Les plantes ont la capacité à former de nouveaux organes grâce à une croissance continue assurée par une réserve de cellules souches au sein de structures spécifiques, les méristèmes. Les méristèmes floraux diffèrent des méristèmes végétatifs par leur caractère déterminé aboutissant à la production des fleurs. Le gène IMA (INHIBITOR OF MERISTEM ACTIVITY) code une protéine contenant un motif «doigt à zinc» (MIF) régulant les processus développementaux de la fleur et des ovules chez la tomate. En effet, IMA inhibe la prolifération cellulaire au cours de la terminaison florale en agissant sur l’expression du gène WUSCHEL, responsable du maintien du pool de cellules souches et contrôle le nombre de carpelles (Sicard et al., 2008). De plus, les protéines IMA et son orthologue chez Arabidopsis, MIF2, modulent la réponse à certaines phytohormones. De manière identique à la protéine MIF1 (Hu and Ma, 2006), IMA/MIF2 régule négativement la réponse aux brassinostéroïdes, à l’auxine, aux cytokinines et aux gibbérellines mais positivement la réponse à l’acide abscissique suggérant une fonction commune des protéines MIF dans les voies de réponse aux phytohormones. Un criblage d’une banque d’ADNc par la technique de double hybride a permis de révéler l’interaction entre les protéines IMA/MIF2 et une sous-unité du complexe signalosome, CSN5. De façon intéressante, les plantes mutantes csn5 d’Arabidopsis montrent de nombreuses altérations phénotypiques telles qu’un aspect buissonnant résultant de la perte de la dominance apicale, et une altération de la réponse à l’obscurité et à l’auxine. Ces phénotypes sont fortement ressemblants aux phénotypes des plantes MIF1OE d’Arabidopsis (Hu and Ma, 2006) et des plantes IMAOE de tomate (Sicard et al., 2008). Les résultats obtenus au cours de ce projet montrent que la protéine IMA inhibe la fonction du complexe signalosome grâce à son interaction avec la protéine CSN5. / Plants have the ability to form new organs as a result of indeterminate growth ensured by specific regions of pluripotent cells, called meristems. Flowers are produced by the activity of floral meristems which differ from vegetative meristems in their determinate fate. The INHIBITOR OF MERISTEM ACTIVITY (IMA) gene encoding a Mini Zinc Finger (MIF) protein from tomato (Solanum lycopersicum) regulates the processes of flower and ovule development. IMA inhibits cell proliferation during floral termination, controls the number of carpels during floral development and acts as a repressor of the meristem organizing centre gene WUSCHEL (Sicard et al., 2008). We demonstrated that IMA and its Arabidopsis ortholog MIF2 is also involved in a multiple hormonal signalling pathway, as a putative conserved feature for plant MIF proteins (Hu and Ma, 2006). Alike Arabidopsis MIF1, IMA/MIF2 regulates negatively BR, auxin, cytokinin and gibberellin signalling and positively ABA signaling. Using yeast two-hybrid screening experiments, we identified a strong protein-protein interaction between IMA and the signalosome subunit 5 (CSN5). Interestingly the csn5 mutant in Arabidopsis displays pleiotropic developmental defects such as a bushy phenotype originating from the loss of apical dominance and the alteration in sensitivity to darkness and auxin signals. These phenotypes are strikingly similar to what was described for Arabidopsis MIF1 (Hu and Ma, 2006) and tomato IMA overexpressors plants (Sicard et al., 2008), respectively. Taken together our data strongly suggest that IMA may act as an inhibitor of CSN function through its physical interaction with SlCSN5. The observed converse effects of IMA/MIF2 overexpression or deregulation on plant development and the abundance of developmental marker genes further support the notion of a CSN inhibitory control, since the COP9 signalosome through the specific deneddylation activity of the CSN5 subunit regulates plant hormone signalling.

