Thesis (Ph. D.)--University of Rhode Island, 2006. / Typescript. Includes bibliographical references (leaves 136-153).

Thesis (Ph. D.)--University of Rhode Island, 2005. / Typescript. Includes bibliographical references (leaves 121-133).

Correct regulation of transcription is essential for maintaining a healthy cellular state. During transcription RNA polymerase II (Pol II) proceeds in a regulated manner through several transitions to ensure appropriate control of synthesis and enable correct processing of the pre-RNA. Shortly after initiation Pol II is caused to pause by the binding of factors, DSIF and NELF. To enable transition of Pol II into the elongation phase CDK9/cyclin T phosphorylates the C-terminal domain (CTD) of Pol II, DSIF and NELF. This phosphorylation releases the paused state and provides an alternative set of post-transcriptional modifications on the CTD to generate a binding platform for elongation, histone modifying and termination factors. CDK9/cyclin T is itself regulated within multicomponent complexes. A small activated complex, containing Brd4, recruits CDK9/cyclin T to active sites of transcription, thereby promoting the elongation of transcription. The role of CDK9/cyclin T in the regulation of transcription has resulted in its validation as a drug target against several disease states including cancer, HIV and cardiac hypertrophy. In this thesis, I present the crystallographic structures of a series of 2-amino-4-heteroaryl-pyrimidine compounds and the roscovitine derivative, (S)-CR8, bound to CDK9/cyclin T and CDK2/cyclin A. In combination with thermal denaturation data and kinetic analysis, these structures have suggested chemical modifications that might be made to increase the CDK9 specificity of these compounds. I have also validated the use of a mutated form of cyclin T for use in the development of CDK9/cyclin T inhibitors. In addition, I present both structural and kinetic analysis of the Brd4-CDK9/cyclin T interaction. I show that C-terminal fragments of Brd4 enhance the in vitro kinase activity of CDK9/cyclin T against the Pol II CTD. Furthermore, I demonstrate that this enhancement may be inhibited by Plk1-mediated phosphorylation of Brd4. Finally, I show that Brd4 binds to a site that spans CDK9 and cyclin T and I propose detailed molecular models of the Brd4-cyclin T interaction.

SRMS (Src-Related tyrosine kinases lacking C-terminal Regulatory tyrosine and N terminal Myristoylation Sites) belongs to a family of non-receptor tyrosine kinases, which also includes breast tumor kinase (BRK). SRMS was first identified in 1994 in a screen for the genes that regulate the growth and differentiation of neuroepithelial cells. This 54 kDa protein spanning 488 amino acids, consists of the prototypical Src homology 3 (SH3), Src homology 2 (SH2) and a tyrosine kinase domain. While BRK has been documented for its expression in over 60 % of breast carcinomas, information on SRMS on similar grounds remains absent from the literature. Furthermore, unlike BRK, knowledge of how SRMS regulates its enzymatic activity as well as the identification of its substrates remains unknown. The work in this thesis demonstrates that SRMS is potentially expressed in the majority of breast carcinomas. To understand the biochemical and cellular functions of SRMS, a series of mutants comprising point mutations as well as the deletion of the N-terminal region and the functional, SH3 and SH2 domains, were generated and assessed for enzymatic activity in cells. This study demonstrates for the first time that the wild type protein is apparently constitutively active and that its N-terminal region regulates its enzymatic activity. As well, three critical amino acid residues in the protein namely, lysine 258 (ATP binding site), tyrosine 380 (auto-phosphorylation site) and tryptophan 223 (intramolecular interaction) have been characterized. All three residues have been determined to be essential for the enzymatic activity of SRMS. Finally, the adapter protein Dok1 has been characterized as a novel substrate of SRMS. The results from the present study underscore the potential significance of the catalytically active non-receptor tyrosine kinase, SRMS that should serve as a foundation upon which further research may ensue in the context of breast tumorigenesis.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 4 uppsatser.

