Histones are proteins found in the nuclei of eukaryotic cells where they are complexed to DNA in chromatin. Rephcation-dependent histones are expressed only during S-phase. Regulation of expression of replication-dependent histone genes requires a highly conserved hairpin RNA element in the 3' untranslated region of histone mRNAs. Replication-dependent histone mRNAs are not polyadenylated; their 3' end is formed by an endonucleolytic cleavage event, 3' of a hairpin element, which is recognised by the Hairpin Binding Protein, HBP (also known as Stem-Loop Binding Protein, SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage that generates the mature mRNA 3' end. The 3' hairpin, and presumably HBP, are also required for nucleocytoplasmic transport, translation and stability of histone mRNAs. It is therefore important to understand this interaction. The hairpin is highly conserved and I have demonstrated that residues in the hairpin loop are important for binding the HBP. This complimented structural studies that showed that the same residues are involved in stacking interactions in the RNA loop. In cell culture, expression of replication-dependent histone genes is S phase specific as is the expresion of HBP. Here I demonstrated that in Caenorhabditis elegans the HBP promoter is active in dividing cells during embryonic and postembryonic development. Depletion of HBP by RNAi leads to an embryonic lethal phenotype associated with defects in chromosome condensation. Postembryonic depletion of HBP results in defects in cell fate during late larval development, specifically in vulval development. A similar phenotype was obtained when histone H3 and H2A were depleted by RNAi suggesting that the phenotype of the hbp (RNAi) worms was due to a lack of histone proteins. I have confirmed this by showing that histone proteins are indeed reduced in hbp (RNAi) worms. I have also shown that depletion of HBP leads to a change in expression of a number of other proteins and specifically an up-regulation of a histone H3 like protein with an apparent molecular mass of 34 kDa. I have evidence that suggests that this protein is the centromer specific protein, CENP-A. As this protein was up-regulated when RNAi was used to deplete histones proteins, this suggests that there could be a compensatory mechanism that helps the animal to deal with the shortage of histone proteins.

Pseudomonas aeruginosa is an infectious Gram-negative bacillus that is found in environments ranging from aerobic to anaerobic, soil to water, plant tissues to human tissues, and even found thriving on plastics and medical implant devices. P. aeruginosa is a major concern for individuals who have cystic fibrosis, chronic obstructive pulmonary disorder, diabetes, have recently undergone surgery, have recently experienced severe burns, or have experienced other ailments that resulted in a compromised immune system, such as Human Immunodeficiency Virus (HIV). P. aeruginosa evades the host immune response by expressing a myriad of virulence factors, and it is through stringent gene regulation of virulence factors that allow P. aeruginosa to initiate acute infections and persist as a chronic infection of its host. The expression of virulence factors is controlled by a complex regulatory system comprised of Two-Component Systems (TCS), post-transcriptional regulators, small non-coding RNAs (sRNA), and others. A significant post-transcriptional regulator involved in this regulatory network is the Regulator of Secondary Metabolites (RsmA). RsmA belongs to the CsrA family of mRNA binding proteins found in many Gram-negative bacteria. Much is known about the targets of RsmA and its functions; however, little is known about how RsmA itself is regulated. Leader sequences, 5’ and 3’, have been demonstrated to have regulatory roles. Using bioinformatics, we have observed potential for the formation of a stem-loop secondary structure in the 5’ leader sequence of rsmA. We propose that this stem-loop plays an important role in the expression of RsmA in P. aeruginosa. In this study, we constructed rsmA leader fusions using the lacUV5 promoter and lacZ reporter to measure translation with and without the secondary structure present. Secondly, we introduced point mutations in the stem of the stem-loop of the leader fusions to disrupt the formation of the stem-loop. Finally, we performed Site-Directed Mutagenesis on the rsmA leader to examine protein levels in vivo via western blot analysis using an HA-tagged rsmA. Our data shows that when the stem-loop formation is disrupted or deleted, translation of RsmA increases. This data suggests that the stem-loop provides a regulatory function in the expression of RsmA.

