Thesis--Auburn University, 2009. / Abstract. Vita. Includes bibliographical references (p. 224-238).

The mitochondrial tyrosyl tRNA synthetases (mtTyrRS) from certain fungii are found to be bifunctional enzymes that aid in group I intron splicing in addition to charging tRNA[superscript Tyr]. This splicing activity is conferred by several insertions that are unique to these mtTyrRS. Initial biochemical evidence suggested the similar tertiary structures of the tRNA and the intron enable binding of the protein to both. However, a recently solved co-crystal structure showed that the tRNA and intron were bound on opposite faces of the protein. The intron was bound almost exclusively by a novel surface formed by several insertions in the protein. This work presents the structure of the C-terminal domain of the A. nidulans mtTyrRS (PDB ID -- 2ktl). NMR results show that the C-terminal domain contains an S4 fold with a mixed [beta]-sheet and two anti-parallel [alpha]-helices that pack against these strands. The strands [beta]1 and [beta]5 are parallel, and [beta]2 to [beta]5 are arranged anti-parallel to each other. The C-terminal domain from A. nidulans mtTyrRS has three insertions in its sequence that make it almost twice the size of bacterial TyrRS. NMR results show that insertion 3 at the N-terminus of the domain is flexible. Insertion 4 is contained in the loop connecting [beta]2-[beta]3 and does not have a well defined structure. Insertion 5 and the C-terminal extension form two helices, [alpha]5 and [alpha]6 that fold away from the core of the protein. An extended helix ([alpha]4) between strands [beta]3 and [beta]4 was identified by NMR. Based on structural alignments with bacterial TyrRS, this helix was classified as a novel insertion 4b in the C-terminal domain. Conserved positively charged residues used to bind the tRNA are found in the turn between the anti-parallel [alpha]-helices and the turn connecting strands [beta]4-[beta]5. Based on a comparison with other TyrRS structures, the three insertions are positioned away from the tRNA binding site. The insertions form a novel RNA binding surface that could interact with the intron. Since these insertions are found in loop and termini regions, they could be a structural adaptation acquired by these splicing mtTyrRS. NMR spectra of the full length TyrRS from B. stearothermophilus and mtTyrRS from A. nidulans indicate that the motion of the C-terminal domain is coupled to that of the full length protein. This provides new information regarding the organization of the full length TyrRS. / text

Dissertation (Ph.D.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographic references.

Transcription of human protein-coding genes and most small nuclear RNA genes is mediated by RNA Polymerase II (Pol II). During a cycle of transcription, Pol II recruits a variety of factors that facilitate transcription elongation, RNA processing and termination, through its long, unstructured C-terminal domain (CTD). The CTD in humans comprises 52 tandem heptapeptide repeats with the consensus sequence Y₁S₂P₃T₄S₅P₆S₇. Each amino acid of the heptapeptide can be chemically modified, which influences the recruitment of other protein factors to the transcription machinery. Not all enzymes that modify the CTD have been discovered. Recent studies have identified a novel CTD phosphatase: RPAP2 in humans and its yeast homologue Rtr1, which dephosphorylate phospho-Ser5 of the heptapeptide repeats. RPAP2 has been shown to stimulate 3' end cleavage of nascent snRNAs through recruitment of the Integrator complex, and unpublished work suggests the involvement of RPAP2 in regulating vertebrate developmental programs. However, the exact mechanisms that regulate the function of human RPAP2, and thus impact on CTD modification, are not well-understood. This thesis presents a novel mechanism whereby RPAP2 recruits protein phosphatase 1 (PP1) to snRNA genes, where PP1 is postulated to activate P-TEFb to phosphorylate Ser2 of the CTD. At the same time, P-TEFb may have a role in activating the phosphatase activity of RPAP2. Furthermore, RPAP2 itself is shown to be recruited to a number of gene promoters by the RPRD1A protein, which also stimulates its phosphatase activity. RPAP2 was shown to have another role in regulating transcription termination: by recruiting the Integrator complex, which is shown here to mediate termination of snRNA genes, and by a so far unknown mechanism on a long protein-coding gene. An attempt was made to purify and crystallise the human RPAP2 to obtain a crystal structure, however the crystallisation trials were not successful. Finally, a correlation was found in human embryonic stem cells and induced pluripotent stem cells between low levels of RPAP2 and high levels of CTD Ser5P, suggesting a potential involvement of RPAP2 in regulating transcription at a key developmental stage. The results presented here contribute to the understanding of human transcriptional mechanisms and the numerous interactions within the transcription machinery. In particular, the mechanism of terminating the transcription of snRNA genes is identified. An interesting possibility is the regulation of development and stem cell differentiation by RPAP2; however the exact pathways by which this occurs are yet to be discovered.

