A team led by Penn State researchers created images of a sirtuin enzyme bound to a nucleosome, a tightly packed complex of DNA and proteins called histones. This demonstrates how the enzyme navigates the nucleosome complex to access DNA and histone proteins and clarifies how it functions in humans and other animals.
Sirtuins are an enzyme found in animals ranging from bacteria to humans that play critical roles in aging, DNA damage detection, and tumor suppression in various malignancies. Pharmaceutical companies are investigating their potential for biomedical applications due to their diverse functions. Much attention has been paid to some sirtuins’ potential to reduce gene expression by removing a chemical flag from histone proteins.
Song Tan, Verne M. Willaman Professor of Molecular Biology at Penn State, said, “In our cells, DNA is not naked like we see it in textbooks; it is spooled around proteins called histones within a large complex called the nucleosome. This packaging can also contribute signals for turning on or turning off genes: Adding an ‘acetyl’ chemical flag to the histone packaging material turns on a gene while removing the acetyl flag turns the gene off. Sirtuins can silence gene activity by removing the acetyl flag from histones packaged into nucleosomes. Understanding how sirtuins interact with the nucleosome to remove this flag could inform future drug discovery efforts.”
Previous research has focused on how sirtuins interact with small segments of histones in isolation. However, the nucleosome is a hundred times larger than the standard histone peptides used in these experiments and hence significantly more difficult to control.
Jean-Paul Armache, assistant biochemistry, and molecular biology professor at Penn State, said, “We have visualized a sirtuin enzyme called SIRT6 on its physiologically relevant substrate, the entire nucleosome. And we found that SIRT6 interacts with multiple parts of the nucleosome, not only the histone where the acetyl flag is to be modified.”
The researchers identified how SIRT6 positions itself on the nucleosome to remove an acetyl group from the K9 position on the histone H3 using cryo-electron microscopy with instruments at the Penn State Cryo-Electron Microscopy Facility, the National Cancer Institute, and the Pacific Northwest Cryo-EM Centre.
The researchers discovered that SIRT6 connects to the nucleosome via an “arginine anchor.” Tan’s lab described this sort of binding in 2014. It is exploited by a range of proteins that target a particularly acidic patch on the nucleosome’s surface. In this scenario, an extended loop structural feature of SIRT6 nestles into a depression in the acidic patch, similar to a pipe resting in a ditch.
He said, “The arginine anchor is a common paradigm for how many chromatin proteins interact with the nucleosome. When we mutated the SIRT6 arginine anchor, the activity at the K9 position was severely affected, supporting a critical role for the SIRT6’s arginine anchor. Surprisingly, this mutation also impacted SIRT6’s enzymatic activity at a different position, K56, located much further away.”
SIRT6 may attach to the nucleosome in two separate ways to access the two different histone locations, or it may bind to access K9 in a way that also provides access to K56.
Armache said, “SIRT6 binds to a partially unwrapped nucleosome, with DNA displaced from the end of the nucleosome. This exposes the K56 position, and it is possible that SIRT6 could essentially lean down to reach that position. We want to validate this hypothesis in the future. We also hope to explore how SIRT6 works alongside other enzymes and better understand its role in response to DNA damage.”
The National Institutes of Health in the United States and the Pennsylvania Department of Health funded this study using Tobacco CURE money.