Biochemistry & Molecular Biology Department Theses and Dissertations

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Functional Analysis of Two Novel DNA Repair Factors, Metnase and Pso4
(2008-10-13T18:49:36Z) Beck, Brian Douglas; Lee, Suk-Hee
Metnase is a novel bifunctional protein that contains a SET domain and a transposase domain. Metnase contains sequence-specific DNA binding activity and sequence non-specific DNA cleavage activity, as well as enhances genomic integration of exogenous DNA. Although Metnase can bind specifically to DNA sequences containing a core Terminal Inverted Repeat sequence, this does not explain how the protein could function at sites of DNA damage. Through immunoprecipitation and gel shift assays, I have identified the Pso4 protein as a binding partner of Metnase both in vitro and in vivo. Pso4 is essential for cell survival in yeast, and cells containing a mutation in Pso4 show increased sensitivity to DNA cross-linking agents. In addition, the protein has sequence-independent DNA binding activity, favoring double-stranded DNA over single-stranded DNA. I demonstrated that the two proteins form a 1:1 stochiometric complex, and once formed, Metnase can localize to DNA damage foci as shown by knockdown of Pso4 protein using in vivo immunofluorescence. In conclusion, this shows that Metnase plays an indispensable role in DNA end joining, possibly through its cleavage activity and association with DNA Ligase IV.
Development and Application of a Mass Spectrometry-Based Quantitative Assay for Apolipoprotein M in Human and Mouse Serum
(2008-10-13T19:13:53Z) Copeland, Marci Lynn; Wang, Mu
Apolipoprotein M (apoM) is necessary for the formation of lipid-poor preβ-HDL particles, the initial precursor of HDL and acceptors of cholesterol efflux from peripheral cells. An assay to quantify apoM in serum is not widely-available, hampering the efforts to further understand apoM and to develop therapeutic methods to increase circulating levels of apoM. An antibody-free, high throughput mass spectrometry (MS)-based assay was developed to quantitatively measure apoM from a variety of species including human, mouse, and rat. Apolipoproteins were enriched by selectively binding to Liposorb, an affinity resin, followed by enzymatic digestion. This peptide mixture was separated by HPLC coupled in-line with tandem MS/ MS. Signal intensities from the MS/ MS fragmentation of apoM-specific peptides were measured simultaneously in a targeted method spanning many commonly used species. The same amount of purified human apolipoprotein A-IV uniformly labeled with 15N was spiked into all samples and was used as an internal standard to correct for any variation in sample handling and recovery. Assay variability and accuracy was statistically validated in a three-day spike recovery experiment to determine the working range of the assay. The concentration range for quantification of apoM using this assay was 11.2-500 nM, whereas average concentration of human apoM measured from a large sampling (n>100) was 370 nM. This assay was used to measure changes in apoM in mouse serum from a pre-clinical study that was designed to evaluate the effects of a microsomal triglyceride transfer protein (MTTP) inhibitor. All measured lipoproteins and apolipoproteins showed a dose-dependent decrease in concentration and the response of apoM closely followed the response of HDL. In a clinical application of the assay, apoM was measured in human serum to evaluate the effects of two cholesterol-lowering compounds, a statin drug and an experimental PPAR-α agonist. ApoM levels did not change with PPAR-α agonist or combination treatments, but significantly decreased with atorvastatin. The measurement of apoM provided additional information on the effects of these drug treatments that previously could not be measured. The availability of a quantitative assay for apoM provides a valuable tool in the development of cardio-protective therapeutics and understanding the mechanisms of these drugs.
Loss of SIMPL increases TNFα sensitivity during hematopoiesis
(2008-10) Benson, Eric Ashley; Harrington, Maureen A.; Goebl, Mark; Clapp, Wade; Skalnik, David
The innate and adaptive immune responses are critical for host survival. The TNFα/NF-κB signaling pathway is a major regulator of the immune response. The TNFα/NF-κB signaling pathway has also been proposed to play a role in the regulation of hematopoiesis. In the TNFα signaling pathway, full induction of NF-κB (specifically the p65 subunit) dependent transcription is regulated by a co-activator SIMPL. The biological significance of SIMPL in TNFα dependent responses is poorly understood. To study SIMPL in vitro and in vivo in mammalian cells, a knockdown system utilizing shRNA (short hairpin RNA) was used. Analysis of hematopoietic progenitor cells infected with a retrovirus encoding the SIMPL shRNA was used to study the role of SIMPL in hematopoiesis. The ability of progenitor cells lacking SIMPL to grow and differentiate was not compromised. In contrast in the progenitors cells lacking SIMPL, TNFα mediated inhibition of colony formation was significantly enhanced. These growth inhibitory effects of SIMPL were not due to an increase in apoptosis. The enhanced inhibitory affects were specific for TNFα and not found in other common hematopoietic inhibitors (TGF-β1 and IFNγ). Results of this work reveal that SIMPL is a component of the hematopoiesis that is required for TNFα dependent effects upon myeloid progenitors.
