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published_or_final_version / Zoology / Master / Master of Philosophy

G-protein coupled receptors (GPCRs) have been shown to interact with an array of accessory proteins that modulate their function. I hypothesize that the GLP-1R, a B-class GPCR, similarly has interacting proteins that regulate its signaling. An unliganded human GLP-1R was screened using a membrane-based split ubiquitin yeast two-hybrid (MYTH) assay and a human fetal brain cDNA prey library to reveal 38 novel interactor proteins. These interactions were confirmed by co-immunoprecipitation and immunofluorescence. When co-expressed with the GLP-1R in cell lines, 15 interactors significantly attenuated GLP-1-induced cAMP accumulation. Interestingly, SiRNA-mediated knock down of three selected novel interactors, SLC15A4, APLP1 and AP2M1, significantly enhanced GLP-1-stimulated insulin secretion from the MIN6 beta cells. In conclusion, this present work generated a novel GLP-1R-protein interactome, identifying several interactors that suppress GLP-1R signaling; and the inhibition of these interactors may serve as a novel strategy to enhance GLP-1R activity.

G-protein coupled receptors (GPCRs) have been shown to interact with an array of accessory proteins that modulate their function. I hypothesize that the GLP-1R, a B-class GPCR, similarly has interacting proteins that regulate its signaling. An unliganded human GLP-1R was screened using a membrane-based split ubiquitin yeast two-hybrid (MYTH) assay and a human fetal brain cDNA prey library to reveal 38 novel interactor proteins. These interactions were confirmed by co-immunoprecipitation and immunofluorescence. When co-expressed with the GLP-1R in cell lines, 15 interactors significantly attenuated GLP-1-induced cAMP accumulation. Interestingly, SiRNA-mediated knock down of three selected novel interactors, SLC15A4, APLP1 and AP2M1, significantly enhanced GLP-1-stimulated insulin secretion from the MIN6 beta cells. In conclusion, this present work generated a novel GLP-1R-protein interactome, identifying several interactors that suppress GLP-1R signaling; and the inhibition of these interactors may serve as a novel strategy to enhance GLP-1R activity.

The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes. Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes. The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level. In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

Understanding normal and cancer cell biology requires the development and application of systems biology approaches capable of probing the functional human proteome, and the protein-protein interactions (PPIs) within it. Such technologies will facilitate our understanding of how molecular events drive phenotypic outcomes, and how these processes are perturbed in disease conditions. In this thesis, I first describe the development of a mammalian, Gateway compatible, lentivirus-based protein-fragment complementation assay (magical-PCA), for the in vivo high-throughput identification of PPIs in mammalian cells. This technology provides a vast improvement over current PCA methodologies by allowing for pooled, proteome-scale mapping of PPIs in any mammalian cell line of interest, using any bait protein of interest. A proof-of-concept pooled genome-scale screen using the magical-PCA approach was performed using the human mitochondrial protein TOMM22 as a bait, providing evidence that this technology is amenable to proteome-wide screens. Moreover, the TOMM22 screens offered novel insight into links between TOMM22 and proteins involved in mitochondrial organization, apoptosis, and cell cycle dynamics. Second, I performed a pooled genome-scale magical-PCA screen with the oncoprotein BMI1, a component of the E3 ubiquitin ligase complex involved in histone H2A mono-ubiquitination and gene silencing, to identify novel BMI1 protein interactors. Consequently, I have uncovered a novel physical and functional association between BMI1 and components of the mammalian splicing machinery. I further discovered that BMI1 knockdown influenced the alternative splicing of a number of cellular pre-mRNAs in colon cancer cell lines, suggesting that the association between BMI1 and cellular splicing factors impinges on pre-mRNA processing. Importantly, BMI1 expression was shown to influence the alternative splicing of the SS18 oncoprotein towards an exon 8-excluded isoform, which was shown in this study to promote cell proliferation when assessed in an anchorage-independent growth assay. Together, these studies highlight the development of a new methodology for the detection and proteome-scale screening of mammalian PPIs. A proof-of-concept screen with human TOMM22 highlighted the utility of the approach, as I was able to detect both strong and weak or transient PPIs. Application of my screening methodology to BMI1 provided crucial insight into the function of this oncoprotein, and BMI1-driven tumorigenesis.

