Actively proliferating cells constantly monitor and re-adjust their metabolic pathways to ensure the replenishment of phospholipids necessary for membrane biogenesis and intracellular trafficking. In Saccharomyces cerevisiae, multiple studies have suggested that lysine acetylation has a role in coordinating phospholipid metabolism, yet its contribution towards phospholipid homeostasis remains uncharacterized. In this study we undertook a genetic screen to explore the connection between lysine acetylation and phospholipid homeostasis. We found that mutants of the lysine acetyltransferase complex, NuA4, shared a negative genetic interaction with a mutant of Sec14, a lipid-binding protein that regulates Golgi phospholipid composition. Through transcriptome, genetic, cell biology, and chemical analysis, we discovered that the growth defects between NuA4 and Sec14 mutants is likely derived from impaired fatty acid biosynthesis suggesting a role for NuA4 as a positive regulator of fatty acid biosynthesis. Secondly, we discovered that acetylation on the conserved lysine residue K109 inhibits the localization and function of the Oxysterol-Binding Protein Osh4- a lipid-binding protein that antagonizes the function of Sec14 at the Golgi. Furthermore, regulation of Oxysterol-Binding Proteins by acetylation may be a conserved mechanism as we found that Osh1, a homologue of Osh4, was also acetylated on the equivalent lysine residue. Altogether, we have demonstrated that lysine acetylation can target multiple different phospholipid metabolic pathways which implies that it has a very important role for the regulation of phospholipid homeostasis.

In 1996, scientists discovered a connection between the gene for the human protein frataxin (FXN) and the neurodegenerative disease Friedreich’s ataxia (FRDA). Decreased FXN levels result in a variety of aberrant phenotypes including loss of activity for iron-sulfur containing enzymes, mitochondrial iron accumulation, and susceptibility to oxidative stress. These symptoms are the primary focus of current therapeutic efforts. In contrast our group is pursuing an alternate strategy of first defining FXN function at a molecular level then using this information to identify small molecule functional replacements. Recently, our group has discovered that FXN functions as an allosteric activator for the human Fe-S cluster assembly complex. The work presented here helps to further define molecular details of FXN activation and explain how FRDA missense mutants are functionally compromised. First, the FRDA missense mutants L182H and L182F were investigated. Unlike other characterized FRDA missense mutants, the L182F variant was not compromised in its ability to bind and activate the Fe-S assembly complex. The L182H variant exhibited an altered circular dichroism signature; suggesting a change in secondary structure relative to native FXN, and rapidly degraded. Together these studies suggest that L182 variants are less stable than native FXN and are likely prone to degradation in FRDA patients. Second, as a regulatory role of FXN suggests that its function is likely controlled by environmental stimuli, different maturation forms of FXN as well as post-translational modification mimics were tested as mechanisms to control FXN regulation. Here experiments were designed to test if a larger polypeptide form of FXN represents a functional form of the protein. Kinetic and analytical ultracentrifugation studies revealed a complex heterogeneous mixture of species some of which can activate the Fe-S assembly complex. A previously identified acetylation site was also tested using mutants that mimic acetylation. These mutants had little effect on the ability of FXN to bind and activate the assembly complex. Third, mutagenesis experiments were designed in which the FXN surface residues were replaced with alanine and the resulting variants were tested in binding and activity assays. These experiments revealed a localized “hot-spot” on the surface of FXN that suggests small cyclic peptide mimics might be able to replace FXN and function as FRDA therapeutics. Unexpectedly, one of the FXN variants exhibited significantly tighter binding and could have relevance for therapeutic development.

No description available.

Accurate DNA replication is vital for maintaining genomic stability. Consequently, the machinery required to drive this process is designed to ensure the meticulous maintenance of information. However, random misincorporation of errors reduce the fidelity of the DNA and lead to pre-mature aging and age-related disorders such as cancer and neurodegenerative diseases. Some of the incorporated errors are the result of the error prone DNA polymerase alpha (Pol a), which initiates synthesis on both the leading and lagging strand. Lagging strand synthesis acquires an increased number of polymerase a tracks because of the number of Okazaki fragments synthesized per round of the cell cycle (~50 million in mammalian cells). The accumulation of these errors invariably reduces the fidelity of the genome. Previous work has shown that these pol a tracks can be removed by two redundant pathways referred to as the short and long flap pathway. The long flap pathway utilizes a complex network of proteins to remove more of the misincorporated nucleotides than the short flap pathway which mediates the removal of shorter flaps. Lysine acetylation has been reported to modulate the function of the nucleases implicated in flap processing. The cleavage activity of the long flap pathway nuclease, Dna2, is stimulated by lysine acetylation while conversely lysine acetylation of the short flap pathway nuclease, FEN1, inhibits its activity. The major protein players implicated during Okazaki fragment processing (OFP) are known, however, the choice of the processing pathway and its regulation by lysine acetylation of its main players is yet unknown. This dissertation identifies three main findings: 1) <i>Saccharomyces cerevisiae</i> helicase, petite integration frequency (Pif1) is lysine acetylated by Esa1 and deacetylated by Rpd3 regulating its viability and biochemical properties including helicase, binding and ATPase activity ii) the single stranded DNA binding protein, human replication protein A (RPA) is modified by p300 and this modification stimulates its primary binding function and iii) lysine acetylated human RPA directs OFP towards the long flap pathway even for a subset of short flaps.

Under environmental stress, such as glucose deprivation, cells form stress granules - the accumulation of cytoplasmic aggregates of repressed translational initiation complexes, proteins, and stalled mRNAs. Recent research implicates stress granules in various diseases, such as neurodegenerative disease, but the exact regulators responsible for the assembly and disassembly of stress granules are unknown. Studies detect post-translational modifications on core stress granule proteins. One modification is lysine acetylation, in which a substrate is regulated by a lysine acetyltransferase (KAT) and lysine deacetylase (KDAC). My project deciphers the impact of lysine acetylation on an essential protein found in stress granules, poly(A) binding protein (Pab1) in Saccharomyces cerevisiae. In this work, I demonstrated that acetylation mimic of Pab1-K131 reduces stress granule formation upon glucose deprivation, and other stressors such as ethanol, raffinose, and vanillin. A potential KDAC that might be facilitating this role is Rpd3. Further, electromobility shift assay studies suggest that acetylation mimic of Pab1-K131 negatively impacts poly(A) RNA binding. This work will be useful when exploring therapeutic options when combating diseases linked to stress granules.