Herpes simplex virus type 1 (HSV-1) is a virus commonly causing cold sores in humans, however, virulent infections are known to produce debilitating encephalitis and death. HSV-1 transcription is carried out by the host cell RNA polymerase II in a tightly regulated temporal cascade. The first genes transcribed, the a genes, are activated in the absence of viral DNA synthesis. Transcription of the other temporal classes, the β, βγ, and γ genes is dependent upon the protein products of the a genes for activation. The purpose of this study was to investigate the factors that contribute to this rigid regulation of HSV-1 transcription. This investigation sought to identify some of the cellular and viral transcription factors that activate transcription of genes of the later kinetic classes. Two separate approaches were utilized in these investigations. 1) In vitro transcription using a soluble, cell free system to study the transcriptional regulation of the VP5 gene, and 2) DNA competition binding assays to identify and characterize the protein-DNA complexes resulting from interaction between the cisacting DNA sequences of the VP5 gene, other viral genes, and the proteins that bind to them. Attempts at in vitro transcription of β, βγ, and γ genes were unsuccessful. Because these genes require a products for activation, it was necessary to prepare nuclear extracts from infected cells. However, HSV-1 contains endogenous RNase activities which are components of the biochemical machinery by which the virus directs host transcription to the synthesis of viral molecules. The uses of virus deficient in the host shut-off function and various drugs were unsuccessful. Previous work in the Millette laboratory demonstrated a sequence in the VP5 promoter that played a significant role in the up regulation of expression of that gene. DNA binding competition studies using a number of HSV-1 sequences exhibiting partial homology to this sequence demonstrated that these sequences all compete for the binding of the same protein factor. Similarly, a piece of the human immunodeficiency virus (HIV) exhibiting a seven base pair homology also exhibited weak competition.

The glycine decarboxylase complex (GDC) of Succharomyces cerevisiae composed of four subunits (P, H, T and L) and plays an important role in the interconversion of serine and glycine and balancing the one-carbon unit requirements of the cell. It also enables the cell to use glycine as sole nitrogen source. This study was concerned with characterising the molecular mechanism of transcriptional regulation of the GCVgenes encoding the subunits of the GDC. The important findings of this work can be summarised as follows: i) Transcription of the GCV genes are regulated by glycine and rich nitrogen sources, which are mediated by different cis-acting elements. The LPDl gene did not show a glycine response since its transcriptional regulation is distinct from that of the other genes encoding the GDC subunits. ii) Glycine analogues or serine did not affect expression of GCV2, and therefore glycine probably needs to be metabolised to effect the glycine response of the GCV genes. iii) The repression of the GCV2 gene expression by rich nitrogen sources is mediated by a sequence between -227 and -205 of GCV2, and NCR-regulatory mutant studies showed that repression is not directly controlled by the known NCR system. iv) The glycine response of GCV2 is mediated by a motif (the glycine regulatory region; GRR; 5'-CATCN7CTTCTT-3') with CTTCTT at its core. Additional sequence immediately 5' of this motif (between -310 to -289) plays a minor role for the gene's full glycine response. v) The GRR of the GCV genes can mediate the glycine response by either activation or repression, indicating that the transcription factor(s) mediating the glycine response is/are dual-functional in nature. vi) Studies of GCV2 gene expression using different regulatory mutants showed that expression of the gene is further modulated by other transcription factors such as and Baslp which are distinct from the glycine response and possibly involved in setting up the basal expression level. vii) I n vitro studies of the GRR-protein interaction revealed THF affects the affinity of the DNA-binding protein(s) for the GRR. The importance of THF in regulation of the GCV2 gene was also shown in vivo using a foll mutant that is unable to synthesise any folates. THF or a C1-bound derivative of it acts as a ligand for the transcription factor, thus influencing transcription of the GCV genes in the appropriate