<p> Non-homologous end joining (NHEJ) is the predominant mode of DNA double strand break (DSB) repair pathway in mammalian cells. At the heart of this repair pathway is Xrcc4-DNA ligase IV complex, which mediates ligation of the broken DNA strands. The C-terminal tandem BRCT repeats of human DNA ligase IV spanning residues 654-911 in complex with the functional fragment of Xrcc4 comprised of residues 1-203 were crystallized by the hanging drop vapour diffusion method at 20°C. Generation of single, well-packed, diffraction quality crystals suitable for structure determination involved usage of an Xrcc4 point mutant (A60E). Arriving at the crystallization condition included optimization of pH, variation of the precipitant concentration, investigation of the effects of small molecules, and alteration of the amount of crystal seed used as initial nuclei. A Crystal of selenomethionine-derived protein complex was grown using the above optimization steps and diffracted to 2.4 A resolution. Data processing revealed that the crystal belonged to space group P1 with unit cell dimensions a= 67.33 b = 86.00 c = 111.52; a= 67.37 ~ = 83.00 y = 74.56. The crystal structure of Xrcc4-DNA ligase IV complex was solved by single-wavelength anomalous diffraction using data collected at a wavelength of 0.9785A corresponding to peak energy. </p> <p> The structure maintains a 2:1 stoichiometry of Xrcc4 to the C-terminal domain of DNA ligase IV. The structure of the complex not only confirms the overall novel mode of interaction first observed in the 3.9 A structure of the yeast ortholog liflp-lig4p complex, but it also discloses additional key features such as the DNA binding surface of the complex and the striking conformational changes occurring within Xrcc4 upon interaction with DNA ligase IV. Together, the structural information procured forms an important basis for a better understanding of the mechanism involved in the NHEJ repair pathway. </p> / Thesis / Master of Science (MSc)

L’Integrase du VIH est une ADN recombinase catalysant deux réactions qui permettent l'intégration de l'ADN viral dans l'ADN hôte. L’intégrase du VIH comprend 3 domaines : N-terminal impliqué dans la réaction de « 3' processing » et le transfert de brin, le domaine catalytique contenant le site actif et le domaine C-terminal liant l'ADN non-spécifiquement (CTD). Des recherches récentes mettent en évidence l'importance du CTD dans la liaison avec d'autres protéines virales comme la transcriptase inverse. Le but de la thèse était de comprendre les rôles et l'importance du domaine C-terminal de l’intégrase dans deux contextes : l'intégration dans la chromatine et la coévolution, avec l'objectif de comprendre le rôle de la multimerisation dans la fonction de l’intégrase. Globalement, les résultats de mon projet indiquent que l'IN-CTD joue un rôle important, en contribuant à la formation de multimères d'ordre supérieur importants pour la fonction de l’IN. / HIV Integrase is a DNA recombinase that catalyzes two endonucleolytic reactions that allow the viral DNA integration into host DNA for replication and subsequent viral protein production. HIV Integrase consists of 3 structural and functional domains: The N-terminal zinc domain involved in 3’ processing and strand transfer, the catalytic core domain which contains the active site, and the C-terminal domain that binds DNA non- specifically. Recent research highlights the importance of the CTD in binding with other viral proteins such as Reverse Transcriptase. The aim of the thesis was to understand the roles and importance of the C-terminal domain of HIV-1 Integrase in two contexts: chromatin integration, and co-evolution, with the overall purpose of understanding the role of multimerization in IN function. Overall, results from my project indicate that the IN-CTD plays an important role, by contributing to the formation of higher order multimers that are important for IN functionality.

