Abstract
The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity.
Highlights
The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription
To quantitatively assess the strength of nucleosome binding, we analyzed the complexes formed in electrophoretic mobility shift assays (EMSAs) when purified SIRT6 was added to recombinant 601-positioned nucleosome core particles (NCPs; Fig. 1a and Supplementary Fig. 1a
Two distinct, bound complexes were evident as SIRT6 was titrated into a fixed level of NCPs: the lower bound complex appeared and saturated at much lower SIRT6 concentrations, while the slower migrating species appeared at higher concentrations of SIRT6 (Fig. 1a)
Summary
The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. We describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. We show that SIRT6 associates with nucleosomes through two asymmetric binding sites using multiple contact points, including an intrinsically disordered C-terminus that associates with nucleosomal DNA Together, these multivalent interactions promote high affinity engagement with substrate, leading to productive deacetylation in cells. Unlike most histone deacetylases and acetyltransferases that require multi-subunit complexes, our studies reveal that SIRT6 harbors the intrinsic capacity to bind tightly and efficiently catalyze the removal of acetyl-groups from nucleosomes without the need to form elaborate protein complexes
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