physiological manner. viii) Using heparin-Sepharose chromatography fractions, four complex formations (complex I to IV) were observed with the GRR. The protein responsible for one of these was separable from the others. EMSA profiles using the GRR of the GCVI and GCV2 genes (in the presence or absence of THF) were very similar, indicating that these genes bind the same proteins and are regulated in a similar manner. ix) Mutation of the CTTCTT motif within the GRR caused significant reduction in in vitro DNA-protein complex formation, however, THF addition overcame this reduction. x) Only complex II formation was observed with a DNA fragment spanning -322 to -295, and THF affected this complex formation. xi) Footprinting analyses of complex I revealed that the binding protein protected the GRR of the GCV2 gene from DNaseI activity. This protein is an excellent candidate for the glycine response regulatory protein. Titration experiments using EMSA showed that this protein can dimerise. A preliminary genome-wide analysis of the S. cerevisiae transcriptome was carried out using miniarray membrane hybridisation. This investigated the global transcriptional changes within the cell in response to the addition of glycine into the medium. Identification of genes related to various cellular processes including onecarbon metabolism gave an insight into the regulation of the cellular metabolic flow, especially that of one-carbon metabolism. The results indicated that: xii) Glycine is transported into mitochondria to be used as substrate for the GDC which (with mitochondria1 SHMT) produces serine that is subsequently utilised for the various one-carbon metabolic pathways, such as methionine synthesis and purine synthesis. xiii) A gene of unknown function (YER183C) which showed homology to the gene for human 5,lO-CH-THF synthetase was identified from gene-array analysis to be upregulated on glycine addition, indicating the protein encoded by this gene may be involved in balancing the metabolic flow between methionine and purine synthesis when THF pools are disturbed by glycine addition. xiv) Addition of glycine to the medium also triggers the expression of other metabolic genes related to amino acid biosynthetic pathways and that of many other genes which are not directly related to one-carbon metabolism. This may be due to prolonged culturing with glycine in the medium resulting in altered expression of genes mediated by one or more secondary factors. These may reflect an adaptive response rather than a direct consequence of glycine induction. On the basis of the above data, a model for the mechanisms regulating glycine response is presented.

The cytochrome P450 (CYP) superfamily of enzymes catalyses the oxidative metabolism of lipophilic xenobiotics such as drugs and environmental chemicals, and also plays an essential role in the biosynthesis and metabolism of endogenous compounds such as cholesterol and bile acids, vitamins, steroids, arachidonic acid and eicosanoids. Cytochrome P450 2J2 (CYP2J2) is a recently identified member of the human CYP protein family that is highly expressed in the heart, vasculature, liver and other tissues. CYP2J2 metabolises arachidonic acid (AA) into epoxyeicosatrienoic acids (EETs), which have a number of potent biological activities including cytoprotective, vasodilatory and anti-inflammatory effects. Given its widespread tissue distribution and the biological actions of EETs, CYP2J2 is likely to play an important role in cellular physiology, and altered expression of CYP2J2 may have pathophysiological consequences. Indeed, recent literature studies have indicated that CYP2J2 protein levels are decreased in vascular endothelial cells exposed to hypoxia and reoxygenation, and that maintenance of CYP2J2 expression enhances cell survival. Thus, CYP2J2 expression may be impaired in diseases or conditions associated with decreased oxygen availability, such as ischaemic heart disease, stroke and atherosclerosis, and this may contribute to their pathogenic consequences. Despite its likely importance in human physiology and pathophysiology, very little is known about the regulation of CYP2J2 gene expression. The aim of this study was to investigate the molecular mechanisms that control expression of the CYP2J2 gene. In particular, this study was designed to identify factors that regulate the expression of the CYP2J2 gene in the liver-derived HepG2 cell line during normoxia and hypoxia. A 2.4 kb fragment of the 5???