Biochemistry Commons^™

Runx1 Loss Leads To An Epithelial To Mesenchymal Transition In Breast Cancer By Regulating Target Gene Expression., Dorcas Lohese

Graduate College Dissertations and Theses

Breast cancer is the second leading cause of cancer death among women in the United States. Due to the various advancements in treatment, the five-year survival rate is greater than 90% among women with non-metastatic breast cancer. However, among patients with metastatic breast cancer, the five-year survival rate quickly drops to 22%. Recognizing early signs of metastasis is essential for targeting cancer before it disseminates. The epithelial-to-mesenchymal transition (EMT) is hypothesized to be a vital process for large-scale cell movement by disrupting cell-cell adhesion, allowing metastatic breast cancer cells to become more migratory. The progression of breast cancer EMT involves …

Characterization And Manipulation Of O-Glcnacylation In Granulosa Cells Of Bovine Ovarian Antral Follicles, Abigail Marie Maucieri

Graduate College Dissertations and Theses

Glucose is widely recognized as the preferred energy substrate for metabolism by granulosa cells (GCs). Yet in most cells, 2-5% of glucose is shunted through the hexosamine biosynthesis pathway (HBP) for O-linked N-acetylglucosaminylation (O-GlcNAcylation). O-GlcNAcylation is an evolutionarily-conserved, post-translational process that modifies serine and threonine residues on a variety of proteins. O-GlcNAcylation is also considered a nutrient sensor that can regulate cellular processes such as metabolism, signal transduction, and proliferation. In this respect, O-GlcNAcylation may be similar to, and possibly mediate, AMP-activated protein kinase (AMPK) signaling and its nutrient-sensing actions. However, the occurrence of O-GlcNAcylation and its relative importance to …

Exploring The Mechanisms Of Pkg1-Α Activation By Synthetic Peptides, Connor Cronin

Graduate College Dissertations and Theses

Cyclic GMP-dependent protein kinases (PKG’s) are essential signaling macromolecules which play a pivotal role in vascular physiology and smooth muscle tone regulation. As principle downstream effectors of the secondary messenger cyclic 3’, 5’-guanosine-monophosphate (cGMP), PKG isoforms are expressed in high levels in all types of smooth muscle cells. The broad range of cellular functions effected by PKG include platelet aggregation, hypertrophy, apoptosis, neuronal plasticity, gene expression, differentiation, vasorelaxation, vascular remodeling, calcium homeostasis, and cardiac function. Recently, a newly characterized helical switch domain within the alpha isoform of PKG (PKG1-α) has led to the development of S1.1, a novel cGMP-independent peptide …

Characterization Of Tau Disease-Associated Mutation, R5l, On Microtubule Bound Tau Behavoir And Function, Alisa Cario

Graduate College Dissertations and Theses

Proper coordination of the neuronal cytoskeleton is necessary for the health of the nervous system. Regulation of the microtubule cytoskeleton is achieved, in part, through microtubule associated proteins (MAPs). MAP-Tau, an intrinsically disordered protein highly expressed in axons, functions in signaling cascades, regulation of motor motility, as well as the direct regulation of microtubule dynamics. Tau misregulation and mutations are linked to a class of neurodegenerative diseases called Tauopathies, characterized by the aggregation of Tau. These include progressive supranuclear palsy (PSP), Pick's disease, and Alzheimer's disease. Many of the disease-associated mutations in Tau are found in the microtubule-binding domain, in …

Characterizing The Interaction Of Polymerase Θ Helicase-Like Domain With Dna, Scott Vanson

Graduate College Dissertations and Theses

DNA damaging events occur every day in every cell of all living organisms andsome may result in double-stranded breaks (DSB). Human DNA polymerase θ (Pol θ) is a large, 290 kDa DNA repair enzyme and is the only known protein to contain both a polymerase domain and a helicase-like domain (HLD) as one molecule. Pol θ is the key mediator of the error-prone DSB repair pathway, Theta-mediated End Joining. This enzyme has been identified as a potential therapeutic target as it may be conferring a survival advantage to subsets of homologous recombination (HR)-deficient cancers, which display elevated expression levels of …