Thesis (Ph. D.)--University of Hawaii at Manoa, 2005. / Includes bibliographical references (leaves 162-188). / Also available by subscription via World Wide Web / xvi, 188 leaves, bound ill. (some col.) 29 cm

Termination of protein synthesis occurs in response to the translocation of a stop codon (UAA, UAG or UGA) into the A site of the ribosome. Unlike sense codons, stop signals in the mRNA are recognized by two classes of specialized proteins called release factors (RFs): the class I or decoding RF, which recognizes the stop codon and promotes peptidyl-tRNA hydrolysis and class II RF, a G-protein that promotes the dissociation of the decoding RF from the ribosome. The discovery that stop codons are decoded by a protein factor rather than a specific tRNA opened up the possibility that the signal for termination of protein synthesis might extend beyond the stop codon itself. Biochemical and genetic experiments in prokaryotes confirmed that bias in nucleotide usage around stop codons correlates with translation termination efficiency. The objective of the current investigation was to define the eukaryotic termination signal by determining the bias in the nucleotide sequence surrounding eukaryotic stop codons and to identify whether this was a determinant of translation termination efficiency. Bioinformatic analysis of five diverse eukaryotic genomes was undertaken to identify potential eukaryotic translation termination signal elements. Significant nucleotide bias was identified both 5� and 3� of the stop codon in all the genomes investigated. Correlations were identified between nucleotide bias and gene expression levels, and between nucleotide bias and natural recoding sites predicting that nucleotides 5� and 3� of the stop codon affect termination efficiency. These correlations were common to all organisms investigated and suggested the existence of a eukaryotic termination signal. Termination signals identified from the bioinformatic analysis were assayed to determine the efficiency of termination in an in vitro dual luciferase reporter assay. Results indicated that nucleotides both 5� and 3� of the stop codon could significantly alter termination signal efficiency, although readthrough did not vary by greater than 1%. The effect of nucleotides 3� to the stop codon on termination efficiency was investigated further in mammalian cultured cells using the dual luciferase reporter assay. Results showed a significant relationship between the identity of these nucleotides and observed termination efficiencies with nucleotides at positions +4 and +8 giving the strongest correlation. Termination sequence elements of the form UGA CUN NCN mediated up to 5% readthrough in cultured cells. Investigations into the underlying mechanisms that were responsible for the variation in termination efficiency were also undertaken. Co-transfection of specific suppressor tRNAs enhanced but did not change the pattern of observed termination efficiency, indicating that the mechanisms mediated by the termination signal element was not mediated through suppressor tRNA binding. Alignments of 18S rRNA sequences indicated potential extensive interactions between the rRNA and the mRNA termination signal element. Experiments that assessed the effect of eRF1 levels on termination at inefficient termination signals in vitro revealed that increased levels of eRF1 could improve termination efficiency. These results indicate that, as in prokaryotes, specific nucleotides beyond the stop codon modulate translation termination efficiency in eukaryotes, and that the translation termination signal should be considered a sequence element.

Bibliography: leaves 139-158. / vii, 158, [44] leaves, [33] leaves of plates : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Hypothesises that p160 and p67 proteins repress the functional activities of c-Myb . Their ability to interact with the c-jun basic-leucine zipper (bZIP region) and their existence amongst the murine cell lines is examined. The complete cloning of cDNA encoding both p160 and p67, and the characterisation of these proteins, including the determination of their relationship is described. / Thesis (Ph.D.)--University of Adelaide, Dept. of Genetics, 1998?

Thesis (M.S.)--University of Texas at El Paso, 2007. / Title from title screen. Vita. CD-ROM. Includes bibliographical references. Also available online.