Date of Award

2017

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Biochemistry & Molecular Biophysics

First Advisor

Roberto Dominguez

Abstract

Chromatin remodeling complexes (remodelers) alter chromatin structure to regulate access to DNA. Remodelers belong to four families, but each are assembled around a catalytic subunit, featuring a conserved, DNA-dependent ATPase domain flanked by family-specific domains. These can intra-molecularly interact with the ATPase domain to regulate its function and can also recruit auxiliary subunits for additional regulation. Sth1, the catalytic subunit of the yeast SWI/SNF-family remodeler RSC, recruits a heterodimer of actin-related proteins (Arps) 7 and 9 through an N-terminal helicase/SANT-associated (HSA) domain. An additional auxiliary subunit, Rtt102, co-purifies with Arp7/9. In this dissertation, I sought to understand how Arp7/9 binding to the HSA domain of Sth1 regulates the structure and function of the central ATPase domain, and how this regulation is modulated by Rtt102. Using Isothermal Titration Calorimetry (ITC), Small angle X-ray scattering (SAXS) and X-ray crystallography. I discovered that Rtt102 binds with nanomolar affinity to stabilize a compact conformation of the Arp7/9 heterodimer, which is required for full binding to the HSA domain and formation of a stable complex with the ATPase domain. The crystal structure of the Rtt102-Arp7/9 complex reveals that ATP binds to Arp7 to help stabilize the compact conformation of Rtt102-Arp7/9 required for tight association with the HSA domain. To correlate these findings to remodeler function, I designed a novel biochemical assay to test for the effects of Arp7/9-binding on intramolecular interactions within Sth1. This approach revealed that two conserved sequences, Protrusion-1 (P1) within the ATPase domain and a region adjacent to the HSA domain known as the post-HSA (pHSA) domain, interact directly with each other. Binding of Arp7/9 to the HSA domain weakens this interaction in an Rtt102-dependent manner. Fluorescence anisotropy experiments further showed that the weakening of P1-pHSA interaction by Rtt102-Arp7/9 reduces the affinity of the ATPase domain for DNA. Taken together, Rtt102 thus emerges as an important factor that stabilizes Arp7/9, allowing it to modulate regulatory intra-molecular interactions within Sth1 and thereby control DNA binding to the ATPase domain. As such, this work establishes a novel molecular mechanism for regulation of the RSC remodeler.

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