Lcms-Based Analysis Explains The Basis Of Oxidative Resistance In Selenium-Containing Thioredoxin Reductase, Daniel Haupt

Graduate College Dissertations and Theses

Selenocysteine (Sec) is referred to as the 21st proteogenic amino acid and is found in place of the redox-sensitive amino acid cysteine (Cys) in a small number of proteins. Sec and Cys carry out similar chemistry and are structural isomers save for a single atom difference; the former contains selenium (Se), while the latter contains sulfur (S) in the identical position. Sec poses a high bioenergetic cost for its synthesis and subsequent incorporation into protein not shared by Cys. Since Sec’s discovery in 1976, scientists have debated why certain proteins express Sec while others express Cys. In recent years, it …

Designer Biologics Composed Of Hepatocyte Growth Factor, Fibroblast Growth Factor 2 And Immunoglobulin G For Treatment Of Acute Myocardial Infarction, Benjamin Liebman

Graduate College Dissertations and Theses

ABSTRACT Coronary artery disease leading to myocardial infarction (a.k.a. MI, heart attack) is one of the leading causes of death globally. Each year an estimated 605,000 Americans suffer a heart attack, which equates to one MI every 40 seconds. As such, MI represents one of the largest health burdens to society. The current standard of care is revascularization therapy achieved by fibrinolytics and Percutaneous Coronary Intervention (PCI); both of which re-open occluded proximal arteries to restore blood flow to the affected areas. Despite revascularization therapy, 30-50% of patients exhibit a form of reperfusion injury termed “no/low-reflow” in which the blood …

Glutathionylation/Glutaredoxin Axis And The Regulation Of Epithelial Cell Plasticity And Fibroblast Activation In Airway Fibrosis, Shi Biao Chia

Graduate College Dissertations and Theses

Asthma is a complex lung disorder that affects more than 200 million people across the globe. About 10% of asthmatics have severe disease accompanied by structural airway remodeling, including subepithelial fibrosis, airway smooth muscle cell hyperplasia, goblet metaplasia, and increased vascularization. Oxidative stress has been well-linked to asthma pathogenesis; however, the precise redox mechanisms governing the pathological states are slowly being teased apart in the recent years. Protein S-glutathionylation (PSSG) is a posttranslational modification where a three amino acid-peptide, glutathione, forms a disulfide bond with reactive cysteines of a protein thereby potentially changing the protein’s biological functions. Glutaredoxins are members …

Tsrna Involvement In Promoting Breast Cancer Phenotypes, Stephanie Scalia

Graduate College Dissertations and Theses

The overall 5-year survival rate for woman diagnosed with breast cancer has increased significantly over the last 20 years. However, prognosis for women with stage IV, metastatic disease remains very poor. Women diagnosed with stage 0-III breast cancer have above an 85% chance of survival over a 5-year period while women diagnosed with stage IV breast cancer have a 5-year survival of less than 30%. A better understanding of the molecular mechanisms driving aggressive breast cancer is essential for the potential discovery of more targeted therapies to increase the survival rates for women diagnosed with stage IV breast cancer.

Previous …

Investigations Into Signaling Mechanisms Of The Dcbld Receptor Family, Anna Schmoker

Graduate College Dissertations and Theses

Cells communicate to drive all biological processes during organismal development, homeostasis, and disease. Communication, or signaling, is carried out through an orchestration of complex sequential molecular interactions. A signal is typically initiated by an extracellular cue binding to a receptor on the cell membrane, which induces an intracellular response, resulting ultimately in cellular phenotypes such as growth, proliferation, migration, apoptosis or survival. Adaptor proteins are critical to signal transduction, as they facilitate the formation of protein complexes that transduce signals. CT10 regulator of kinase (CRK) and CRK-like (CRKL) form a family of adaptors that facilitate complex formation during developmental signaling, …

