PHDS, Stress, And Starvation: The Identification Of A New RPD3 Deacetylase Complex Involved In The Yeast Oxidative Stress And Metabolism Pathways
type: CreativeWork
description: The cellular pathways that govern survival in the face of diverse stresses rely on gene expression changes as one mechanism to respond to or protect against internal and external threats. Because eukaryotic DNA is packaged into chromatin, these gene expression changes depend on the targeting of regulatory proteins to specific regions of the genome to alter chromatin structure, promoting or repressing transcription. One protein domain involved in targeting chromatin regulators is the plant homeodomain, or PHD finger, a module that preferentially interacts with either methylated or unmethylated lysines on histones, and has important functions in human health. Despite recent advances in identifying the histone ligands for some PHD fingers as well as the functions of the proteins that contain them, for many other PHD fingers, including some of the 17 PHD fingers of the budding yeast Saccharomyces cerevisiae, these questions remain unanswered. In the research presented in this thesis, I sought to gain insight into the ligands and functions for three yeast PHD finger proteins, the Yng1 subunit of the NuA3 acetyltransferase complex, Jhd2, and Ecm5, the latter two both being homologous to the mammalian JARID family of histone demethylases. In Chapter 2, I demonstrate that the PHD fi ngers of these proteins interact with histone H3 enriched for different sites of methylation depending on the PHD and present results of an in vitro assay used to test whether any yeast PHD fi ngers possess ubiquitin E3 ligase activity, a function ascribed to the PHD-related RING domain. In Chapter 3, I discuss experiments performed to identify the protein interaction partners of Jhd2 and Ecm5,culminating in the discovery that Ecm5 interacts with the PHD finger protein Snt2 as well as the Rpd3 deacetylase, forming a complex I have named Rpd3(T). I also discuss experiments showing that the ecm5 knockout strain does not have obvious defects in many yeast pathways. In Chapter 4, I present evidence …
abstract: The cellular pathways that govern survival in the face of diverse stresses rely on gene expression changes as one mechanism to respond to or protect against internal and external threats. Because eukaryotic DNA is packaged into chromatin, these gene expression changes depend on the targeting of regulatory proteins to specific regions of the genome to alter chromatin structure, promoting or repressing transcription. One protein domain involved in targeting chromatin regulators is the plant homeodomain, or PHD finger, a module that preferentially interacts with either methylated or unmethylated lysines on histones, and has important functions in human health. Despite recent advances in identifying the histone ligands for some PHD fingers as well as the functions of the proteins that contain them, for many other PHD fingers, including some of the 17 PHD fingers of the budding yeast Saccharomyces cerevisiae, these questions remain unanswered. In the research presented in this thesis, I sought to gain insight into the ligands and functions for three yeast PHD finger proteins, the Yng1 subunit of the NuA3 acetyltransferase complex, Jhd2, and Ecm5, the latter two both being homologous to the mammalian JARID family of histone demethylases. In Chapter 2, I demonstrate that the PHD fi ngers of these proteins interact with histone H3 enriched for different sites of methylation depending on the PHD and present results of an in vitro assay used to test whether any yeast PHD fi ngers possess ubiquitin E3 ligase activity, a function ascribed to the PHD-related RING domain. In Chapter 3, I discuss experiments performed to identify the protein interaction partners of Jhd2 and Ecm5,culminating in the discovery that Ecm5 interacts with the PHD finger protein Snt2 as well as the Rpd3 deacetylase, forming a complex I have named Rpd3(T). I also discuss experiments showing that the ecm5 knockout strain does not have obvious defects in many yeast pathways. In Chapter 4, I present evidence …
author: Baker, Lindsey A
keywords: chromatin regulation, PHD finger proteins, histone modifications, oxidative stress, yeast genetics, Rpd3 complex, Life Sciences
date published: 2012-01-01T08:00:00Z
date modified: 2026-07-24T04:11:51Z
provider: Rockefeller
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Rockefeller