<p>The protein degradation process is of vital importance for the cell to maintain cellular functions. An important enzyme in this process is the multimeric tripeptidyl-peptidase II (TPP II). It removes tripeptides from a free N-terminus of the substrates. TPP II has broad substrate specificity and wide-spread distribution, suggesting that the TPP II gene is a house-keeping gene. However, the levels of both mRNA and TPP II protein varies during different conditions and the TPP II gene promoter was therefore identified and characterized. It is a 215 bp fragment just upstream of the coding sequence. This fragment lacks a TATA-box but contains an initiator, two inverted CCAAT-boxes and an E-box. The CCAAT-boxes and the E-box were found to bind the nuclear factor Y (NF-Y) and upstream stimulatory factor-1 (USF-1) respectively. The CCAAT-boxes appear to be most important for the transcriptional activation. Furthermore, several silencer element were identified further upstream of the 215 bp promoter and the octamer binding factor Oct-1 was found to bind one of these fragments. If Oct-1 is responsible for the inhibition of the transcription of the TPP II gene remains to be investigated. In addition, the substrate specificity was investigated. For this purpose an expression system using <i>Pichia pastoris</i> was developed. The purified recombinant TPP II was found to have the same enzymatic properties as the native enzyme. In order to identify the amino acids involved in the binding of the N-terminus of the substrate, wild-type murine TPP II and four mutants E305Q, E305K, E331Q and E331K were purified. Steady-state kinetic analysis clearly demonstrated that both Glu-305 and Glu-331 are important for this binding as the K_M^app is more than 10² higher for the mutants than wild-type. Finally, the pH-dependence for cleavage of two chromogenic substrates was compared for TPP II from different species.</p>

Cytochrome P450 enzymes (CYPs), found in almost all organisms, are involved in endobiotic metabolism and detoxification of xenobiotic compounds, such as drugs, pollutants, and insecticides. In insects, CYPs play a major role in conferring resistance to various insecticides including DDT. In Drosophila and other insects, DDT-resistant strains exhibit increased expression of multiple P450 genes; however, the mechanism of overexpression is unknown. Since many CYP genes including Cyp6a8 of Drosophila are induced by caffeine and other xenobiotics, these chemicals are used as tools to understand the regulation of these genes. Previously it was shown that the 0.8-kb (-1/-732) and 0.2-kb (-1/-170) upstream DNA of Cyp6a8 of the DDT-resistant 91-R strain support caffeine, DDT, and Phenobarbital induction in adult flies and S2 cells, the 0.2-kb DNA has many transcriptionally important sequence motifs. In the present investigation, site-directed mutagenesis was performed on the putative TATA box and CREB/AP-1 motifs located at the -97/-101, -57/-61, -43/-47, and -6/-10 regions of the 0.2- and 0.8 DNAs to determine their cis-regulatory role in caffeine and PB induction in S2 cells using luciferase reporter system. Results showed that all four deletions in 0.2- and 0.8-kb DNA decreased both basal and caffeine-induced activities, but maximum effect was seen with the -57/-61 deletion. Second, the TATA mutations greatly decreased basal activity, but they did not decrease caffeine-inducibility as much as the -57/-61 mutations. Third, the effects of other three deletions on basal activities were not as pronounced in the 0.8-kb environment as were seen in the 0.2-kb environment. Taken together these results suggest that of all four putative CREB/AP1 sites the one located at -57/-61 region is most important for both basal and caffeine-induced activities. The results also suggest that the additional 600 bases upstream of -1/-170 have distal elements that interact with the proximal promoter in the 0.2-kb DNA and boost basal transcription. A model suggesting interactions of all cis elements with the basal promoter for basal and induced transcription has been proposed.