C2H2-zinc fingers (ZFs) are commonly found in transcription factors that code for nearly 3% of gene products in the human genome. ZF proteins are commonly involved in gene regulation during development, cell differentiation, and tumor suppression. Each "finger" is a domain composed of approximately 30 amino acids. Since the discovery of these domains over 25 years ago, several groups have contributed to the structural and biochemical knowledge to understand their DNA-binding properties. Taking advantage of the simplicity of manipulating the DNA-binding potential of a ZF, the technology has now evolved to make sequence-specific Zinc Finger Nucleases (ZFNs), Artificial Transcription Factors (ATFs), Zinc Finger Recombinases, and DNA detection tools. ZFPs have been used for various applications, ranging from regulating genes by ZF-ATFs to manipulating genomes in diverse organisms. ZFNs have remarkably revolutionized the field of genome engineering. ZFN-modified T-cells have now advanced into human clinical trials for cell-based therapies as a treatment against HIV. Despite the advances in the ZFN technology, one of the challenges in the field is obtaining effective ZFNs using publicly available tools. The traditional method of synthesizing custom ZF arrays was using modular assembly (MA). In this method, preselected ZFs from publicly available one-finger archives can be assembled modularly to make long arrays. MA of ZFNs provides a rapid method to create proteins that can recognize a broad spectrum of DNA sequences. However, three- and four-finger arrays often fail to produce active nucleases. The low success rate of MA ZF arrays was attributed to the fact that they suffer from finger-finger incompatibility referred to as context-dependent effects. However, we hypothesized that the low affinity of MA arrays was the limiting factor. The work presented in this dissertation describes our efforts at addressing these fundamental methodological challenges. We developed the Extended Modular Assembly method that overcomes the limitations of both the previous Modular Assembly. We performed a systematic investigation of number and composition of modules on ZFN activity and analyzed ZFN specificity both in vitro and in vivo. Our current experiments apply the ZFNs produced by our method to study the role of genetic variation in human disease.

The Krüppel-associated box (KRAB) zinc finger protein (ZFP) genes comprise one of the largest gene families in the mammalian genome, encoding transcription factors with an N-terminal KRAB domain and C-terminal zinc fingers. The KRAB domain interacts with a co-repressor protein, KAP-1, which can recruit various factors causing transcriptional repression of genes to which KRAB ZFPs bind. Little is currently known about the gene targets of the ~400 human and mouse KRAB ZFPs. Many KRAB ZFPs interact with factors other than KAP-1. To identify proteins that may interact with one particular KRAB ZFP, Zfp647, I previously carried out a yeast two-hybrid screen using the full-length Zfp647 sequence and a mouse embryonic cDNA library. I have now tested the interactions from this screen for their specificity for Zfp647. I show that Zfp647 can interact with itself and at least 20 other KRAB ZFPs through their zinc finger domains, and have confirmed the Zfp647 self-interaction by in vitro co-immunoprecipitation. In my yeast two-hybrid screen, Zfp647 bound to KAP-1 as well as another related protein, ARD1/Trim23. Zfp647 also interacts with proteins that function in ubiquitylation. I have found evidence to suggest that Zfp647 may also interact with proteins encoding jumonji domains both by yeast two-hybrid assay and by co-immunoprecipitation from NIH/3T3 cell extracts. We have previously found that Zfp647 localises to non-heterochromatic nuclear foci in differentiated ES cells, which also contain KAP-1 and HP1, and which lie adjacent to PML nuclear bodies in a high proportion of cells. I have found that these foci are also visible in pMEFs, but not NIH/3T3 tissue culture cells. Immunofluorescence studies with antibodies against proteins from the yeast twohybrid screen have not shown any significant co-localisation with Zfp647. KAP-1 is sumoylated ex vivo, as are two human KRAB ZFPs. Because Zfp647 lies adjacent to PML nuclear bodies and can associate with proteins involved in posttranslational modification, I tested whether Zfp647 is also modified. I characterised a sheep _-Zfp647 antibody previously created in the lab and have shown that it detects Zfp647 by western blot, but not by immunofluorescence. I show that treatment of NIH/3T3 cells with NEM, which prevents the removal of protein modifications, leads to the appearance of higher molecular weight forms of Zfp647. Modification of Zfp647 is not dependent on KAP-1, which is known to function as a SUMO E3 ligase. Attempts to classify the modification as either ubiquitin, SUMO or NEDD8 have suggested that Zfp647 may be mono-ubquitylated. The larger modified forms of Zfp647 are present in both NIH/3T3 and ES cells. Interestingly, I found that the modification profile of the protein changes over the course of ES cell differentiation, during which time Zfp647 relocalises to punctate nuclear foci; thus Zfp647 modification may be involved in this process.