Identification of a Minimal Cis-element and Cognate Trans-factors Required for the Regulation of Rac2 Gene Expression during K562 Cell Differentiation
(2009-03-18T18:48:49Z) Muthukrishnan, Rajarajeswari; Skalnik, David; Herring, B. Paul; Rhodes, Simon J.; Wek, Ronald C.
This dissertation examines the molecular mechanisms regulating Rac2 gene expression during cell differentiation and identification of a minimal cis-element required for the induction of Rac2 gene expression during K562 cell differentiation. The Rho family GTPase Rac2 is expressed in hematopoietic cell lineages and is further up-regulated upon terminal myeloid cell differentiation. Rac2 plays an important role in many hematopoietic cellular functions, such as neutrophil chemotaxis, superoxide production, cytoskeletal reorganization, and stem cell adhesion. Despite the crucial role of Rac2 in blood cell function, little is known about the mechanisms of Rac2 gene regulation during blood cell differentiation. Previous studies from the Skalnik lab determined that a human Rac2 gene fragment containing the 1.6 kb upstream and 8 kb downstream sequence directs lineage-specific expression of Rac2 in transgenic mice. In addition, epigenetic modifications such as DNA methylation also play important roles in the lineage-specific expression of Rac2. The current study investigated the molecular mechanisms regulating human Rac2 gene expression during cell differentiation using chemically induced megakaryocytic differentiation of the human chronic myelogenous leukemia cell line K562 as the model system. Phorbol 12-myristate 13-acetate (PMA) stimulation of K562 cells resulted in increased Rac2 mRNA expression as analyzed by real time-polymerase chain reaction (RT-PCR). Luciferase reporter gene assays revealed that increased transcriptional activity of the Rac2 gene is mediated by the Rac2 promoter region. Nested 5’- deletions of the promoter region identified a critical regulatory region between -4223 bp and -4008 bp upstream of the transcription start site. Super shift and chromatin immunoprecipitation assays indicated binding by the transcription factor AP1 to three distinct binding sites within the 135 bp minimal regulatory region. PMA stimulation of K562 cells led to extensive changes in chromatin structure, including increased histone H3 acetylation, within the 135 bp Rac2 cis-element. These findings provide evidence for the interplay between epigenetic modifications, transcription factors and cis-acting regulatory elements within the Rac2 gene promoter region to regulate Rac2 expression during K562 cell differentiation.
Pyruvate Dehydrogenase Kinase 4 Deficiency and Hepatic Steatosis
(2009-06-23T21:37:16Z) Hwang, Byounghoon; Harris, Robert A.; Roach, Peter J.; Thurmond, Debbie C.; Elmendorf, Jeffrey S.; Considine, Robert V.
Regulation of the pyruvate dehydrogenase complex (PDC) is important for glucose homeostasis and control of fuel selection by tissues. Knocking out pyruvate dehydrogenase kinase 4 (PDK4), one of four kinases responsible for regulation of PDC activity, lowers blood glucose levels by limiting the supply of three carbon compounds for gluconeogenesis. Down regulation of PDK4 expression is also important for control of blood glucose by insulin. The primary goal was to determine whether PDK4 should be considered a target for the treatment of diabetes. A major concern is that inhibition of fatty acid oxidation by PDK4 deficiency may promote fat accumulation in tissues and worsen insulin sensitivity. This was examined by feeding wild type and PDK4 knockout mice a diet rich in saturated fat. Fasting blood glucose levels were lower, glucose tolerance was better, insulin sensitivity was greater, and liver fat was reduced in PDK4 knockout mice. The reduction in liver fat is contradictory to the finding that fibrate drugs increase PDK4 expression but ameliorate hepatic steatosis in rodents. To investigate this phenomenon, wild type and PDK4 knockout mice were fed the high saturated fat diet with and without clofibric acid. The beneficial effect of clofibric acid on hepatic steatosis was greater in the PDK4 knockout mice, indicating up regulation of PDK4 is not necessary and likely opposes the effect of clofibric acid on hepatic steatosis. Clofibric acid dramatically lowered the amount of hepatic CD36, a plasma membrane translocase required for fatty acid import, suggesting a novel mechanism for prevention of hepatic steatosis by fibrates. PDK4 deficiency had no effect on CD36 expression but reduced the enzymatic capacity for fatty acid synthesis, suggesting clofibric acid and PDK4 deficiency ameliorate hepatic steatosis by independent mechanisms. Investigation of the mechanism by which insulin regulates PDK4 expression revealed a novel binding site for hepatic nuclear factor 4α (HNF4α) in the PDK4 promoter. The stimulatory effect of HNF4α was sensitive to inhibition by Akt which is activated by insulin. The findings suggest PDK4 is a viable target for the treatment of hepatic steatosis and type 2 diabetes.