Caught In Motion: Structural Studies Of Nucleic Acid Repair Enzymes, Brittany Carroll

Graduate College Dissertations and Theses

Cells synthesize proteins, the molecular instruments of all cellular processes, via

intermediate biomolecules that are susceptible to damage at every step. Known as the

central dogma of molecular biology, genes encoded in deoxyribonucleic acid (DNA) are

transcribed, spliced, and matured into messenger ribonucleic acid (mRNA). These

nucleic acids direct protein synthesis by the pairing of nucleotide triplets with transfer

RNA (tRNA). tRNAs concomitantly decode the so-called codon, as they escort the

correct amino acid to the ribosome for extension of the nascent polypeptide chain.

Damage to any of these intermediate biomolecules can be highly damaging to protein

synthesis, leading to …

Maintenance Of Mammary Epithelial Phenotype By Transcription Factor Runx1 Through Mitotic Gene Bookmarking, Joshua Rose

Graduate College Dissertations and Theses

Breast cancer arises from a series of acquired mutations that disrupt normal mammary epithelial homeostasis and create multi-potent cancer stem cells that can differentiate into clinically distinct breast cancer subtypes. Despite improved therapies and advances in early detection, breast cancer remains the leading diagnosed cancer in women.

A predominant mechanism initiating invasion and migration for a variety of cancers including breast, is epithelial-to-mesenchymal transition (EMT). EMT— a trans-differentiation process through which mammary epithelial cells acquire a more aggressive mesenchymal phenotype—is a regulated process during early mammary gland development and involves many transcription factors involved in cell lineage commitment, proliferation, and …

Studies On The Molecular Mechanism Of S-Tide Mediated Activation Of Pkg-Iα, Joseph William Charles

Graduate College Dissertations and Theses

cGMP-dependent protein kinases (PKG) are key players in intracellular second messenger signaling within many cellular systems throughout the body. Most notably PKG is known for its role in smooth muscle relaxation (Pfeiffer et.al, 1999). The Iα PKG isozyme has been identified as the primary effector of the nitric oxide pathway (and serves to be a novel drug target). To date the overall knowledge of structure and function of PKG is lacking in terms of the mechanisms of activation and the structural orientations that coordinate them. Recently, our laboratory has solved the crystal structure of the regulatory domain of PKG Iα, …

Biochemical Characterization Of The Dimerization Domain Of Purine-Rich Element Binding Protein B: An Essential Subdomain Mediating The Repression Of Smooth Muscle Alpha Actin Gene Expression, Lauren Ferris

Graduate College Dissertations and Theses

A number of physiologic processes require the expression of smooth muscle alpha actin (SMαA) to mediate cellular contraction. Stable expression of SMαA in differentiated vascular smooth muscle cells is associated with a contractile phenotype that is essential for regulation of blood flow and pressure. The transient expression of SMαA in myofibroblasts during wound repair facilitates wound closure. Hence, it is no surprise that dysregulation of SMαA gene expression in both cell types can have pathological consequences. Indeed, aberrant SMαA gene regulation has been implicated in diseases such as atherosclerosis and fibrosis. Therefore, a better understanding of the molecular mechanisms that …

Secondary Functions And Novel Inhibitors Of Aminoacyl-Trna Synthetases, Patrick Wiencek

Graduate College Dissertations and Theses

The aminoacyl-tRNA synthetases are a family of enzymes involved in the process of translation, more specifically, ligating amino acids to their cognate tRNA molecules. Recent evidence suggests that aminoacyl-tRNA synthetases are capable of aminoacylating proteins, some of which are involved in the autophagy pathway. Here, we test the conditions under which E. coli and human threonyl-tRNA synthetases, as well as hisidyl-tRNA synthetase aminoacylate themselves. These reactions are ATP dependent, stimulated by Mg2+, and are inhibited by increasing cognate tRNA concentrations. These data represent the foundation for future aminoacylation experiments, specifically delving into the relationship between the autophagy pathway and the …