Pseudomonas aeruginosa is a Gram-negative bacillus found in numerous environments. Gene regulatory mechanisms such as; Two-Component Systems, transcriptional and post-transcriptional regulators, and small non-coding RNAs control the expression of virulence factors that allow P. aeruginosa to initiate acute infections and persist as a chronic infection. A significant post-transcriptional regulator involved in these regulatory networks is the Regulator of Secondary Metabolites (RsmA). In this study, we investigated the contribution of a putative stem-loop on expression of RsmA. We constructed rsmA leader fusions to measure translation with and without the stem-loop present. Secondly, we introduced point mutations to disrupt the formation of the stem-loop. Finally, we performed Site-Directed Mutagenesis on the rsmA leader to examine protein levels in vivo by western blot analysis using an HA-tagged rsmA. Our data suggests that the segment of RNA that contains the putative stem-loop structure serves some function in post-transcriptional regulation of RsmA.

No description available.

Long terminal repeats (LTRs) are non-coding repeats flanking the protein-coding genes of LTR retrotransposons. The variability of LTRs poses a challenge in studying them. Hidden Markov models (HMMs), probabilistic models widely used in pattern recognition, are useful in dealing with this variability. The aim of this work was mainly to study LTRs of retroviruses and LTR retrotransposons using HMMs. Paper I describes the methodology of HMM modelling applied to different groups of LTRs from exogenous retroviruses (XRVs) and endogenous retroviruses (ERVs). The detection capabilities of HMMs were assessed and were found to be high for homogeneous groups of LTRs. The alignments generated by the HMMs displayed conserved motifs some of which could be related to known functions of XRVs. The common features of the different groups of retroviral LTRs were investigated by combining them into a single alignment. They were the short inverted terminal repeats TG and CA and three AT-rich stretches which provide retroviruses with TATA boxes and AATAAA polyadenylation signals. In Paper II, phylogenetic trees of three groups of retroviral LTRs were constructed by using HMM-based alignments. The LTR trees were consistent with trees based on other retroviral genes suggesting co-evolution between LTRs and these genes. In Paper III, the methods in Paper I and II were extended to LTRs from other retrotransposon groups, covering much of the diversity of all known LTRs. For the first time an LTR phylogeny could be achieved. There were no major disagreement between the LTR tree and trees based on three different domains of the Pol gene. The conserved LTR structure of paper I was found to apply to all LTRs. Putative Integrase recognition motifs extended up to 12 bp beyond the short inverted repeats TG/CA. Paper IV is a review article describing the use of sequence similarity and structural markers for the taxonomy of ERVs. ERVs were originally classified into three classes according to the length of the target site duplication. While this classification is useful it does not include all ERVs. A naming convention based on previous ERV and XRV nomenclature but taking into account newer information is advocated in order to provide a practical yet coherent scheme in dealing with new unclassified ERV sequences. Paper V gives an overview of bioinformatics tools for studies of ERVs and of retroviral evolution before and after endogenization. It gives some examples of recent integrations in vertebrate genomes and discusses pathogenicity of human ERVs including their possible relation to cancers. In conclusion, HMMs were able to successfully detect and align LTRs. Progress was made in understanding their conserved structure and phylogeny. The methods developed in this thesis could be applied to different kinds of non-coding DNA sequence element.