Haematopoietic development is a complex process that is strictly hierarchically organized. Here, the phagocyte lineages are a very heterogeneous cell compartment with specialized functions in innate immunity and induction of adaptive immune responses. Their generation from a common precursor must be tightly controlled. Interference within lineage formation programs for example by mutation or change in expression levels of transcription factors (TF) is causative to leukaemia. However, the molecular mechanisms driving specification into distinct phagocytes remain poorly understood. In the present study I identify the transcription factor Interferon Regulatory Factor 8 (IRF8) as the specification factor of dendritic cell (DC) commitment in early phagocyte precursors. Employing an IRF8 reporter mouse, I showed the distinct Irf8 expression in haematopoietic lineage diversification and isolated a novel bone marrow resident progenitor which selectively differentiates into CD8α+ conventional dendritic cells (cDCs) in vivo. This progenitor strictly depends on Irf8 expression to properly establish its transcriptional DC program while suppressing a lineage-inappropriate neutrophile program. Moreover, I demonstrated that Irf8 expression during this cDC commitment-step depends on a newly discovered myeloid-specific cis-enhancer which is controlled by the haematopoietic transcription factors PU.1 and RUNX1. Interference with their binding leads to abrogation of Irf8 expression, subsequently to disturbed cell fate decisions, demonstrating the importance of these factors for proper phagocyte cell development. Collectively, these data delineate a transcriptional program establishing cDC fate choice with IRF8 in its center. / Die Differenzierung von hämatopoietischen Zellen ist ein komplexer Prozess, der strikt hierarchisch organisiert ist. Dabei stellen die Phagozyten eine sehr heterogene Zellpopulation dar, mit hochspezialisierten Funktionen im angeborenen Immunsystem sowie während der Initialisierung der adaptiven Immunreaktion. Ihre Entwicklung, ausgehend von einer gemeinsamen Vorläuferzelle, unterliegt einer strikten Kontrolle. Die Beeinträchtigung dieser Linienentscheidungsprogramme, z.B. durch Mutationen oder Änderungen der Expressionslevel von Transkriptionsfaktoren kann Leukämie auslösen. Die molekularen Mechanismen, welche die linienspezifische Entwicklung steuern, sind allerdings noch nicht im Detail bekannt. In dieser Arbeit zeige ich den maßgeblichen Einfluss des Transkriptionsfaktors Interferon Regulierender Faktor 8 (IRF8) auf die Entwicklung von dendritischen Zellen (DC) innerhalb der Phagozyten. Mittels einer IRF8-Reporter Maus stellte ich die sehr differenziellen Expressionsmuster von Irf8 in der hämatopoietischen Entwicklung dar. Dabei konnte ich eine neue, im Knochenmark lokalisierte, Vorläuferpopulation isolieren, die in vivo spezifisch Differenzierung in CD8α+ konventionelle dendritische Zellen (cDC) steuert. Dieser Vorläufer ist dabei absolut von der Expression von Irf8 abhängig und etabliert auf transkriptioneller Ebene die dendritische Zellentwicklung, während gleichzeitig die Entwicklung neutrophiler Zellen unterdrückt wird. Darüber hinaus zeigte ich, dass Irf8 Expression während der cDC Entwicklung von einem neu charakterisierten cis-regulatorischen Enhancer abhängt, der spezifisch in myeloiden Zellen agiert. Ich konnte zeigen, dass die hämatopoietischen Transkriptionfaktoren PU.1 und RUNX1 mittels dieses Enhancers die Irf8 Expression steuern. Können diese beiden Faktoren nicht mit dem Enhancer interagieren, führt das zu stark verminderter Irf8 Expression, damit zu Veränderungen in den Differnzierungsprogrammen der Zellen, was die Bedeutung dieses regulatorischen Mechanismus unterstreicht. Zusammengefasst beschreiben diese Daten die Etablierung der frühen cDC Entwicklung, in der IRF8 die zentrale Rolle spielt.

The protein degradation process is of vital importance for the cell to maintain cellular functions. An important enzyme in this process is the multimeric tripeptidyl-peptidase II (TPP II). It removes tripeptides from a free N-terminus of the substrates. TPP II has broad substrate specificity and wide-spread distribution, suggesting that the TPP II gene is a house-keeping gene. However, the levels of both mRNA and TPP II protein varies during different conditions and the TPP II gene promoter was therefore identified and characterized. It is a 215 bp fragment just upstream of the coding sequence. This fragment lacks a TATA-box but contains an initiator, two inverted CCAAT-boxes and an E-box. The CCAAT-boxes and the E-box were found to bind the nuclear factor Y (NF-Y) and upstream stimulatory factor-1 (USF-1) respectively. The CCAAT-boxes appear to be most important for the transcriptional activation. Furthermore, several silencer element were identified further upstream of the 215 bp promoter and the octamer binding factor Oct-1 was found to bind one of these fragments. If Oct-1 is responsible for the inhibition of the transcription of the TPP II gene remains to be investigated. In addition, the substrate specificity was investigated. For this purpose an expression system using Pichia pastoris was developed. The purified recombinant TPP II was found to have the same enzymatic properties as the native enzyme. In order to identify the amino acids involved in the binding of the N-terminus of the substrate, wild-type murine TPP II and four mutants E305Q, E305K, E331Q and E331K were purified. Steady-state kinetic analysis clearly demonstrated that both Glu-305 and Glu-331 are important for this binding as the KMapp is more than 102 higher for the mutants than wild-type. Finally, the pH-dependence for cleavage of two chromogenic substrates was compared for TPP II from different species.

