<p> Proper gene expression programs cellular activities, while aberrant manipulation of transcription factors often leads to devastating consequences, such as cancer or cell death. The transcription factor family activator protein-1 (AP-1) plays an important role in many cellular activities including cell transformation, proliferation and survival (Shaulian and Karin 2002). However, little has been done to obtain a global view of the role of individual AP-1 members and how they cooperate in many cellular activities. We have discovered that blocking the AP-1 pathway by a c-Jun dominant negative mutant, TAM67, induced cell death in RSV-transformed primary chicken embryo fibroblasts (CEF), suggesting that AP-1 activity is vital for cell survival upon v-Src transformation. In addition, accumulation of cytoplasmic vesicles was observed in the cytoplasm of a proportion of RSV-transformed CEF expressing TAM67. Oil-red staining of these vesicles indicated the presence of lipid droplets in these cells, suggesting that the inhibition of AP-1 promotes the adipogenic conversion of v-Src transformed CEF. To understand the role of individual members of the AP-1 family, a retroviral-based shRNA expressing system was designed to stably downregulate individual AP-1 members. This retroviral-based RNAi system provided sustained gene downregulation of AP-1 family members. Reduction of the c-Jun protein level by shRNA induced senescence in normal CEF, while it modestly downregulated AP-1 activity in RSV -transformed CEF indicating that c-Jun is not the main component of the AP-1 complex in RSV-transformed CEF. Inhibition of JunD expression induced apoptosis and was deleterious to both normal and RSV-transformed CEF, suggesting that JunD is crucial for the survival of CEF. Transient express10n reporter-assays also showed that loss-of-function of JunD by shRNA dramatically repressed AP-1 activity. Hence JunD is the main component of the AP-1 complex that regulates the survival of CEF. Furthermore, we determined that loss of JunD expression resulted in an elevated level of tumour suppressor p53. Co-inhibition of p53 and JunD restored the transforming ability of v-Src transformed CEF, as indicated by foci formation in soft agar assays. Hence, repression of p53 induction was able to bypass the death signal released as a result of AP-1 inhibition in v-Src transformed CEF. Downregulation of Fra-2 (Fos-related antigen 2) level by shRNA did not affect the proliferation of normal CEF. However, RSV -transformed CEFs expressing fra -2 shRNA were transformation-defective with the presence of multiple vesicles in cytoplasm. Oil-red staining of these vesicles indicated the presence of lipid droplets, which resembles the effect of T AM67 in RSV -transformed CEF indicating that Fra-2 blocks differentiation. These findings help us to understand the role of individual members of the AP-1 transcription factor family in normal and RSV -transformed CEF. Importantly, global gene profiling of v-Src transformed CEF expressing shRNA for individual AP-1 members will improve our knowledge of the transformation process. Functional characterization of the cascade will rely on the use of retroviral-based shRNA expressing system as described above. </p> / Thesis / Doctor of Philosophy (PhD)

<p>Stress responsive genes play a key role in shaping the manner in which plants process and respond to environmental stress. Their gene products are linked to DNA transcription and its consequent translation into a response product. However, whilst these genes play a significant role in manufacturing responses to stressful stimuli, transcription factors coordinate access to these genes, specifically by accessing a gene&rsquo / s promoter region which houses transcription factor binding sites. Here transcriptional elements play a key role in mediating responses to environmental stress where each transcription factor binding site may constitute a potential response to a stress signal. Arabidopsis thaliana, a model organism, can be used to identify the mechanism of how transcription factors shape a plant&rsquo / s survival in a stressful environment. Whilst there are numerous plant stress research groups, globally there is a shortage of publicly available stress responsive gene databases. In addition a number of previous databases such as the Generation Challenge Programme&rsquo / s comparative plant stressresponsive gene catalogue, Stresslink and DRASTIC have become defunct whilst others have stagnated. There is currently a single Arabidopsis thaliana stress response database called STIFDB which was launched in 2008 and only covers abiotic stresses as handled by major abiotic stress responsive transcription