Porcine Epidemic Diarrhea Virus (PEDV) was first detected in Europe in the 1970s, but did not emerge in the United States until 2013. When it arrived, it ran rampant due to the lack of previous exposure, causing the death of 7-8 million neonatal piglets and $900 million to $1.8 billion in losses to the U.S. pork industry in 2013 and 2014. This virus causes diarrhea and vomiting which leads to dehydration and in extreme cases, death. Neonatal piglets rely heavily on passive lactogenic immunity from their mother's milk, thus making them especially vulnerable to this disease. Within 2-3 days of infection during the initial outbreak, there was a 90-95% mortality rate among these weaning piglets. Additionally, this virus is highly contagious, with high rates of fecal shedding during infection. To control the outbreak, the USDA had approved two emergency-relief vaccines, but both have proved to be ineffective at preventing disease or reducing fecal shedding. These vaccines are still available today. As such, it is necessary to develop a vaccine that will be effective at preventing illness and viral shedding. PEDV is a single-stranded RNA virus made of four major subunits: a structural spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. The one most studied and of particular interest is the S protein as it facilitates the virus' attachment and entry into the host cell. The S protein is made of two domains, the S1 domain which allows for protein interactions between the virus and the host cell, and the S2 domain which allows for membrane fusion. Because of the S1's role in protein interaction, it is often the target of potential vaccines. Within the S1 domain, it's C-terminal domain encodes for the receptor binding domain (RBD), which is why the S1 CTD is the target of this study. In this study we focused on the expression, purification, and immunogenicity testing of the CTD protein using T7 Express E. coli as the expression host. We used PCR, gel electrophoresis, Sanger Sequencing, western blots, and mass spectrometry to ensure that the protein was being expressed properly. The future goal is to use this protein as the antigen in a future nanoparticle-based PEDV vaccine. / Master of Science / In 2013, Porcine Epidemic Diarrhea Virus (PEDV) emerged in the United States, causing an estimated $900 million to $1.8 billion in damages to the pork industry and the death of 7 to 8 million newborn piglets in just one year. This virus causes diarrhea and vomiting which causes dehydration and death, and newborn piglets are particularly vulnerable. During the initial outbreak, two emergency-relief vaccines were approved but have not been proven effective against the disease. Thus, it is of great importance to develop a vaccine that is both effective and safe. Therefore, our task was to express, purify, and test the immunogenicity of a segment of the PEDV spike protein to be used as the antigen of a future nanoparticle-based vaccine.