-flanking region of the CYP2J2 gene (corresponding to nucleotides -2341 to +98, relative to the translation start site) was isolated from a human genomic library. Automated searching of the upstream regulatory region of CYP2J2 identified several putative binding sites for the transcription factor activator protein-1 (AP-1). Because AP-1 activity is altered in hypoxia, the possibility that AP-1 may participate in the regulation of CYP2J2 expression in hypoxia was explored. Cell culture studies examined the relationship between the expression of CYP2J2, and the AP-1 genes c-fos and c-jun, in HepG2 cells cultured in normoxia and hypoxia. Down-regulation of CYP2J2 mRNA and protein in hypoxic HepG2 cells was associated with the pronounced up-regulation of c-Fos protein from an undetectable level in normoxic cells; c-Jun protein levels were readily detectable in normoxia, and were also increased in hypoxia. Transient transfection studies revealed distinct effects of Fos and Jun proteins on CYP2J2 promoter activity. While the CYP2J2 promoter was strongly activated by c-Jun, c-Fos was inactive, and also abolished gene transactivation elicited by c-Jun. These results suggest that the constitutively expressed c-Jun is important in the maintenance of CYP2J2 expression in normoxic cells. The up-regulation of c-Fos in hypoxia stimulates the formation of c-Fos/c-Jun heterodimers, which do not support CYP2J2 transcription, leading to gene down-regulation. Experiments with CYP2J2 promoter deletion constructs revealed that the region between -152 to -50 bp relative to the translation start site was crucial for activation of CYP2J2 by c-Jun. Electrophoretic mobility shift assays (EMSAs) and transfection studies identified two distinct elements within this region that were involved in c-Jun-dependent transactivation: an AP-1-like element at -56 to -63 bp, and an atypical AP-1 element at -105 to -95 bp. c-Jun homodimers interacted specifically with both elements. Separate mutagenesis of either element significantly impaired c-Jun-dependent transactivation of CYP2J2, while mutagenesis of both elements eliminated c-Jun-responsiveness. EMSAs established that c-Jun, but not c-Fos, interacted with both elements in normoxic HepG2 cells. Furthermore, mutagenesis of either c-Jun-response element significantly decreased the basal transcriptional activity of the CYP2J2 promoter in HepG2 cells, while mutagenesis of both elements almost completely suppressed basal promoter activity. These findings indicate a pivotal role for c-Jun in the maintenance of CYP2J2 expression in normoxic cells. Transfection studies indicated that c-Fos suppresses c-Jun-dependent activation of CYP2J2 at both the -56/-63 bp and -105/-95 bp c-Jun-response elements. However, c-Fos-dependent inhibition appears to be mediated by distinct mechanisms at these two regulatory elements. While both elements interacted with c-Jun homodimers, only the -105/-95 bp element was able to interact with c-Fos/c-Jun heterodimers. Thus, the up-regulation of c-Fos in hypoxia, and the shift from c-Jun homodimers to c-Fos/c-Jun heterodimers, directly decreased c-Jun binding and transactivation at the -56/-63 bp element. In contrast, up-regulation of c-Fos in hypoxia altered the composition of proteins bound at the -105/-95 bp element from c-Jun to c-Fos/c-Jun. Inhibition of promoter activity occurs because c-Fos/c-Jun heterodimers can occupy, but not transactivate, the CYP2J2 promoter via the -105/-95 bp element. In summary, this thesis provides novel information on the molecular mechanisms that control the differential expression of the human CYP2J2 gene in normoxia and hypoxia. In particular, this study has established that the AP-1 proteins c-Jun and c-Fos play a crucial role in modulating the transcriptional activation of the CYP2J2 promoter in response to cellular stress. Binding of c-Jun to two distinct c-Jun-response elements within the CYP2J2 proximal promoter induces transcriptional activation of the CYP2J2 gene and is essential for maintenance of CYP2J2 expression in normoxic cells. The up-regulation of c-Fos in hypoxia promotes the formation of c-Fos/c-Jun heterodimers, which inhibit transcriptional activation of the CYP2J2 promoter by c-Jun, thus contributing to decreased CYP2J2 expression in hypoxia. Impaired expression of CYP2J2 may contribute to cellular injury in diseases such as atherosclerosis and stroke, and a greater understanding of the mechanisms responsible for mediating altered CYP2J2 expression may eventually lead to therapeutic strategies that manipulate the expression of this important human gene.

