhibit DNA transcription and recombination(ref).”
There is still more to be said about SIRT6 and the other sirtuins. And there is more that can be said about DNA repair. Also, I have not touched here on another important topic related to genomic stability: changes in the epigenome that occur in aging. There appears to be no end to possible topics for future blog entries.