RNA polymerase II (Pol II) is the enzyme responsible for the synthesis of all mRNAs in eukaryotic cells. As the central component of the eukaryotic transcription machinery, Pol II is the final target of transcription regulatory pathways. While the role for different Pol II associated proteins, co-activators and general transcription factors (GTFs) in regulation of transcription in response to different stimuli is well studied, a similar role for some subunits of the core Pol II is only now being recognized. The studies reported in this thesis address the role of the fourth largest subunit of Pol II, Rpb4, in transcription and stress response using Saccharomyces cerevisiae as the model system. Rpb4 is closely associated with another smaller subunit, Rpb7 and forms a dissociable complex (Edwards et al. 1991). The rpb4 null mutant is viable but is unable to survive at extreme temperatures (>34ºC and <12ºC) (Woychik and Young, 1989). This mutant has also been shown to be defective in activated transcription and unable to respond adequately to several stress conditions (Pillai et al. 2001; Sampath and Sadhale, 2005). In spite of wealth of available information, the exact role of Rpb4 in transcription process remains poorly understood. In the present work, we have used genetic, molecular and biochemical approaches to understand the role of Rpb4 as described in three different parts below: I. Role of Rpb4 in various pathways related to Transcription Elongation The genome-wide recruitment study of RNA pol II in presence and absence of Rpb4 has indicated role of Rpb4 in transcription elongation (Verma-Gaur et al. 2008). However, a recent proteomics based report has argued against it (Mosley et al. 2013). To address this conflict and understand Rpb4 functions, we monitored recruitment of RNA pol II on a few individual long genes in wild type and rpb4∆ cells. It was observed that RNA pol II recruitment on genes with longer coding regions is not significantly affected in rpb4∆ as compared to wild type thus ruling out role of Rpb4 in transcription elongation of these genes. However, our genetic interaction studies have shown a strong interaction (synthetic lethality) between RPB4 and the PAF1 and SPT4 genes, the products of which code for well-known transcription elongation factors. The studies based on Rpb4 overexpression in mutants for elongation factors, 6-Azauracil sensitivity of cells, effect of Dst1 overexpression in rpb4∆ cells and mitotic recombination rate in rpb4∆ cells have indicated functional interactions of Rpb4 with many of the transcription elongation factors. II. Studies on Genetic and Functional Interactions of Rpb4 with SAGA Complex in Promoter- Specific Transcription Initiation To carry out transcription, RNA pol II depends on several general transcription factors, mediators, activators, co-activators and chromatin remodeling complexes. In the present study, we explored the genetic and functional relationships between Rpb4 and the SAGA complex of transcription machinery, to gain some insight on the role of Rpb4 during transcription. Our chromatin immunoprecipitation data suggest that RNA pol II does not associate with promoters of heat shock genes during transcription activation of these heat stress induced genes in absence of Rpb4. SAGA coactivator complex is required for RNA pol II recruitment and transcription activation of these genes (Zanton and Pugh, 2004). However, recruitment of the SAGA complex at promoters of these heat shock genes was not affected in rpb4∆ cells after heat stress. Our genetic interaction analysis between RPB4 and components of SAGA complex (spt20∆) showed synthetic lethality indicating that fully functional Rpb4 and SAGA complex are required for cellular functions in the absence of heat stress and the simultaneous deletion of factors in the two complexes leads to cell death. III. Role of Rpb4 in phosphorylation cycles of Rpb1-CTD The C-Terminal Domain (CTD) of Rpb1 protein of RNA pol II undergoes several rounds of phosphorylation cycles at Ser-2 and Ser-5 residues on its heptad repeats during transcription. These phosphorylation marks are to be erased before the start of next round of transcription. Using protein pull down assay, we observed that hyperphosphorylated form of Rpb1 is reduced in rpb4∆ as compared to that seen in wild type cells among the free RNA pol II molecules. The level of Rpb2 protein was unaffected in both wild type and rpb4∆. These preliminary data hints at role of Rpb4 in the regulation of Rpb1 phosphorylation.

Molecular modeling is a term referring to the study of proteins, nucleic acids, lipids, and other bio- or macro- or small molecules at the atomistic level using a combination of computational methods, physico-chemical principles, and mathematical functions. It can be generally sub-divided into two areas: molecular mechanics, which is the treatment of atoms and bonds as Newtonian particles and springs, and quantum mechanics, which models electronic behaviors using the Schrödinger equation and wavefunctions. Each technique is a powerful tool that, when used alone or in combination with wet lab experiments, can yield useful results, the products of which have broad applications in studying human disease models, oxidative damage, and other biomolecular processes that are otherwise not easily observed by experiment alone. Within this document, we study seven different such systems. This includes the mode of inhibitor binding to the enzyme monoamine oxidase B, the active site mechanism of that same enzyme, the dynamics of the unstructured p53 C-terminal domain in complex with globular, structured proteins, the process of the viral protein B2 unbinding from double-stranded RNA, and a focus on the dynamics of a variable loop in the antigenic peanut protein Ara h 2. In addition to those conventional molecular modeling studies, several of which were done in tandem with wet lab experiment, we also discuss the validation of charges and charge group parameters for small molecules used in molecular mechanics, and the development of software for the analysis of lipid bilayer systems in molecular mechanics simulations. As computational resources continue to evolve, and as more structural information becomes available, these methods are becoming an integral part of the study of biomolecules in the context of disease. / Ph. D.

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