factor families. Its data was sourced from microarray expression databases, contains numerous omissions as well as numerous erroneous entries and has not been updated since its inception.The Dragon Arabidopsis Stress Transcription Factor database (DASTF) was developed in response to the current lack of stress response gene resources. A total of 2333 entries were downloaded from SWISSPROT, manually curated and imported into DASTF. The entries represent 424 transcription factor families. Each entry has a corresponding SWISSPROT, ENTREZ GENBANK and TAIR accession number. The 5&rsquo / untranslated regions (UTR) of 417 families were scanned against TRANSFAC&rsquo / s binding site catalogue to identify binding sites. The relational database consists of two tables, namely a transcription factor table and a transcription factor family table called DASTF_TF and TF_Family respectively. Using a two-tier client-server architecture, a webserver was built with PHP, APACHE and MYSQL and the data was loaded into these tables with a PYTHON script. The DASTF database contains 60 entries which correspond to biotic stress and 167 correspond to abiotic stress while 2106 respond to biotic and/or abiotic stress. Users can search the database using text, family, chromosome and stress type search options. Online tools have been integrated into the DASTF&nbsp / database, such as HMMER, CLUSTALW, BLAST and HYDROCALCULATOR. User&rsquo / s can upload sequences to identify which transcription factor family their sequences belong to by using HMMER. The website can be accessed at http://apps.sanbi.ac.za/dastf/ and two updates per year are envisaged.</p>

<p>Stress responsive genes play a key role in shaping the manner in which plants process and respond to environmental stress. Their gene products are linked to DNA transcription and its consequent translation into a response product. However, whilst these genes play a significant role in manufacturing responses to stressful stimuli, transcription factors coordinate access to these genes, specifically by accessing a gene&rsquo / s promoter region which houses transcription factor binding sites. Here transcriptional elements play a key role in mediating responses to environmental stress where each transcription factor binding site may constitute a potential response to a stress signal. Arabidopsis thaliana, a model organism, can be used to identify the mechanism of how transcription factors shape a plant&rsquo / s survival in a stressful environment. Whilst there are numerous plant stress research groups, globally there is a shortage of publicly available stress responsive gene databases. In addition a number of previous databases such as the Generation Challenge Programme&rsquo / s comparative plant stressresponsive gene catalogue, Stresslink and DRASTIC have become defunct whilst others have stagnated. There is currently a single Arabidopsis thaliana stress response database called STIFDB which was launched in 2008 and only covers abiotic stresses as handled by major abiotic stress responsive transcription factor families. Its data was sourced from microarray expression databases, contains numerous omissions as well as numerous erroneous entries and has not been updated since its inception.The Dragon Arabidopsis Stress Transcription Factor database (DASTF) was developed in response to the current lack of stress response gene resources. A total of 2333 entries were downloaded from SWISSPROT, manually curated and imported into DASTF. The entries represent 424 transcription factor families. Each entry has a corresponding SWISSPROT, ENTREZ GENBANK and TAIR accession number. The 5&rsquo / untranslated regions (UTR) of 417 families were scanned against TRANSFAC&rsquo / s binding site catalogue to identify binding sites. The relational database consists of two tables, namely a transcription factor table and a transcription factor family table called DASTF_TF and TF_Family respectively. Using a two-tier client-server architecture, a webserver was built with PHP, APACHE and MYSQL and the data was loaded into these tables with a PYTHON script. The DASTF database contains 60 entries which correspond to biotic stress and 167 correspond to abiotic stress while 2106 respond to biotic and/or abiotic stress. Users can search the database using text, family, chromosome and stress type search options. Online tools have been integrated into the DASTF&nbsp / database, such as HMMER, CLUSTALW, BLAST and HYDROCALCULATOR. User&rsquo / s can upload sequences to identify which transcription factor family their sequences belong to by using HMMER. The website can be accessed at http://apps.sanbi.ac.za/dastf/ and two updates per year are envisaged.</p>