Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Les introns de groupe II forment une classe d'ARN connus avant tout pour leur activité ribozymique, qui leur permet de catalyser leur propre réaction d'épissage. Sous certaines conditions, ces introns peuvent s'exciser des ARN précurseurs dont ils font partie et assurer la ligation des exons qui les bordent sans l'aide d'aucune protéine. Les introns de groupe II sont généralement excisés sous forme d'un lariat, semblable à celui formé par les introns des prémessagers nucléaires, dont l'épissage est assurée par le spliceosome. De telles similarités dans le mécanisme d'épissage suggèrent que les introns de groupe II et les introns des prémessagers nucléaires pourraient avoir un ancêtre évolutif commun.Malgré leurs séquences très diverses, les introns de groupe II peuvent être définis par une structure secondaire commune, hautement conservée. Celle-ci est formée de six domaines (domaine I à domaine VI ; D1-D6), émergeant d'une roue centrale. L'épissage des introns de groupe II comprend deux étapes, et autant de réactions de transestérification, qui produisent les exons liés et l'intron excisé sous forme lariat. Il est généralement admis que la structure du ribozyme subit des changements conformationnels entre les deux étapes de l'épissage et que le domaine VI est un acteur clé dans ce phénomène. Cependant, malgré l'identification d'un certain nombre d'interactions tertiaires entre domaines, ni la RMN, ni les études faisant appel à des modifications chimiques ne sont parvenues à déterminer l'environnement immédiat, au niveau du site actif du ribozyme, de l'adénosine qui sert de point de branchement de la structure en lariat, ainsi que des nucléotides qui entourent cette adénosine au sein du domaine VI. A l'aide d'analyses phylogénétiques et d'une modélisation moléculaire tridimensionnelle, nous avons identifié plusieurs sections du ribozyme susceptibles de constituer le site de fixation du domaine VI au cours de l'étape de branchement. Des mutations ont été introduites dans ces sites de fixation potentiels et la cinétique de réaction des ARN mutants résultants a été déterminée. Afin de démontrer formellement l'interaction du domaine VI avec le site récepteur le plus probable, une molécule de ribozyme dont la réaction de branchement est assurée par l'addition d'oligonucléotides ADN ou ARN qui positionnent correctement le domaine VI vis-à-vis de son partenaire a été construite. En combinant l'information apportée par différentes expériences de ce type, nous avons pu générer un modèle à résolution atomique du complexe formé par le domaine VI, son site de branchement et le reste de l'intron au moment où l'épissage est initié.

<p>RNA is the only biological molecule that can function both as a repository of information and as a catalyst. This, together with the ability to self-replicate, led to recognition of RNA as ‘prelude to life’.</p><p>My work highlights some of the important features of RNA as a catalyst, exemplified by RNase P. It addresses questions of evolutionary preservations of residues and structure, involvement of metal ions and finally structure evolution towards minimal catalytically competent RNA motifs.</p><p>RNase P is the only enzyme involved in 5’ end processing of all pre-tRNAs. Until recently, it was believed that the RNA moiety of RNase P is responsible for mediating catalysis only in Bacteria. However, my recent study conclusively demonstrated that eukaryotic RNase P RNA is catalytically competent in vitro in absence of proteins. These findings evidenced evolutionary preservation of RNA-mediated catalysis in RNase P.</p><p>RNase P RNA is a metalloeznyme. In my studies I analyzed the contributions of individual chemical groups at the cleavage site to catalysis. My findings suggested that the 2’OH of N_-1 and the exocyclic amine of G₊₁ are involved in positioning of functionally important metal ions. Additionally, data appointed the function of Pb²⁺ as both structural metal ion and important in generating the nucleophile. My studies further indicate a conformational change upon RNase P RNA -substrate complex formation in keeping with an induced fit mechanism. </p><p>Studying the effects of reducing the ribozyme size upon dissection of bacterial RNase P RNAs, we defined the smallest catalytically competent domain i.e. P15-loop. Derivatives of this autonomous metal ion binding domain, (the smallest being 31nt-s), are able to cleave both whole-length pre-tRNAs as well as hairpin substrates, though with severely reduced rates relative to their parent ribozymes. The study has inferred that partite ES interactions at the cleavage site prove sufficient for catalysis.</p>

The structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).