The species of Brucella were isolated and characterized almost 120 years ago and their genomes sequenced for almost 4 years. Compared to other bacterial pathogens relatively, little is known about the factors contributing to their persistence in hosts and multiplication within phagocytic cells. Also, many aspects of the interactions between Brucella and its host remain unclear. Molecular characterization of intracellular survival processes of Brucella will provide guidance for additional prevention and control measures. One of the features that distinguishes Brucella is that they do not express classic virulence factors. Thus identification of virulence factors has been elusive and some of the identified virulence genes are putative. Disruption of putative virulence genes and studying the consequent effect on attenuation in cell lines or mouse models is a widely used method. However, in most cases it is not apparent whether the mutated genes encode virulence factors or merely affect normal metabolic or biological functions. Some mutations in Brucella can be compensated by redundancy or backup mechanisms. One method for identifying putative virulence genes involved in pathogenesis is to express these genes in a nonpathogenic host and isolate recombinants with increased virulence or survival ability either in cell culture or animal model. We hypothesize that over-expression of Brucella putative virulence genes in the non-pathogenic and close phylogenic relative Ochrobactrum anthropi should enhance its survival in infection models in vivo. O. anthropi is one of the closest Brucella relatives based on DNA, rRNA, and protein analyses but it is unable to establish chronic infection and considered as opportunistic pathogen that, under certain circumstances, may produce disease in immunocompromised humans. Therefore, we established enhanced expression system in Brucella and Ochrobactrum to identify B. suis virulence genes. We created an enhanced expression system that can be used for cloning and expression of heterologous genes in Brucella and Ochrobactrum. We studied the transcriptional activity of several promoters and created some tools to enhance the expression, detection and purification of Brucella recombinant protein in Ochrobactrum. The presumable importance of alkyl hydroperoxide reductases encoded by ahpC and ahpD genes and their contribution to intracellular survival of Brucella were studied by over-expressing them. The recombinant O. anthropi expressing B. suis ahpC and ahpD genes were able to resist in vitro killing by H2O2 and or cumene hydroperoxide and survived longer in the macrophage J774 A.1 cell line. The control O. anthropi was cleared from BALB/c mice in five days while the recombinants were recovered from spleens, livers and lungs of infected mice up to eight days post-infection. We tested the contribution of B. suis cyclic glucan synthetase gene (cgs) to virulence by over-expressing it in O. anthropi. We studied the ability of the recombinant O. anthropi to resist killing in vitro and in vivo. We generated evidence that B. suis cgs when over-expressed in O. anthropi increased the amount of cyclic glucans synthesized and accumulated in the periplasmic space. This accumulation changed the virulence of the microorganism from a soil bacterium that cleared from mice in less than five days into a pathogenic organism that could survive up to 9 days and at higher doses killed the mice. In summary, several vectors have been constructed for gene expression and protein purification in Brucella and Ochrobactrum. Novel useful tools for enhancement of heterologous gene expression were created and demonstrated to work in Brucella and Ochrobactrum. Brucella putative virulence genes were studied in Ochrobactrum using the newly constructed vectors and tools. Ochrobactrum as a gain of function model for studying putative virulence genes of intracellular pathogens in general and for Brucella in particular proved to be a very useful model. / Ph. D.