La chromatine chez les eucaryotes, porte des informations génétiques et épigénétiques. Les mécanismes garantissant le maintien de ces informations lors de la division cellulaire ou la réparation de l’ADN sont encore mal connus et ils constituent l’enjeu principal du projet de thèse. Plus particulièrement, l’objectif du projet de thèse est de chercher à comprendre comment les chaperons d’histones coordonnent leur action avec des partenaires associés à la fourche de réplication pour conserver les marques épigénétiques portées par les histones parentales et les reporter sur les histones nouvellement synthétisées. Cette thèse décrit précisément comment ASF1 (Anti Silencing Function 1) coopère avec le complexe CAF-1 (Chromatin Assembly Factor 1) et la sous-unité de l’hélicase réplicative MCM2 (Mini Chromosome Maintenance 2), pour la prise en charge des H3-H4 dans la réplication et la réparation de l’ADN.La thèse s’intéresse également à la régulation de l’activité de ces chaperons d’histones par des kinases activées suite à des stress réplicatifs ou des dommages de l’ADN. En particulier nous avons cherché à mieux comprendre comment l’ajout de groupements phosphate sur ASF1 par une enzyme appelée TLK (Tousled Like Kinase) module son activité au cours du cycle cellulaire et en réponse aux dommages de l’ADN. La caractérisation de l'importance des sites phosphorylés sur les propriétés de liaison du chaperon, permet de mieux comprendre le rôle joué par différent forme d’ASF1 dans l’assemblage des histones sur l’ADN et le maintien des informations épigénétiques. Le travail de thèse contient d’analyses biochimiques et structurales par une combinaison de techniques (SEC-MALS, AUC, ITC, RMN, cristallographie des rayons X) et d’analyses fonctionnelles sur des modèles cellulaires. / In eukaryotes, chromatin carries both, the genetic and epigenetic information. Mechanisms implicated in maintenance of these information during cell division or DNA repair remain poorly understood and they constitute the main issue of this thesis project. More specifically, the goal of the project is to understand how histone chaperones coordinate their action with partners associated with the replication fork to recognize and preserve the epigenetic marks carried by parental histones and to copy on the newly synthesized histones. The work unravels how ASF1 (Anti-Silencing Function 1) cooperates with the CAF-1 complex (Chromatin Assembly Factor 1) and with the replicative helicase subunit MCM2 (Mini Chromosome Maintenance 2), for the management of H3-H4 histones in DNA replication and repair.Moreover, this thesis investigates the regulation of histone chaperones activities by kinases activated after a replicative stress or DNA damage. In particular, we analyzed the consequences of ASF1 phosphorylation by the enzyme called TLK (Tousled like kinase). The activity of TLK is modulated during the cell cycle and after DNA damage. Characterization of the importance of phosphorylated sites on the chaperone binding properties, allows a better understanding of the role played by different forms of ASF1 in the assembly of histones on DNA and maintenance of epigenetic information. The thesis work included biochemical and structural analysis with a combination of different techniques (SEC-MALS, AUC, ITC, NMR, X-ray crystallography) and functional analysis in cellular models.

Aurora A and B are the major kinases that control key events in mitosis, such as centrosome function, spindle assembly, chromosome segregation and cytokinesis, through phosphorylation of multiple proteins. These kinases share identical consensus target motifs, so the substrate specificity is determined by distinctive sub-cellular localization of the Auroras. Many proteins have been identified as targets of either Aurora A, or Aurora B, or both kinases by mass spectrometry studies. However, only a few of the identified phosphorylation sites in these targets have a characterized function in vivo. Therefore, the molecular mechanisms underlying the regulation of certain mitotic events by Aurora kinases remain unclear. The objective of my work was to develop a tool for identifying new substrates of both Aurora kinases. More specifically, I aimed to identify the molecular targets of Aurora A at the kinetochores, and determine how Aurora A contributes to the error correction near spindle poles. I first demonstrated that the outer kinetochore protein HEC1/Ndc80, phosphorylated by Aurora B at kinetochores, can also be phosphorylated by Aurora A close to the centrosomes (Chapter 2). My finding showed that Aurora kinases can share substrates in the cells and revealed the mechanism by which Aurora A contributes to the error-correction near spindle poles. To identify and characterise novel substrates of Aurora kinases, I developed a bioinformatic approach in collaboration with the Centre Bioinformatician, Alastair Kerr. This bioinformatic method uses the Auroras’ shared consensus motifs combined with several parameters that control the substrate specificity of Aurora kinases. I tested the phosphorylation of the chosen candidates in vitro using radiolabelled kinase assays. In my study, five proteins were validated - SPICE1, TTLL4, AHCTF1, CLASP2 and an uncharacterized protein KIAA1468 - as in vitro substrates of Aurora A and Aurora B kinases (Chapter 3). I then focussed on the Aurora kinases-dependent regulation of spindle and centriole-associated protein, SPICE1, in cells (Chapter 4). Using either site-directed mutagenesis of SPICE1 or inhibition of Aurora kinases with small molecule inhibitors, I found that the predicted phosphorylation of the SPICE1 C terminus had the function in cells of directing the SPICE1 localization on the spindle MTs. My results demonstrate the high accuracy of this genome-wide bioinformatics approach. By complementing mass spectrometry studies, here lies a potential for the identification of other unknown substrates, which is important for the general understanding of how Aurora kinases regulate the mitotic apparatus.

TRPA1 is a thermosensitive ion channel from the ankyrin subfamily of Transient Receptor Potential (TRP) receptors. These proteins play essential roles in the transduction of wide variety of environmental and endogenous signals. TRPA1, which is abundantly expressed in primary nociceptive neurons, is an important transducer of various noxious and irritant stimuli and is also involved in the detection of temperature changes. Similarly to other TRP channels, TRPA1 is comprised of four subunits, each with six transmembrane segments (S1-S6), flanked by the cytoplasmic N- and C-terminal ends. In native tissues, TRPA1 is supposed to be regulated by multiple phosphorylation sites that underlie TRPA1 activity under physiological and various pathophysiological conditions. Using mutational approach, we predicted and explored the role of potential phosphorylation sites for protein kinase C in TRPA1 functioning. Our results identify candidate residues, at which phosho-mimicking mutations affected the channel's ability to respond to voltage and chemical stimuli, whereas the phospho-null mutations to alanine or glycine did not affect the channel activation. Particularly, we identify the serine 602 within the N-terminal ankyrin repeat domain 16, the substitution of which to aspartate completely abolished the TRPA1...