RNA is the only biological molecule that can function both as a repository of information and as a catalyst. This, together with the ability to self-replicate, led to recognition of RNA as ‘prelude to life’. My work highlights some of the important features of RNA as a catalyst, exemplified by RNase P. It addresses questions of evolutionary preservations of residues and structure, involvement of metal ions and finally structure evolution towards minimal catalytically competent RNA motifs. RNase P is the only enzyme involved in 5’ end processing of all pre-tRNAs. Until recently, it was believed that the RNA moiety of RNase P is responsible for mediating catalysis only in Bacteria. However, my recent study conclusively demonstrated that eukaryotic RNase P RNA is catalytically competent in vitro in absence of proteins. These findings evidenced evolutionary preservation of RNA-mediated catalysis in RNase P. RNase P RNA is a metalloeznyme. In my studies I analyzed the contributions of individual chemical groups at the cleavage site to catalysis. My findings suggested that the 2’OH of N-1 and the exocyclic amine of G+1 are involved in positioning of functionally important metal ions. Additionally, data appointed the function of Pb2+ as both structural metal ion and important in generating the nucleophile. My studies further indicate a conformational change upon RNase P RNA -substrate complex formation in keeping with an induced fit mechanism. Studying the effects of reducing the ribozyme size upon dissection of bacterial RNase P RNAs, we defined the smallest catalytically competent domain i.e. P15-loop. Derivatives of this autonomous metal ion binding domain, (the smallest being 31nt-s), are able to cleave both whole-length pre-tRNAs as well as hairpin substrates, though with severely reduced rates relative to their parent ribozymes. The study has inferred that partite ES interactions at the cleavage site prove sufficient for catalysis.

AIDS is caused by a lentivirus, HIV-1. In addition to antiretroviral drugs that are currently in use for HIV/AIDS therapy, a number of gene therapy strategies have been designed as alternative therapies. Most of these therapies target HIV RNA/proteins, which are subject to high rate of mutation, resulting in escape mutants. Viral entry is mediated by CCR5 co-receptor in most routes of transmission. To downregulate CCR5 as a gene therapy approach, we targeted seven unique sites within the CCR5 mRNA by a multimeric hammerhead ribozyme, Rz1-7. Hammerhead ribozyme is a small RNA that cleaves a target RNA upon binding to it. Expressing the Rz1-7 from HIV-1- and MSCV-based vectors in otherwise susceptible cells inhibited replication of a CCR5-tropic strain of HIV-1 by 99-100%. The Rz1-7 will be tested for inhibition of HIV-1 replication in the CD4+ T-lymphoid and myeloid progeny of transduced human CD34+ hematopoietic progenitor stem cells. It may be preferable to interfere HIV-1 life cycle at the DNA level since a one-time inactivation might suffice to confer a complete and permanent inhibition of virus replication in the gene modified cells and their progeny. This is what other strategies that target the HIV-1 RNA/protein can hardly offer. For this purpose, group II introns, which are able to splice out and get incorporated into a specific DNA sequence, can be designed/modified to gain novel DNA targeting specificities. As a novel approach, we have examined whether insertion of a modified intron into an infectious HIV-1 clone at two sites within the integrase domain of HIV-1 pol gene could inhibit virus replication. Intron insertion into the HIV-1 clone was induced and mammalian cells were transfected with intron-inserted HIV-1 clones. Although similar amounts of HIV-1 RNA, protein, and progeny virus were produced from the clones as from wild-type HIV-1 provirus DNA, in the absence of a functional integrase, the HIV-1 reverse-transcribed DNA failed to integrate and virus replication was aborted. These results demonstrate that modified group II introns can confer complete inhibition of virus replication at the level of second round of infection. We are now developing vectors to assess whether intron insertion can take place in mammalian cells.