Potassium ion channels play a key role in the generation and propagation of action potentials. The S4-S5 linker peptide (L45) is believed to be responsible for the anesthetic/alcohol response of voltage-gated K+ channels. We investigated this region to define the structural basis of 1-alkanol binding site in dShaw2 K+ channel. L45 peptides derived from dShaw2 and hKv3.4 K+ channel, which, if part of the complete channel, demonstrate different sensitivity to 1-alcohols. Specifically, dShaw2 is alcohol sensitive and hKv3.4 is alcohol resistant. Structural analysis of L45 with NMR and CD suggested a direct correlation between alpha-helicity and the inhibition of dShaw2 channel by 1-butanol. We used CD and NMR to determine the structure of L45 peptides in micelles and vesicles. We measured spin-lattice relaxation time (T1) and determined the location and surface accessibility of L45 in micelles. These experiments confirm that L45 of dShaw2 adopts an α-helical conformation, partially buried in the membrane and parallel to the surface. The binding and accumulation of rev proteins to an internal loop of RRE (rev responsive element) of unspliced mRNA precursors is a key step of propagation of human immunodeficiency (HIV) virus. Molecules that interfere with this process can be expected to show anti-HIV activity. Our work is based on an assumption that zinc fingers could compete with rev proteins, therefore impeding the life cycle of HIV and stopping its infection. We studied the influence of different cations, anions, and the concentration of salts and osmolytes on the binding affinity with Polyacrylamide Gel Electrophoresis (PAGE) and Isothermal Titration Calorimetry (ITC). We conclude that the types of anions and/or cations and their concentrations affect the enthalpy and entropy of the binding interacitons. Using a gel assay, we confirm that there are three products in RNA-Protein reaction, and both EDTA and salts (and their concentrations) in the gel or samples interfere with RNA-protein complex mobility.

Following pathogen recognition, nitric oxide (NO) is rapidly produced in plants, this small molecule has emerged as a key signal in plant defence responses. S-nitrosylation is the major route of NO signal transduction in plants, a redox-based modification by addition of an NO moiety on cysteine thiol to form an S-nitrosothiol (SNO). S-nitrosoglutathione reductase (GSNOR) regulates cellular levels of S-nitrosylation and displays a key role in regulating the plant defence response. In this context, NO is important to orchestrate both defence gene expression and the hypersensitive response (HR) during attempted microbial infection. However, how the plant immune system recognizes NO and how NO level could elicit plant defence responses are poorly understood. The Arabidopsis thaliana (Arabidopsis) mutant NO overproducing 1 (nox1) was employed to characterize how NO level elicits defence dynamics. In response to microbial infection, resistance (R) gene-mediated defence and basal resistance were found to be compromised in the nox1 mutant relative to wild type Col-0 plants. Interestingly, nox1 mutant exhibit similar levels of HR and pathogen susceptibility to the GSNOR loss-of-function mutant atgsnor1-3. This phenomenon suggests that NO might regulate defence responses via GSNOR-mediated S-nitrosylation. Therefore, the nox1 atgsnor1-3 double mutant was generated and characterized to clarify this hypothesis. Accelerated HR and increased pathogen susceptibility are shown in the double mutant, which implies that increased NO mediated by nox1 and elevated SNOs resulting from atgsnor1-3, are additive with respect to the plant defence response. To identify genes responsible for NO perception, forward genetic screens were developed to identify Arabidopsis mutants with abnormal NO recognition. NO marker genes for genetic screens were identified from both lab and open source microarray data. Two genes, At3g28740 and At1g76600 were selected and experimentally confirmed to be strongly induced by NO. Transgenic Arabidopsis plants were generated carrying a NO reporter cassette, which consist of a luciferase reporter gene (LUC) driven by the promoter of NO marker gene. This forward genetic approach might be a powerful tool to identify genes integral to NO signal transduction. Three C2H2 zinc finger transcription factors (ZnTFs) ZAT7, ZAT8 and ZAT12 were identified as being rapidly and strongly induced by NO donors, which could be modulators of redox/NO-dependent signalling pathway. T-DNA insertion mutants within these ZnTFs have been identified. Basal resistance against Pseudomonas syringae pv tomato (Pst) DC3000 is compromised in all single knockout lines. Therefore, the full characterisation of defence phenotype of these mutants would be necessary to explore the role of these TFs in the plant defence. Furthermore, zat8 mutant is more sensitive to nitrosative stress when compared to wild type Col-0. This suggests that ZAT8 may be involved in protecting plants against nitrosative stress. However, the molecular mechanisms that underpin this function remain to be determined. In conclusion, NO and SNOs might regulate plant disease resistance via distinct pathways. Our work has also established NO-reporter lines to identify genes responsible for NO perception. In addition, three NO-induced ZnTFs have been identified that participate in regulation of basal resistance, which might unveil aspects of NO signalling related to the regulation of transcription.