Selenium In Thioredoxin Reductase: Resistance To Oxidative Inactivation, Oxidation States, And Reversibility Of Chemical Reactions, Drew Barber

Graduate College Dissertations and Theses

Selenium is a required trace element which was originally discovered by the Swedish chemist Jons Jacob Berzelius in 1817. It was initially believed to be a toxin as it was identified as being the cause of hoof maladies and excessive hair loss in horses that feed upon plants with high selenium content. It wasn’t until 1957 that the potential contributions of selenium to physiology were first demonstrated. Selenium is now known to play a critical role in the maintenance of human health. Interestingly, unlike other trace metals/semi-metals, selenium is directly incorporated into proteins in the form of the amino acid …

The A-Site In The Pkg Iα Regulatory Domain Controls Both Cgmp- And Oxidative-Dependent Activation, Jessica Lynne Sheehe

Graduate College Dissertations and Theses

The type Iα cGMP-dependent protein kinase (PKG Iα) is an essential regulator of vascular tone and systemic blood pressure. Located in the smooth muscle of resistance vessels, PKG Iα stimulates vasodilation through the phosphorylation of multiple intracellular substrates. Its primary regulator is the small molecule, 3',5'-cyclic guanosine monophosphate (cGMP); however, the Iα isoform can also be activated by oxidation. Despite the established physiological importance of PKG Iα, the structural underpinnings of these two activation mechanisms are largely unknown.

The work presented in this dissertation demonstrates the importance of the cGMP-binding domain A (CBD-A) in regulating both of these mechanisms of …

Methylation Controlled J Protein Is A Master Regulator Of Mitochondrial Metabolism, Devin Pierre Champagne

Graduate College Dissertations and Theses

Methylation controlled J protein (MCJ) is a negative regulator of mitochondrial metabolism that has a substantial impact on overall cell metabolism and function. MCJ is highly expressed by naïve CD8+ T cells, however its role in their immune effector functions was unknown. In this dissertation, it will be demonstrated that MCJ restricts the mitochondrial metabolism of CD8+ T cells, in part by reducing respiratory supercomplex formation. MCJ deficiency enhances the immune effector functions and memory responses of CD8+ T cells in a mitochondrial ATP dependent manner. As a consequence, protection to influenza virus infection is substantially improved. Reduced expression of …

A Proximity-Dependent Biotin Labeling Based Screen For Protein Kinase A Anchoring Proteins Within Focal Adhesion Complexes, Hannah Naughton

Graduate College Dissertations and Theses

Protein kinase A (PKA) regulates a diverse array of cellular activities including metabolism, differentiation, actomyosin contractility, and migration. The multifunctionality of this ubiquitous enzyme is achieved, in part, through subcellular targeting mediated by the A Kinase Anchoring Proteins (AKAP) family of proteins. AKAPs serve as scaffolding proteins that localize PKA to various cellular compartments and bring together specific targets and modulators of PKA activity.

The importance of spatially restricted PKA signaling is particularly apparent in the context of cell motility. It has been observed that both anchoring through AKAPs and the subsequent localized activation of PKA at the leading edge …

Molecular Mechanisms Of Mrna Transport By A Class V Myosin And Cytoplasmic Dynein, Thomas Edward Sladewski

Graduate College Dissertations and Theses

mRNA localization ensures correct spatial and temporal control of protein synthesis in the cell. Using a single molecule in vitro approach, we provide insight into the mechanisms by which localizing mRNAs are carried by molecular motors on cytoskeletal tracks to their destination.