AIDS is caused by a lentivirus, HIV-1. In addition to antiretroviral drugs that are currently in use for HIV/AIDS therapy, a number of gene therapy strategies have been designed as alternative therapies. Most of these therapies target HIV RNA/proteins, which are subject to high rate of mutation, resulting in escape mutants. Viral entry is mediated by CCR5 co-receptor in most routes of transmission. To downregulate CCR5 as a gene therapy approach, we targeted seven unique sites within the CCR5 mRNA by a multimeric hammerhead ribozyme, Rz1-7. Hammerhead ribozyme is a small RNA that cleaves a target RNA upon binding to it. Expressing the Rz1-7 from HIV-1- and MSCV-based vectors in otherwise susceptible cells inhibited replication of a CCR5-tropic strain of HIV-1 by 99-100%. The Rz1-7 will be tested for inhibition of HIV-1 replication in the CD4+ T-lymphoid and myeloid progeny of transduced human CD34+ hematopoietic progenitor stem cells. It may be preferable to interfere HIV-1 life cycle at the DNA level since a one-time inactivation might suffice to confer a complete and permanent inhibition of virus replication in the gene modified cells and their progeny. This is what other strategies that target the HIV-1 RNA/protein can hardly offer. For this purpose, group II introns, which are able to splice out and get incorporated into a specific DNA sequence, can be designed/modified to gain novel DNA targeting specificities. As a novel approach, we have examined whether insertion of a modified intron into an infectious HIV-1 clone at two sites within the integrase domain of HIV-1 pol gene could inhibit virus replication. Intron insertion into the HIV-1 clone was induced and mammalian cells were transfected with intron-inserted HIV-1 clones. Although similar amounts of HIV-1 RNA, protein, and progeny virus were produced from the clones as from wild-type HIV-1 provirus DNA, in the absence of a functional integrase, the HIV-1 reverse-transcribed DNA failed to integrate and virus replication was aborted. These results demonstrate that modified group II introns can confer complete inhibition of virus replication at the level of second round of infection. We are now developing vectors to assess whether intron insertion can take place in mammalian cells.