Biomarker Discovery in Early Stage Breast Cancer Using Proteomics Technologies
(2009-06-24T12:49:22Z) Qi, Guihong; Wang, Mu
Characterization of the Mitochondrial Proteome in Pyruvate Dehydrogenase Kinase 4 Wild-Type and Knockout Mice
(2009-06-24T12:51:58Z) Ringham, Heather Nicole; Wang, Mu; Harris, Robert; Witzmann, Frank
The goal of this study was to determine the effect of a PDK4 (pyruvate dehydrogenase kinase isoenzyme 4) knock-out on mitochondrial protein expression. A 2-D gel based mass spectrometry approach was used to analyze the mitochondrial proteomes of PDK4 wild-type and knockout mice. Mitochondria were isolated from the kidneys of mice in both well-fed and starved states. Previous studies show PDK4 increases greatly in the kidney in response to starvation and diabetes suggesting its significance in glucose homeostasis. The mitochondrial fractions of the four experimental groups (PDK4+/+ fed, PDK4+/+ starved, PDK4-/- fed, and PDK4-/- starved) were separated via large- format, high resolution two-dimensional gel electrophoresis. Gels were scanned, image analyzed, and ANOVA performed followed by a pair-wise multiple comparison procedure (Holm-Sidak method) for statistical analysis. The abundance of a total of 87 unique protein spots was deemed significantly different (p<0.01). 22 spots were up- or down-regulated in the fed knockout vs. fed wild-type; 26 spots in the starved knockout vs. starved wild-type; 61 spots in the fed vs. starved wild-types; and 44 in the fed vs. starved knockouts. Altered protein spots were excised from the gel, trypsinized, and identified via tandem mass spectrometry (LC-MS/MS). Differentially expressed proteins identified with high confidence include ATP synthase proteins, fatty acid metabolism proteins, components of the citric acid cycle and electron transport chain. Proteins of interest were analyzed with Ingenuity Pathway Analysis (IPA) to examine relationships among the proteins and analyze biological pathways, as well as ontological analysis with Generic Gene Ontology (GO) Term Mapper. IPA found a number of canonical pathways, biological functions, and functional networks associated with the 87 proteins. Oxidative phosphorylation was the pathway associated with a majority of the proteins, while the largest network of proteins involved carbohydrate metabolism and energy production. Overall, the effects of starvation were more extensive on mitochondrial protein expression than the PDK4 knockout.
Human carboxylesterase 2 splice variants: expression, activity, and role in the metabolism of irinotecan and capecitabine
(2009-02) Schiel, Marissa Ann; Bosron, William F.; Chiorean, E. Gabriela; Flockhart, David A.; Harrington, Maureen A.; Sanghani, Sonal P.
Carboxylesterases (CES) are enzymes that metabolize a wide variety of compounds including esters, thioesters, carbamates, and amides. In humans there are three known carboxylesterase genes CES1, CES2, and CES3. Irinotecan (CPT-11) and capecitabine are important chemotherapeutic prodrugs that are used for the treatment of colorectal cancer. Of the three CES isoenzymes, CES2 has the highest catalytic efficiency for irinotecan activation. There is large inter-individual variation in response to treatment with irinotecan. Life-threatening late-onset diarrhea has been reported in approximately 13% of patients receiving irinotecan. Several studies have reported single nucleotide polymorphisms (SNPs) for the CES2 gene. However, there has been no consensus on the effect of different CES2 SNPs and their relationship to CES2 RNA expression or irinotecan hydrolase activity. Three CES2 mRNA transcripts of approximately 2kb,3kb, and 4kb have been identified by multi-tissue northern analysis. The expressed sequence tag (EST) database indicates that CES2 undergoes several splicing events that could generate up to six potential proteins. Four of the proteins CES2, CES2458-473, CES2+64, CES21-93 were studied to characterize their expression and activity. Multi-tissue northern analysis revealed that CES2+64 corresponds to the 4kb and 3kb transcripts while CES21-93 is located only in the 4 kb transcript. CES2458-473 is an inactive splice variant that accounts for approximately 6% of the CES2 transcripts in normal and tumor colon tissue. There is large inter-individual variation in CES2 expression in both tumor and normal colon samples. Characterization of CES2+64 identified the protein as normal CES2 indicating that the signal peptide is recognized in spite of the additional 64 amino acids at the N-terminus. Sub-cellular localization studies revealed that CES2 and CES2+64 localize to the ER, and CES21-93 localizes to the cytoplasm. To date CES2 SNP data has not provided any explanation for the high inter-individual variability in response to irinotecan treatment. Multi-tissue northern blots indicate that CES2 is expressed in a tissue specific manner. We have identified the CES2 variants which correspond to each mRNA transcript. This information will be critical to defining the role of CES2 variants in the different tissues.