Budding yeast serves as a model system for studying the mechanisms of mRNA transport because localizing mRNAs are moved on actin tracks in the cell by a single class V myosin motor, Myo4p. Molecular motors that specialize in cargo transport are generally double-headed so that they can "walk" for many microns without dissociating, a feature known as processivity. …

Understanding The Role Of Runx2 In A Breast Cancer Progression Cell Model, Alexandra Ojemann

Graduate College Dissertations and Theses

Runx2 is a transcription factor required for bone formation and osteoblastic differentiation during normal development and is implicated in metastatic disease during breast cancer progression. Runx2 is highly expressed in many metastatic breast cancers and breast cancer cell lines Knockdown of Runx2 in various breast cancer cell lines restores epithelial characteristics and reduces proliferation, migration, and invasion. However, the role of Runx2 in breast cancer progression from early to late stages is not well understood. The MCF10A derived breast cancer progression model provides the opportunity to study the role of Runx2 in a series of cell lines that progress from …

Changes In Threonyl-Trna Synthetase Expression And Secretion In Response To Endoplasmic Reticulum Stress By Monensin In Ovarian Cancer Cells, Jared Louis Hammer

Graduate College Dissertations and Theses

Aminoacyl-tRNA synthetases (ARS) are a family of enzymes that catalyze the charging of amino acids to their cognate tRNA in an aminoacylation reaction. Many members of this family have been found to have secondary functions independent of their primary aminoacylation function. Threonyl-tRNA synthetase (TARS), the ARS responsible for charging tRNA with threonine, is secreted from endothelial cells in response to both vascular endothelial growth factor (VEGF) and tumor necrosis factor-α (TNF-α), and stimulates angiogenesis and cell migration. Here we show a novel experimental approach for studying TARS secretion, and for observing the role of intracellular TARS in the endoplasmic reticulum …

The Biochemical Characterization Of Human Histidyl-Trna Synthetase And Disease Associated Variants, Jamie Alyson Abbott

Graduate College Dissertations and Theses

Human histidyl-tRNA synthetase (HARS) is an aminoacyl-tRNA synthetase (AARS) that catalyzes the attachment of the amino acid histidine to histidyl-tRNA (tRNAHis) in a two-step reaction that is essential for protein translation. Currently, two human diseases, Usher Syndrome IIIB (USH3B) and an inherited peripheral neuropathy, Charcot Marie Tooth Syndrome (CMT), have been linked genetically to single point mutations in the HARS gene. The recessive HARS USH3B mutation encodes an Y454S substitution localized at the interface between the anticodon-binding domain and the catalytic domain of the opposing subunit. Patients with Usher Syndrome IIIB lose their sight and hearing during their second decade …

Myo2 Motor Function In The Contractile Ring And The Regulation Of Fission Yeast Cytokinesis, Luther Woodrow Pollard

Graduate College Dissertations and Theses

Animals, fungi, and amoebas require an actomyosin contractile ring at the division site to perform cytokinesis. The contractile ring initiates and guides the invagination of the plasma membrane as it forms new barriers between the nuclei at the cell equator. Defects in the contractile ring can result in misdirected, delayed, or premature cytokinesis, which leads to abnormal chromosome numbers. Aneuploidies resulting from failed cytokinesis sometimes lead to aggressive forms of cancer. This dissertation was motivated by the goal of better understanding the properties of the contractile ring and how it drives cytokinesis.

Actomyosin is initially recruited to the cell equator …

Functional And Mechanistic Consequences Of Dual Oxidase 1 Suppression In Lung Cancer, Andrew Charles Little

Graduate College Dissertations and Theses

The NADPH oxidase homolog, dual oxidase 1 (DUOX1), is an H2O2 producing transmembrane enzyme highly expressed in the airway epithelium. DUOX1-dependent redox signaling has been characterized to regulate many homeostatic processes in the lung epithelium, such as host defense, wound healing, and type II immune responses. Intriguingly, DUOX1 has been found to be suppressed in many epithelial cancers, including lung cancer, by hypermethylation of its promoter. Epigenetic silencing of DUOX1 in cancer is paradoxical to the understanding that tumors harbor elevated levels of reactive oxygen species (ROS), suggesting that DUOX1 may be a tumor suppressor.