Suppressor of Hairy-wing [Su(Hw)] is a twelve zinc-finger (ZF), DNA binding transcription factor. Su(Hw) has been well characterized as critical component of the gypsy insulator complex, required for the enhancer blocking and the barrier activity of the insulator. In addition to gypsy, Su(Hw) localizes to ~3,000 binding sites in the Drosophila genome, with association to a subset of sites required for female germline development. Loss of Su(Hw) results in activation of a developmental checkpoint and apoptosis at mid- oogenesis, with a critical role during oogenesis in down-regulation of neural genes. Studies of Su(Hw) function have identified transcriptional activator, repressor and insulator roles at distinct binding sites. Current investigations aim to understand the factors that dictate the regulatory output of Su(Hw) at individual sites in the Drosophila genome, with a focus on the ZF domain. A genetic screen was completed to generate novel mutations in su(Hw). After screening more than 8,000 mutagenized chromosomes, we identified four new su(Hw) alleles, including two deletion mutations and two amino acid substitutions disrupting individual ZFs (ZF4 and ZF8). Studies of the ZF4 mutant, Su(Hw)M4M393, revealed that Su(Hw) requires this ZF for female fertility, but notgypsy insulator function. To achieve a comprehensive understanding of the Su(Hw) ZF domain, we generated Su(Hw) mutant proteins carrying disruptions in individual ZFs. Analyses utilizing these proteins have defined the requirement for each ZF in DNA association in vitro. To complement extant ZF alleles, Su(Hw) ZF mutants were expressed in vivo. Analyses of these mutants established how each ZF contributes to SBS occupancy, gypsy insulator function and female fertility. Gene expression and ChIP analyses suggest that some Su(Hw) ZFs may execute roles apart from direct DNA recognition. Genome-wide binding analyses of Su(Hw)M4M393, combined with previous studies, found that the SBS binding motif contains three DNA sequence cores (termed upstream, central and downstream). Analyses of these sequence cores in combination with Su(Hw) ZF mutants have outlined which ZFs associate with each core. Interestingly, the class containing all three sequence cores represents high occupancy SBSs that are enriched for protein factors from functional classes including transcriptional repression, nucleosome remodeling and DNA replication. The class containing the upstream and central core correlates with insulator function, while the class containing the central and downstream cores correlates with activation or repression of Su(Hw) target genes. Finally, in vitro studies of Su(Hw) ZF mutants revealed a DNA bound conformation distinct from wild type Su(Hw). Su(Hw) is a versatile transcription factor able to act as an insulator, activator and repressor. Analyses of SBSs with these functions suggest that DNA sequence, ZF usage, protein partnership and Su(Hw) conformation, combine to dictate regulatory output. Together, these studies provide insight into how discrete ZFs contribute to the roles of a multifunctional, polydactyl transcription factor.

The zinc finger protein, zBED6, is a transcriptional regulator of IGF2 along with hundreds of other genes relating to development and growth. Studies on the growth of commercially bred pigs discovered a single nucleotide substitution in the third intron of IGF2 which disrupts the binding of zBED6 and is responsible for the three-fold upregulation of IGF2 in skeletal muscle. The mutation is linked to decreased subcutaneous fat deposition, larger organ size, and increased skeletal muscle mass. Three different constructs of the zBED6 protein made by Björklund 2018 were expressed and purified to characterize their binding affinity, where one contained both zinc finger domains and two of the constructs contained only one zinc finger domain each. Electrophoretic mobility shift assay protocol was optimized to determine the apparent Kd (= 210 ± 31nM) for the full-length construct C13 and to determine which zinc finger domain was sensitive to the mutation in the IGF2 gene. The first zinc finger domain seems to be more specific in its binding target. Preliminary microscale thermophoresis results were highly variable, needing further optimization of the protocol in order to obtain a full binding curve. The next steps involve site directed mutagenesis of residues binding DNA to determine which interactions are the most significant and possibly crystallization studies as well.

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references. Also available on the World Wide Web.