Since plants can not escape their predators by walking, they use some other defense systems, like induction or repression of defense genes. A microarray experiment performed with barley attacked by the bird cherry-oat aphid (Rhopalosiphum padi), led to the hypothesis that contig 16360 (similar to ser/thr kinases) could be linked with the resistance of barley against R. padi, and contig 6519 (similar to WIR 1A) with the susceptibility. Time course experiments showed that contig16360 and AJ250283 (similar to BCI-4) are almost induced in the same way, each, by two different aphids (R. padi and Metopolophium dirhodum). Genomic PCR was used to test the hypothesis that when plants have the gene for contig 16360, they are more likely to be resistant against aphid attack, and when plants have the gene for contig 6519, they are more likely to be susceptible. This test was performed with 69 barley lines: wild, commercial or breeding lines. Results were that the presence of WIR 1A gene has no correlation with the susceptibility, while presence of ser/thr kinase seems to be correlated with resistance.

The aerial plant body is derived from undifferentiated cells in the shoot apical meristem that in Arabidopsis thaliana is active throughout the plant life cycle. Upon transition to flowering the activity of the meristem is altered and the meristem starts to produce secondary inflorescences and floral meristems instead of leaves. Both the activity of the meristem and the decision of when to flower are processes strictly regulated by several mechanisms. In this thesis I describe the function of two genes that are active in the regulation of meristem function and in the regulation of when to shift to reproductive development. First, the Arabidopsis gene encoding TERMINAL FLOWER2 (TFL2), homologous to HETEROCHROMATIN PROTEIN1, was isolated and characterised. Mutations in TFL2 result in plants that are dwarfed, flowers early, have reduced sensitivity to day length and terminate the inflorescence in an apical flower. As homologues from other organisms TFL2 is active in gene regulation by gene repression. I show that the gene affect flowering time by the autonomous and the photoperiod pathways, two of four floral inductive pathways. TFL2 act to repress the activity of genes that are promoters of floral meristem identity and interacts genetically with factors known to alter the chromatin state. Further tfl2 is shown to have altered levels of and response to auxin. All together this shows that TFL2 is active as a regulator of several different processes during plant development. Second, I have characterised and studied the function of three genes encoding APETALA2 LIKE proteins in Norway spruce (Picea abies). In spruce these genes are expressed in meristems and reproductive tissues. When constitutively expressed in Arabidopsis two of the genes delays flowering time and alter the function of shoot apical and floral meristems. Together this suggests a function similar to the Arabidopsis homologues.

Methylation of CpG islands located at the promoter regions is a mechanism which controls gene silencing and expression. Hyper or hypo methylation of these sites on promoter sequences have been associated with many diseases, like cancer. Even though promoter CpG islands and their methylation profiles are important regulators of gene expression, the exact mechanism of gene silencing through methylation is not known. Here, we have investigated the status of promoter CpG methylation under various evolutionary pressures by calculating the differences in promoter CpG content and methylation profiles at different pass points. In order to determine the list of genes under each category we have analyzed and compared the orthologs among 58 genomes available through ENSEMBL. The total number of CpG dinucleotides at the promoter regions of all groups of genes have been calculated and compared. Additionally, we have compared the experimentally determined methylation profiles of these CpG&#039 / s between human blood cells and fibroblast cells. While the promoter CpG content changed through common to newer genes, the number of the CpG units methylated found to be consistent. Here, we present the functional level analysis of common gene lists at different pass points and report the differences of the promoter CpG content and the methylation profiles among these groups with distinct evolutionary conservation status. We have also observed the conservation status of individual methylated CpG units on the low and high methylated genes. Our analysis revealed that the surrounding methylation content had a positive effect on the conservation of individual CpG&rsquo / s.

Stimulation or repression of gene expression by genome-wide regulatory mechanisms is an important epigenetic regulatory function which can act to efficiently regulate larger regions or specific groups of genes, for example by compensating for loss or gain of chromosome copy numbers. In Drosophila melanogaster there are two known chromosome-wide regulatory systems; the MSL complex, which mediates dosage compensation of the single male X-chromosome and POF, which stimulates expression from the heterochromatic 4th chromosome. POF also interacts with the heterochromatin inducing protein HP1a, which represses expression from the 4th chromosome but which also has been assigned stimulatory functions. In addition to these two, there is another more elusive and less well-characterized genome-wide mechanism called buffering, which can act to balance transcriptional output of aneuploidy regions of the genome (i.e. copy number variation). In my thesis, I describe the presence of a novel physical link between dosage compensation and heterochromatin; mediate by two female-specific POF binding sites, proximal to roX1 and roX2 on the X chromosome (the two non-coding RNAs in the MSL complex). These sites can also provide clues to the mechanisms behind targeting of chromosome-specific proteins. Furthermore, to clarify the conflicting reports about the function of HP1a, I have suggested a mechanism in which HP1a has adopted its function to different genomic locations and gene types. Different binding mechanisms to the promoter vs. the exon of genes allows HP1a to adopt opposite functions; at the promoter, HP1a binding opens up the chromatin structure and stimulates gene expression, whereas the binding to exons condense the chromatin and thus, represses expression. This also causes long genes to be more bound and repressed by HP1a. Moreover, I show that buffering of monosomic regions is a weak but significant response to loss of chromosomal copy numbers, and that this is mediated via a general mechanism which mainly acts on differentially expressed genes, where the effect becomes stronger for long genes. I also show that POF is the factor which compensates for copy number loss of chromosome 4.