Since DUOX1 loss occurs in …

Mechanisms And Dynamics Of Oxidative Dna Damage Repair In Nucleosomes, Wendy J. Cannan

Graduate College Dissertations and Theses

DNA provides the blueprint for cell function and growth, as well as ensuring continuity from one cell generation to the next. In order to compact, protect, and regulate this vital information, DNA is packaged by histone proteins into nucleosomes, which are the fundamental subunits of chromatin. Reactive oxygen species, generated by both endogenous and exogenous agents, can react with DNA, altering base chemistry and generating DNA strand breaks. Left unrepaired, these oxidation products can result in mutations and/or cell death. The Base Excision Repair (BER) pathway exists to deal with damaged bases and single-stranded DNA breaks. However, the packaging of …

Novel Mechanisms Governing Autoregulation Of The Src Family Kinase Fyn And Its Crosstalk With Protein Kinase A, Marion Weir

Graduate College Dissertations and Theses

ABSTRACT

Phosphorylation is a post-translational modification important for regulating protein activity and protein binding capacity. It is used in many different signaling pathways within the cell. Src Family Kinases and Protein Kinase A (PKA) are two prototyptical non-receptor tyrosine and serine/ threonine kinases, respectively, which are found in canonical signaling pathways. These two kinases are critical for signaling in essentially every cell of a multicellular organism, and are particularly important in development, cell migration and proliferation. Although both proteins have been intensely studied for many decades, an understanding of the molecular mechanisms which govern their regulation and the regulation that …

Defining Platelet-Derived Components Regulating The Prothrombinase Enzyme Complex, Francis Ayombil

Graduate College Dissertations and Theses

At sites of vascular injury, the critical blood clotting enzyme thrombin is generated from prothrombin via Prothrombinase, a macromolecular, Ca2+-dependent enzymatic complex consisting of the serine protease factor Xa and the non-enzymatic cofactor factor Va, assembled on the membranes of activated platelets. Platelets regulate thrombin formation by providing specific binding sites for the components of Prothrombinase and by releasing a platelet-derived factor V/Va molecule that is more procoagulant than its plasma counterpart and partially resistant to proteolytic inactivation. This dissertation identifies and characterizes the subpopulation of platelet-derived factor V/Va that is responsible for the observed protease resistance, and the mechanism …

The Role Of Src Kinase Activation In Lung Epithelial Alterations In Response To The A,B-Unsaturated Aldehyde Acrolein, Robert Bauer

Graduate College Dissertations and Theses

Cigarette smoke (CS) exposure is the leading cause of preventable death in the United States contributing to over 480,000 deaths a year with over 300 billion dollars in CS related costs spent per year. While the dangers of CS exposure have been studied and characterized for decades being largely attributed to reactive oxygen species and oxidative stress, increasing evidence suggests that reactive aldehydes in CS, specifically the α,β-unsaturated aldehyde acrolein, are responsible for many of the negative pathologies associated CS exposure. Previous work has shown that acrolein can bind directly to a number of cellular proteins containing redox sensitive cysteine …

Characterization Of A Non-Canonical Function For Threonyl-Trna Synthetase In Angiogenesis, Adam Christopher Mirando

Graduate College Dissertations and Theses

In addition to its canonical role in aminoacylation, threonyl-tRNA synthetase (TARS) possesses pro-angiogenic activity that is susceptible to the TARS-specific antibiotic borrelidin. However, the therapeutic benefit of borrelidin is offset by its strong toxicity to living cells. The removal of a single methylene group from the parent borrelidin generates BC194, a modified compound with significantly reduced toxicity but comparable anti-angiogenic potential. Biochemical analyses revealed that the difference in toxicities was due to borrelidin's stimulation of amino acid starvation at ten-fold lower concentrations than BC194. However, both compounds were found to inhibit in vitro and in vivo models of angiogenesis at …