Two novel and highly related C₂H₂ zinc finger proteins (CTIP1/BCL11A/EVI9 and CTIP2/BCL11B/Rit1) have been implicated in COUP-TF signaling, etiology of myeloid and lymphoid malignancies, and hematopoietic cell development. However, the precise cellular function(s) and the contribution of these proteins to neoplastic processes and hematopoietic cell development remain unknown. The goal of the studies described herein was to elucidate the molecular mechanisms underlying the transcriptional repression mediated by these proteins to understand their biological properties, and ultimately, their cellular function(s). CTIP proteins repressed transcription of a reporter gene in a TSA-insensitive manner, suggesting that this repression mechanism(s) may not involve TSA-sensitive histone deacetylation catalyzed by member(s) of class I and II HDACs. One possible mechanism is that CTIP proteins may exert ISA-insensitive histone deacetylation catalyzed by TSA-insensitive HDAC(s), such as SIRT1, to repress transcription. In deed, SIRT1 was found to interact with CTIP proteins both in vitro and in mammalian cells, and was recruited to the promoter template in a CTIP-dependent manner. The proline-rich regions of CTIP proteins and the sirtuin homology domain of SIRT1 were found to be essential for mediating CTIPs•SIRT1 interactions. Moreover, column chromatography revealed that SIRT1 and CTIP2 were components of a large complex in Jurkat cell nuclear extracts. Based on the findings that SIRT1 associates with CTIP proteins in mammalian cells, SIRT1 may underlie the transcriptional repression activity of CTIP proteins. The following results support the hypothesis that SIRT1 may underlie the mechanism(s) of CTIP-mediated transcriptional repression. First, CTIP-mediated transcriptional repression was inhibited, at least partially, by nicotinamide, an inhibitor of the NAD⁺-dependent, TSA-insensitive HDACs. Second, the decrease in levels of acetylated histones H3 and/or H4 at the promoter region of a reporter gene was observed upon overexpression of CTIP proteins, and this effect was inhibited, at least partially, by nicotinamide. Third, endogenous SIRT1 was recruited to the promoter template of a reporter gene in mammalian cells upon overexpression of CTIP proteins. Fourth, SIRT1 enhanced the transcriptional repression mediated by CTIP proteins and this enhancement required the catalytic activity of SIRT1. Finally, SIRT1 enhanced the deacetylation of template-associated histones H3 and/or H4 in CTIP-transfected cells. In summary, results described herein strongly suggest that CTIP-mediated transcriptional repression involves the recruitment of SIRT1 to the template, at which the TSA-insensitive, but nicotinamide-sensitive histone deacetylase catalyzes deacetylation of promoter-associated histones H3 and/or H4. These results contribute additional understanding to the molecular mechanisms underlying transcriptional activity of CTIP proteins, which might be helpful for identification and characterization of the target genes under the control of CTIP proteins in cells of hematopoietic system and/or the central nervous system. / Graduation date: 2004

The Hepatitis B virus (HBV) chronically infects 350 million individuals worldwide, leading to mortality by end-stage liver disease, liver cirrhosis, and hepatocellular carcinoma. The vaccine to prevent HBV infection is highly effective but is not extensively available in endemic areas, resulting in high infection rates. Nucleoside analogue treatment of HBV has allowed for higher rates of viral clearance in infected individuals, but most patients must remain on therapy long term and viral resistance to the drugs is growing. The HBV viral genome is an episome in the nucleus of infected hepatocytes. It is called covalently closed circular (ccc) DNA and is highly stable, has a long half-life, and is the template for all viral transcription and progeny production. Nucleoside analogues do not directly target cccDNA, therefore many patients experience rebound when antiviral therapy is stopped. I have designed novel DNA binding proteins called zinc finger proteins (ZFPs) to specifically bind to the cccDNA in infected cells and inhibit viral transcription. Seven ZFPs targeting the model duck HBV (DHBV) and ten ZFPs targeting HBV were developed. Kinetic analyses of the purified ZFPs were performed, characterizing their specificity and binding properties. Using the DHBV tissue culture model system, I have demonstrated that the DHBV-specific ZFPs can specifically inhibit transcription from the viral template, resulting in reduced viral RNA, protein products and progeny virions. The DHBV-specific ZFPs were tested in primary duck hepatocytes (PDH) and in vivo in the Pekin duck model. ZFPs failed to express in PDH transduced by baculovirus vectors when DHBV was present in the cells. In vivo gene delivery of the ZFPs was carried out by portal vein injection of chitosan-based nanospheres. Unfortunately, non-specific reductions in viral levels masked any direct effect by the ZFPs. Testing of the HBV-specific ZFPs in tissue culture was hindered by a lack of transfectable cell culture model. A number of different transfection methods were tested to express the HBV-specific ZFPs, all without success. Further work is being carried out using baculovirus vectors to deliver the HBV-specific ZFPs to HBV-harbouring cell lines and HBV-infected scid-Alb/uPA chimeric mice with human liver cells. / Virology