Effect of Inhibition of S-Nitrosoglutathione Reductase on the NF-κB Pathway
(2009-09-30T19:08:58Z) Fears, Sharry L.; Sanghani, Sonal P.; Sanghani, Paresh C.; Bosron, William F.
S-nitrosoglutathione reductase (GSNOR) also known as glutathione- dependent formaldehyde dehydrogenase (FDH), is a zinc-dependent dehydrogenase. GSNOR oxidizes long chain alcohols to an aldehyde with the help of a molecule of NAD+. GSNOR was initially identified as FDH because of its role in the formaldehyde detoxification pathway. The only S-nitrosothiol (SNO) substrate recognized by GSNOR is GSNO. A transnitrosation reaction transfers NO from nitrosylated proteins or S-nitrosothiols (RSNO) to glutathione to form S-nitrosoglutathione. This GSNO is finally converted to glutathione disulfide (GSSG) by a two step mechanism. Cellular GSNO is a nitric oxide reservoir that can either transfer to or remove from the proteins a NO group. Reduction of GSNO by GSNOR depletes this reservoir and therefore indirectly regulates protein nitrosylation. GSNOR inhibitors which can increase the basal GSNO levels will be another potential therapy. Several GSNOR inhibitors were identified in our laboratory and the aim of this study was to understand their cellular effects. One of the experiments studied the effect of the compound on protein-SNO. The role of nitric oxide in regulation of NF-κB pathway is reviewed by Bove and van der Vliet. We focused on identification of nitrosylated proteins using protein specific antibodies. We identified nitrosylation of IKKβ. So the question raised was whether nitrosylation of IKKβ affects its activity. IKKβ is responsible for phosphorylation of IκBα and phosphorylation of IκBα results in its degradation and activation of NF-κB pathway. Therefore, we studied the phosphorylation of IκBα in the presence of inhibitor C3. Results showed a dose-dependent decrease of pIκB. So the next question was whether the phosphorylation of IKKβ was affected by nitrosylation. We did not detect any change in pIKKβ with different concentrations of C3. The decreased degradation of IκBα caused by C3 translated into decreased NF-κB activity as seen by a dose-dependent decrease in amounts of ICAM-1 with increasing C3 concentration. This data supports the premise that the activity of transcription factor NF-κB is suppressed by inhibiting GSNOR with compound C3
Multiple, Nutrient Sensing Kinases Converge to Phosphorylate an Element of cdc34 That Increases Saccharomyces Cerevisiae Lifespan
(2009-08) Cocklin, Ross Roland; Goebl, Mark G.; Bard, Martin; Harrington, Maureen; Harris, Robert; Wang, Mu
Growth and division are tightly coordinated with available nutrient conditions. Cells of the budding yeast, Saccharomyces cerevisiae, grow to a larger size prior to budding and DNA replication when preferred carbon sources such as glucose, as opposed to less preferred sources like ethanol and acetate, are available. A culture’s doubling time is also significantly reduced when the available carbon and nitrogen sources are more favorable. These physiological phenomena are well documented but the precise molecular mechanisms relaying nutrient conditions to the growth and division machinery are not well defined. I demonstrate here that Cdc34, the ubiquitin conjugating enzyme that promotes S phase entry, is phosphorylated upon a highly conserved serine residue which is part of a motif that defines the family of Cdc34/Ubc7 ubiquitin conjugating enzymes. This phosphorylation is regulated by multiple, nutrient sensing kinases including Protein Kinase A, Sch9 and TOR. Furthermore, this phosphorylation event is regulated through the cell cycle with the sole induction occurring in the G1 phase which is when nutrients are sensed and cells commit to another round of division. This phosphorylation likely activates Cdc34 and in turn propagates a signal to the cell division cycle machinery that nutrient conditions are favorable for commitment to a new round of division. This phosphorylation is critical for normal cell cycle progression but must be carefully controlled when cells are deprived of nutrients. Crippling the activity of Protein Kinase A, SCH9 or TOR increases the proportion of cells that survive stationary phase conditions, which because of the metabolic conditions that must be maintained and the similarity to post-mitotic mammalian cells, is referred to as a yeast culture’s chronological lifespan. Yeast cells expressing Cdc34 mutants that are no longer subject to this regulation by phosphorylation have a reduced chronological lifespan. A precise molecular mechanism describing the change in Cdc34 activity after phosphorylation of this serine residue is discussed.

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