Die Etablierung der Transkription von kompletten Genen auf planaren Oberflächen soll eine Verbindung zwischen der Mikroarraytechnologie und der Transkriptomforschung herstellen. Darüber hinaus kann mit diesem Verfahren ein Brückenschlag zwischen der Synthese der Gene und ihrer kodierenden Proteine auf einer Oberfläche erfolgen. Alle transkribierten RNAs wurden mittels RT-PCR in cDNA umgeschrieben und in einer genspezifischen PCR amplifiziert. Die PCR-Produkte wurden hierfür entweder per Hand oder maschinell auf die Oberfläche transferiert. Über eine Oberflächen-PCR war es möglich, die Gensequenz des Reportergens EGFP direkt auf der Oberfläche zu synthetisieren und anschließend zu transkribieren. Somit war eine Transkription mit weniger als 1 ng an Matrize möglich. Der Vorteil einer Oberflächen-Transkription gegenüber der in Lösung liegt in der mehrfachen Verwendung der immobilisierten Matrize, wie sie in dieser Arbeit dreimal erfolgreich absolviert wurde. Die Oberflächen-Translation des EGFP-Gens konnte ebenfalls zweimal an einer immobilisierten Matrize gezeigt werden, wobei Zweifel über eine echte Festphasen-Translation nicht ausgeräumt werden konnten. Zusammenfassend kann festgestellt werden, dass die Transkription und Translation von immobilisierten Gensequenzen auf planaren Oberflächen möglich ist, wofür die linearen Matrizen direkt auf der Oberfläche synthetisiert werden können. / In vitro mRNA synthesis and in vitro translation are of great interest for biochemical and molecular biological basic research, and also for biotechnology and other applications. Solid phase coupled synthesis is very useful for the development of high throughput procedures to elucidate and manipulate gene products. An artificial gene was constructed combining the T7 promoter and terminator with the EGFP-gene from the plasmid pEGFP. The functionality of the construct was shown by in vitro translation. The gene-construct was immobilised on a planar glass surface. The transcription was performed on the immobilised gene and mRNA was determined by RT-PCR. These results demonstrate that the complete gene is transcribed from the covalently coupled PCR product. Thus, it is possible to transfer a standard transcription technique onto an On-chip reaction. The direct PCR amplification of transcriptionable sequences of EGFP bound on surfaces was successfully used for solid phase transcription. Successful transcriptions were also performed at least to 1 ng of used template. The RNA synthesis was also successful in the second and third reaction on the same slide as observed by signals after RT-PCR. It seems to be possible to transfer the translation of reportergenes in a solid phase coupled synthesis, too. For further integration of cellular procedures on a chip, the cell-free RNA synthesis on immobilised templates is an crucial technical hurdle to conquer. Major advantages of using immobilised templates for transcription are, low risk of contamination occuring in solution, and no necessity of further purification steps for downstream applications of the RNA product.

Killer strains of the yeast Kluyveromyces lactis secrete a heterotrimeric protein toxin (zymocin) to inhibit the growth of sensitive yeasts. The cytotoxicity of zymocin resides in the γ subunit (γ-toxin), however the mechanism of cytotoxicity caused by γ-toxin was previously unknown. This thesis aimed to unravel the mode of γ-toxin action and characterize the interaction between γ-toxin and its substrates. Previous studies suggested a link between the action of γ-toxin and a distinct set of transfer RNAs. In paper I, we show that γ-toxin is a tRNA anticodon endonuclease which cleaves tRNA carrying modified nucleoside 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at position 34 (wobble position). The cleavage occurs 3’ to the wobble uridine and yields 2’, 3’-cyclic phosphate and 5´-hydroxyl termini. In paper II, we identified the determinants in tRNA important for efficient γ-toxin cleavage. The modifications present on the wobble uridines have different effects on tRNA cleavage by γ-toxin. The Saccharomyces cerevisiae wobble modification mcm5 group has a strong positive effect, whereas the Escherichia coli wobble modification 5-methylaminomethyl group has a strong inhibitory effect on tRNA cleavage. The s2 group present in both S. cerevisiae and E. coli tRNAs has a weaker positive effect on the cleavage. The anticodon stem loop (ASL) of tRNA represents the minimal structural requirement for γ-toxin action. Nucleotides U34U35C36A37C38 in the ASL are required for optimal cleavage by γ-toxin, whereas a purine at position 32 or a G at position 33 dramatically reduces the reactivity of ASL. Screening for S. cerevisiae mutants resistant to zymocin led to the identification of novel proteins important for mcm5s2U formation (paper III). Sit4p (a protein phosphatase), Sap185p and Sap190p (two of the Sit4 associated proteins), and Kti14p (a protein kinase) are required for the formation of mcm5 side chain. Ncs2p, Ncs6p, Urm1p, and Uba4p, the latter two function in a protein modification (urmylation) pathway, are required for the formation of s2 group. The gene product of YOR251C is also involved in the formation of s2 group. The involvement of multiple proteins suggests that the biogenesis of mcm5s2U is very complex.

Thesis (M.S.)--Miami University, Dept. of Zoology, 2005. / Title from first page of PDF document. Document formatted into pages; contains [1], ix, 75 p. : ill. Includes bibliographical references (p. 69-75).

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