The vertebrate Dlx gene family consists of multiple convergently transcribed bigene clusters and encodes a group of homeodomain-containing transcription factors crucial for the development of forebrain, branchial arches, sensory organs and limbs. At least four cis-regulatory elements (CREs) are responsible for Dlx expression in the forebrain: URE2 and I12b in the Dlx1/Dlx2 (zebrafish dlx1a/dlx2a) locus, and, I56i and I56ii in the Dlx5/Dlx6 (zebrafish dlx5a/dlx6a) locus. Here, we first show that unlike the other three enhancers, mouse I56ii CRE targets a group of GABAergic projection neurons expressing striatal markers Meis2 and Islet1. Meis2 and Islet1 proteins can activate reporter gene transcription via the I56ii CRE, suggesting that they may be potential upstream regulators of Dlx genes in vivo. To determine whether there exists a dlx-mediated regulatory pathway during zebrafish GABAergic neuron formation, we establish two independent lines of transgenic fish in which the GFP reporter gene is controlled by a 1.4kb dlx5a/dlx6a intergenic sequence (encompassing zebrafish I56i and I56ii) and a 1.1kb fragment containing only I56i CRE, respectively. Our observations reveal that dlx5a/dlx6a regulatory elements exhibit a fairly specific activity in the zebrafish forebrain and may be essential for GABAergic neuron generation, while I56i and I56ii are likely to play distinct roles in modulating this process in different subpopulations of cells. Disruption of dlx1a/dlx2a or dlx5a/dlx6a function leads to a marked decrease of enhancer activity in the diencephalon and midbrain as well as a comparatively lesser extent of reduction in the telencephalon. In order to define the specific contribution of various individual CREs to overall Dlx regulation, we also generate a mutant mouse model in which I12b CRE is selectively deleted. Despite that mice homozygous for I12b loss develop normally and harbor no overt morphological defects in the forebrain, targeted deletion of this enhancer results in a significant reduction of Dlx1/Dlx2 transcript levels and seemingly perturbs cell proliferation in the subpallial telencephalon, particularly in the ventricular and subventricular zones of ganglionic eminences. Taken together, these data illustrate a complex and dynamic Dlx regulation in the early developing forebrain through the implications of multiple Dlx CREs with overlapping and diverse functions.

Plants respond to and defend themselves against a wide range of disease-causing microbes. In order to do so, massive reprogramming of cellular protein expression patterns, which underpin various defense pathways, must occur. A family of basic leucine zipper transcription factors, called TGA factors, has been implicated in mediating this response. The TGA factors themselves are subject to complex regulation; of note, TGA1 and TGA4 are regulated via a reduction of conserved cysteines after treatment with the phenolic signaling molecular salicylic acid, which accumulates following pathogen challenge. Previous studies indicate that TGA factors physically interact in the yeast two-hybrid system with the plant-specific CC-type of glutaredoxin (Grx)-like proteins. Grx are a family of oxidoreductases that are important for maintaining the cellular redox status and often are required to modulate protein activity. The goal of this study was to ascertain the role of these Grx-like proteins in regulating TGA1 redox state. To this end, the expression patterns of several Grx genes were analyzed.<p> Quantitative-reverse-transcriptase PCR (q-RT-PCR) experiments indicated that TGA1 and TGA4 may be involved in down-regulating levels Grx-like gene transcripts after exposure to pathogens or salicylic acid (SA). Furthermore, qRT-PCR experiments also indicated that expression of some Grx-like genes is induced by SA, jasmonic acid (JA), and <i>Pseudomonas syringae</i>. Overexpression of the Grx-like protein, CXXC9, in <i>Arabidopsis thaliana</i> revealed that it is a regulatory factor in the cross-talk between vi theSA/JA pathways as it is able to suppress expression of PDF1.2, a marker for the JA defense pathway, as determined by qRT-PCR. The â-hydroxy ethyl disulfide (HED) assay was utilized to determine if the CC-type of Grx-like proteins have oxidoreductase activity <i>in vitro</i>. These studies revealed that that the Grx-like proteins do not exhibit oxidoreductase activity in this assay.