Structural Biochemistry/Chromatin regulation and genome maintenance by mammalian SIRT6

Introduction

Saccharomyces cerevisia (Sir2) is an NAD⁺-dependent histone deacetylase. It's role within the cell is to link chromatin silencing to genomic stability, cellular metabolism, and lifespan regulation. For example, in mice, if there is a deficiency for SIRT6 (family member of Sir2), the mice experience genomic instability, metabolic defects, and degenerative pathologies in terms of aging, everything opposite of the roles of Sir2. With new insights to the previously ambiguous SIRT6, scientists have discovered that SIRT6 is a very substrate-specific histone deacetylase that promotes proper chromatin function in things like telomere stabilization and DNA repair.

Sir2: a chromatin-aging connection

Sir2 is the founding member of the family of proteins called sirtuins. These proteins provided the first link between chromatin regulation and aging. Sir2 favors chromatin silencing at sub-telomeric DNA, silent mating-type loci, and rDNA repeats. These effects of Sir2 on chromatin is mediated by having Sir2 catalyzing the deacetylation of lysine residues on the amino terminal ends of histones H3 and H4 and also on the globular core of histone (all by NAD⁺-dependent histone deacetylase activity). Deacetylation of H4 lysine 16 and H3K56 mediate the silencing effects of Sir2.
Example: In budding yeast, Sir2 regulates replicative lifespan through a couple of chromatin-silencing processes.

First, Sir2 suppresses recombination between rDNA repeats and this prevents
Second, H4K16 acetylation levels increase at telomeres when replicative age increases; Thus, Sir2 protein levels decrease. These chromatin changes create defects in telomere position-dependent transcriptional silencing and trigger replicative senescence.

A few studies have shown that there are aging-related Sir2 functions that might be chromatin-independent, making the relationship between Sir2 and lifespan regulation even more complex.
For example,Sir2 asymmetrically segregates damaged proteins to the yeast mother cell during cell division; this asymmetry can age the mother cell by forming toxic protein aggregates. Also, Sir2 can block lifespan extension in response to nutrient deprivation of mutations in nutrient-sensing pathways.

Mammalian sirtuin proteins: venturing out from chromatin

SIRT1 is the most closely related to year Sir2 out of the seven SIR2 family members. However, Sir2 appears to deacetylate histones exclusively while SIRT1 appears to more than 40 substrates. SIRT1 deacetylates many non-histone proteins and impacts on many phsysiologic processes like apoptosis.
SIRT1, SIRT6, and SIRT7 are concentrated in different sub-nuclear patterns; SIRT2 is cytoplasmic; SIRT3, SIRT4, and SIRT5 reside in the mitochondria.

SIRTching for a function through knockout mice

SIRT6-deficient mice appear normal when born, but after a couple of weeks, they start to develop degenerative phenotypes like osteoporosis. They also experience metabolic defects - so much that with such low levels of the insulin-like protein IFG-1, these mice die by 1 month.

An orphan enzyme finds its substrates

Through experiments, it was found in vitro that SIRT6 promotes mono-ADP-ribosylation, an alternative NAD⁺-depdendent reaction in sirtuins. Another breakthrough occurred to further understand SIRT6 function through discovery of the enzymatic activity and the first substrate of SIRT6: NAD⁺-depdendent deacetylation of histone H3 lysine 9. SIRT6 specifically deacetylates H3K9, but lacks activity on a lot of other histone tail residues due to its intense specificity.
Two groups were identified independently as the second substrate for SIRT6: lysine 56 of histone H3 (H3K56Ac).

To the core and beyond: biochemical dissection of SIRT6 function

Sirtuin proteins have a conserved central "sirtuin domain" flanked by N- and C- terminal extensions. The sirtuin domain supposedly has an enzymatic core and understanding this domain can show scientists the physiologic regulation of sirtuin proteins.
For SIRT6, a recent study showed that the N- and C- terminal domains regulate SIRT6 function by having the C terminus require proper nuclear localization (but is dispensable for enzymatic activity) and then the N terminus is beneficial for chromatic association and intrinsic catalytic activity.
Why is catalytic activity required for chromatin association in the cell?

It could be possible that histone deacetylation by SIRT6 might be able to stabilize SIRT6 availability at chromatin or it can promote propagation of SIRT6 molecules along chromatin.

At the ends of chromosomes: SIRT6 regulates telomeric chromatin

SIRT6 plays an important role in the chromatin-regulatory context by keeping the integrity of telomeric chromatin stable. Telomeres are specialized DNA-protein structures which protect chromosome ends that are linear from degradation and fusion. SIRT6 plays a huge role at telomeres in humans for a couple of reasons:

First, telomere structures need to be correct in order to maintain genomic stability; chromosomal instability is apparent in cancer cells.

Also, telomere length decreases with cellular age. This shows that SIRT6's role at telomeres correlates with aging.

Conclusion

With many experiments and discoveries, SIRT6 has been determined as a site-specific histone deacetylase, playing very important roles in keeping up telomere integrity, honing aging-associated gene expression programs, preventing the genome to become unstable, and maintaining metabolic homeostasis.
Not only does SIRT6 function at specific sites in the genome, it plays a role in binding to additional gene promotors. Also, there might be interactions between SIRT6 and other sirtuin proteins.
Lastly, SIRT6 might have an impact on cancer due to the fact that there have been links between SIRT6 and cancer by the SIRT6 chromosomal locus.

References

Tennen, Ruth I., and Katrin F. Chua. "Chromatin regulation and genome maintenance by mammalian SIRT6." Trends in Biochemical Sciences 36.1 (2011) 39-46. Academic Search Complete. Web. 05 December. 2012.