Includes bibliography / 219 leaves, [22] leaves of plates : ill ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Biochemistry, 1987

The cytochrome P450 (CYP) superfamily of enzymes catalyses the oxidative metabolism of lipophilic xenobiotics such as drugs and environmental chemicals, and also plays an essential role in the biosynthesis and metabolism of endogenous compounds such as cholesterol and bile acids, vitamins, steroids, arachidonic acid and eicosanoids. Cytochrome P450 2J2 (CYP2J2) is a recently identified member of the human CYP protein family that is highly expressed in the heart, vasculature, liver and other tissues. CYP2J2 metabolises arachidonic acid (AA) into epoxyeicosatrienoic acids (EETs), which have a number of potent biological activities including cytoprotective, vasodilatory and anti-inflammatory effects. Given its widespread tissue distribution and the biological actions of EETs, CYP2J2 is likely to play an important role in cellular physiology, and altered expression of CYP2J2 may have pathophysiological consequences. Indeed, recent literature studies have indicated that CYP2J2 protein levels are decreased in vascular endothelial cells exposed to hypoxia and reoxygenation, and that maintenance of CYP2J2 expression enhances cell survival. Thus, CYP2J2 expression may be impaired in diseases or conditions associated with decreased oxygen availability, such as ischaemic heart disease, stroke and atherosclerosis, and this may contribute to their pathogenic consequences. Despite its likely importance in human physiology and pathophysiology, very little is known about the regulation of CYP2J2 gene expression. The aim of this study was to investigate the molecular mechanisms that control expression of the CYP2J2 gene. In particular, this study was designed to identify factors that regulate the expression of the CYP2J2 gene in the liver-derived HepG2 cell line during normoxia and hypoxia. A 2.4 kb fragment of the 5???-flanking region of the CYP2J2 gene (corresponding to nucleotides -2341 to +98, relative to the translation start site) was isolated from a human genomic library. Automated searching of the upstream regulatory region of CYP2J2 identified several putative binding sites for the transcription factor activator protein-1 (AP-1). Because AP-1 activity is altered in hypoxia, the possibility that AP-1 may participate in the regulation of CYP2J2 expression in hypoxia was explored. Cell culture studies examined the relationship between the expression of CYP2J2, and the AP-1 genes c-fos and c-jun, in HepG2 cells cultured in normoxia and hypoxia. Down-regulation of CYP2J2 mRNA and protein in hypoxic HepG2 cells was associated with the pronounced up-regulation of c-Fos protein from an undetectable level in normoxic cells; c-Jun protein levels were readily detectable in normoxia, and were also increased in hypoxia. Transient transfection studies revealed distinct effects of Fos and Jun proteins on CYP2J2 promoter activity. While the CYP2J2 promoter was strongly activated by c-Jun, c-Fos was inactive, and also abolished gene transactivation elicited by c-Jun. These results suggest that the constitutively expressed c-Jun is important in the maintenance of CYP2J2 expression in normoxic cells. The up-regulation of c-Fos in hypoxia stimulates the formation of c-Fos/c-Jun heterodimers, which do not support CYP2J2 transcription, leading to gene down-regulation. Experiments with CYP2J2 promoter deletion constructs revealed that the region between -152 to -50 bp relative to the translation start site was crucial for activation of CYP2J2 by c-Jun. Electrophoretic mobility shift assays (EMSAs) and transfection studies identified two distinct elements within this region that were involved in c-Jun-dependent transactivation: an AP-1-like element at -56 to -63 bp, and an atypical AP-1 element at -105 to -95 bp. c-Jun homodimers interacted specifically with both elements. Separate mutagenesis of either element significantly impaired c-Jun-dependent transactivation of CYP2J2, while mutagenesis of both elements eliminated c-Jun-responsiveness. EMSAs established that c-Jun, but not c-Fos, interacted with both elements in normoxic HepG2 cells. Furthermore, mutagenesis of either c-Jun-response element significantly decreased the basal transcriptional activity of the CYP2J2 promoter in HepG2 cells, while mutagenesis of both elements almost completely suppressed basal promoter activity. These findings indicate a pivotal role for c-Jun in the maintenance of CYP2J2 expression in normoxic cells. Transfection studies indicated that c-Fos suppresses c-Jun-dependent activation of CYP2J2 at both the -56/-63 bp and -105/-95 bp c-Jun-response elements. However, c-Fos-dependent inhibition appears to be mediated by distinct mechanisms at these two regulatory elements. While both elements interacted with c-Jun homodimers, only the -105/-95 bp element was able to interact with c-Fos/c-Jun heterodimers. Thus, the up-regulation of c-Fos in hypoxia, and the shift from c-Jun homodimers to c-Fos/c-Jun heterodimers, directly decreased c-Jun binding and transactivation at the -56/-63 bp element. In contrast, up-regulation of c-Fos in hypoxia altered the composition of proteins bound at the -105/-95 bp element from c-Jun to c-Fos/c-Jun. Inhibition of promoter activity occurs because c-Fos/c-Jun heterodimers can occupy, but not transactivate, the CYP2J2 promoter via the -105/-95 bp element. In summary, this thesis provides novel information on the molecular mechanisms that control the differential expression of the human CYP2J2 gene in normoxia and hypoxia. In particular, this study has established that the AP-1 proteins c-Jun and c-Fos play a crucial role in modulating the transcriptional activation of the CYP2J2 promoter in response to cellular stress. Binding of c-Jun to two distinct c-Jun-response elements within the CYP2J2 proximal promoter induces transcriptional activation of the CYP2J2 gene and is essential for maintenance of CYP2J2 expression in normoxic cells. The up-regulation of c-Fos in hypoxia promotes the formation of c-Fos/c-Jun heterodimers, which inhibit transcriptional activation of the CYP2J2 promoter by c-Jun, thus contributing to decreased CYP2J2 expression in hypoxia. Impaired expression of CYP2J2 may contribute to cellular injury in diseases such as atherosclerosis and stroke, and a greater understanding of the mechanisms responsible for mediating altered CYP2J2 expression may eventually lead to therapeutic strategies that manipulate the expression of this important human gene.

The cytochrome P450 (CYP) superfamily of enzymes catalyses the oxidative metabolism of lipophilic xenobiotics such as drugs and environmental chemicals, and also plays an essential role in the biosynthesis and metabolism of endogenous compounds such as cholesterol and bile acids, vitamins, steroids, arachidonic acid and eicosanoids. Cytochrome P450 2J2 (CYP2J2) is a recently identified member of the human CYP protein family that is highly expressed in the heart, vasculature, liver and other tissues. CYP2J2 metabolises arachidonic acid (AA) into epoxyeicosatrienoic acids (EETs), which have a number of potent biological activities including cytoprotective, vasodilatory and anti-inflammatory effects. Given its widespread tissue distribution and the biological actions of EETs, CYP2J2 is likely to play an important role in cellular physiology, and altered expression of CYP2J2 may have pathophysiological consequences. Indeed, recent literature studies have indicated that CYP2J2 protein levels are decreased in vascular endothelial cells exposed to hypoxia and reoxygenation, and that maintenance of CYP2J2 expression enhances cell survival. Thus, CYP2J2 expression may be impaired in diseases or conditions associated with decreased oxygen availability, such as ischaemic heart disease, stroke and atherosclerosis, and this may contribute to their pathogenic consequences. Despite its likely importance in human physiology and pathophysiology, very little is known about the regulation of CYP2J2 gene expression. The aim of this study was to investigate the molecular mechanisms that control expression of the CYP2J2 gene. In particular, this study was designed to identify factors that regulate the expression of the CYP2J2 gene in the liver-derived HepG2 cell line during normoxia and hypoxia. A 2.4 kb fragment of the 5???-flanking region of the CYP2J2 gene (corresponding to nucleotides -2341 to +98, relative to the translation start site) was isolated from a human genomic library. Automated searching of the upstream regulatory region of CYP2J2 identified several putative binding sites for the transcription factor activator protein-1 (AP-1). Because AP-1 activity is altered in hypoxia, the possibility that AP-1 may participate in the regulation of CYP2J2 expression in hypoxia was explored. Cell culture studies examined the relationship between the expression of CYP2J2, and the AP-1 genes c-fos and c-jun, in HepG2 cells cultured in normoxia and hypoxia. Down-regulation of CYP2J2 mRNA and protein in hypoxic HepG2 cells was associated with the pronounced up-regulation of c-Fos protein from an undetectable level in normoxic cells; c-Jun protein levels were readily detectable in normoxia, and were also increased in hypoxia. Transient transfection studies revealed distinct effects of Fos and Jun proteins on CYP2J2 promoter activity. While the CYP2J2 promoter was strongly activated by c-Jun, c-Fos was inactive, and also abolished gene transactivation elicited by c-Jun. These results suggest that the constitutively expressed c-Jun is important in the maintenance of CYP2J2 expression in normoxic cells. The up-regulation of c-Fos in hypoxia stimulates the formation of c-Fos/c-Jun heterodimers, which do not support CYP2J2 transcription, leading to gene down-regulation. Experiments with CYP2J2 promoter deletion constructs revealed that the region between -152 to -50 bp relative to the translation start site was crucial for activation of CYP2J2 by c-Jun. Electrophoretic mobility shift assays (EMSAs) and transfection studies identified two distinct elements within this region that were involved in c-Jun-dependent transactivation: an AP-1-like element at -56 to -63 bp, and an atypical AP-1 element at -105 to -95 bp. c-Jun homodimers interacted specifically with both elements. Separate mutagenesis of either element significantly impaired c-Jun-dependent transactivation of CYP2J2, while mutagenesis of both elements eliminated c-Jun-responsiveness. EMSAs established that c-Jun, but not c-Fos, interacted with both elements in normoxic HepG2 cells. Furthermore, mutagenesis of either c-Jun-response element significantly decreased the basal transcriptional activity of the CYP2J2 promoter in HepG2 cells, while mutagenesis of both elements almost completely suppressed basal promoter activity. These findings indicate a pivotal role for c-Jun in the maintenance of CYP2J2 expression in normoxic cells. Transfection studies indicated that c-Fos suppresses c-Jun-dependent activation of CYP2J2 at both the -56/-63 bp and -105/-95 bp c-Jun-response elements. However, c-Fos-dependent inhibition appears to be mediated by distinct mechanisms at these two regulatory elements. While both elements interacted with c-Jun homodimers, only the -105/-95 bp element was able to interact with c-Fos/c-Jun heterodimers. Thus, the up-regulation of c-Fos in hypoxia, and the shift from c-Jun homodimers to c-Fos/c-Jun heterodimers, directly decreased c-Jun binding and transactivation at the -56/-63 bp element. In contrast, up-regulation of c-Fos in hypoxia altered the composition of proteins bound at the -105/-95 bp element from c-Jun to c-Fos/c-Jun. Inhibition of promoter activity occurs because c-Fos/c-Jun heterodimers can occupy, but not transactivate, the CYP2J2 promoter via the -105/-95 bp element. In summary, this thesis provides novel information on the molecular mechanisms that control the differential expression of the human CYP2J2 gene in normoxia and hypoxia. In particular, this study has established that the AP-1 proteins c-Jun and c-Fos play a crucial role in modulating the transcriptional activation of the CYP2J2 promoter in response to cellular stress. Binding of c-Jun to two distinct c-Jun-response elements within the CYP2J2 proximal promoter induces transcriptional activation of the CYP2J2 gene and is essential for maintenance of CYP2J2 expression in normoxic cells. The up-regulation of c-Fos in hypoxia promotes the formation of c-Fos/c-Jun heterodimers, which inhibit transcriptional activation of the CYP2J2 promoter by c-Jun, thus contributing to decreased CYP2J2 expression in hypoxia. Impaired expression of CYP2J2 may contribute to cellular injury in diseases such as atherosclerosis and stroke, and a greater understanding of the mechanisms responsible for mediating altered CYP2J2 expression may eventually lead to therapeutic strategies that manipulate the expression of this important human gene.

Thesis (Ph. D.)--Ohio State University, 2006. / Full text release at OhioLINK's ETD Center delayed at author's request

Thesis (Ph. D.)--University of Chicago, Dept. of Molecular Genetics and Cell Biology, August 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--Rutgers University, 2009. / "Graduate Program in Plant Biology." Includes bibliographical references.

Thesis (Ph. D.)--Rutgers University, 2009. / "Graduate Program in Biomedical Engineering." Includes bibliographical references (p. 82-90).