<p>HDV antigenomic RNA is processed in two distinct pathways; it can be cleaved at the polyA site and polyadenylated to become mRNA for the delta antigens, or the RNA can be cleaved by the antigenomic ribozyme to become full-length antigenomic RNA that is used for synthesis of genomic HDV RNA. The polyA site is located just 33 nucleotides upstream of the ribozyme cleavage site. If processing occurs primarily at the upstream polyA site, there may not be enough full-length antigenomic RNA to support replication. On the other hand, ribozyme cleavage downstream of the polyA site could inhibit polyadenylation by interfering with polyadenylation complex assembly. Thus, it appears that HDV may need a mechanism to control RNA processing so that both products can be generated in the proper amounts during the infection cycle. </p><p>A model has been proposed in which the choice between ribozyme cleavage and polyadenylation is determined by alternative RNA secondary structures formed by the polyA sequence (Wadkins and Been 2002). One of the hypothetical structures, AltP2, is a pairing between part of the upstream polyA sequence and the 3' end of the ribozyme sequence. For this model, the same upstream sequence that forms AltP2 could also form a stem loop, P(-1), within the leader, by pairing with sequences located farther upstream. A processing choice is possible because AltP2 is predicted to inhibit ribozyme cleavage and favor polyadenylation resulting in mRNA production, whereas P(-1) would inhibit polyadenylation and favor ribozyme cleavage resulting in full-length replication product. </p><p>The P(-1) vs. AltP2 model was tested using an antigenomic HDV ribozyme construct with the 60-nucleotide sequence upstream of the ribozyme cleavage site. This leader sequence contains the proposed polyA sequence elements. In vitro analysis of this construct revealed that the kinetic profile of ribozyme self-cleavage was altered in two ways. Relative to the ribozyme without upstream sequences, the fraction of precursor RNA that cleaved decreased to about 50%, but the active ribozyme fraction cleaved faster. Native gel electrophoresis revealed that the active and inactive precursor RNAs adopted persistent alternative structures, and structure mapping with Ribonuclease T1 and RNase H provided evidence for structures resembling P(-1) and AltP2.</p><p>Sequence changes in the 5' leader designed to alter the relative stability of P(-1) and AltP2 increased or decreased the extent of ribozyme cleavage in a predictable way, but disrupting AltP2 did not completely restore ribozyme activity. The analysis of deletion and base change variants supported a second alternative pairing, AltP4, formed by the pyrimidine-rich sequence immediately 5' of the ribozyme cleavage site and a purine-rich sequence from the 5' side of P4. A similar approach was used to test if the effect of disrupting both AltP2 and AltP4 might be additive, and the results suggested that ribozyme precursors with 5' leader sequences could fold into multiple inactive conformations, which can include, but may not be limited to, AltP2, AltP4, or a combination of both.</p><p>Luciferase expression constructs with HDV polyA and ribozyme sequences were used to investigate the effects of RNA structure and ribozyme cleavage on polyadenylation in cells. One hypothesis was that P(-1) could inhibit polyadenylation by making the polyA sequence elements less accessible to polyA factors, but sequence changes designed to alter the stability of the stem loop had no effect on polyadenylation. The model also predicts that the ribozyme sequence downstream of the polyA site could affect polyadenylation, possibly in two different ways. Ribozyme cleavage could interfere with polyadenylation by uncoupling transcription from processing, however, the ribozyme sequence might also influence polyadenylation in a manner independent of the ribozyme cleavage activity. As such, the AltP2 structure could potentially have a positive effect on polyadenylation either by inhibiting ribozyme cleavage or by making the polyA signal sequences more accessible to the polyA factors. To distinguish between the effects of ribozyme cleavage and alternative RNA structures, luciferase expression levels from constructs with an HDV polyA sequence followed by the active wild-type ribozyme or the inactive C76u version of the ribozyme were compared. For the wild-type HDV polyA sequence, the active ribozyme reduced expression, whereas the inactive ribozyme control had no effect on expression. However, for the modified leader sequences, which were efficiently polyadenylated in the absence of ribozyme, there were changes in expression that appeared to be independent of ribozyme cleavage. Based on these findings, two alternative models are proposed. One model predicts that protein factors might affect antigenomic RNA processing, and the other model suggests that additional alternative structures, such as AltP4, might influence the choice between ribozyme cleavage and polyadenylation.</p> / Dissertation

The structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).

Many functional RNAs are required to fold into specific three-dimensional structures. A fundamental property of RNA is that its secondary structure and even some tertiary contacts are highly stable, which gives rise to independent modular RNA motifs and makes RNAs prone to adopting misfolded intermediates. Consequently, in addition to stabilizing the native structure relative to the unfolded species (defined here as stability), RNAs are faced with the challenge of stabilizing the native structure relative to alternative structures (defined as structural specificity). How RNAs have evolved to overcome these challenges is incompletely understood. Self-splicing group I introns have been used to study RNA structure and folding for decades. Among them, the Tetrahymena intron was the first discovered and has been studied extensively. In this work, we found that a version of the intron that was generated by in vitro selection for enhanced stability also displayed enhanced specificity against a stable misfolded structure that is globally similar to the native state, despite the absence of selective pressure to increase the energy gap between these structures. Further dissection suggests that the increased specificity against misfolding arises from two point mutations, which strengthen a local tertiary contact network that apparently cannot form in the misfolded conformation. Our results suggest that the structural rigidity and intricate networks of contacts inherent to structured RNAs can allow them to evolve exquisite structural specificity without explicit negative selection, even against closely-related alternative structures. To explore further how RNAs gain stability from intricate architectures, we examined a novel group I intron from red algae (Bangia). Biochemical methods and computational modeling suggest that this intron possesses general motifs of group IC1 introns but also forms an atypical tertiary contact, which has been reported previously in other subgroups and helps position the reactive helix at the active site. In the Bangia intron, the partners have been swapped relative to known group I RNAs that include this contact. This result underscores the modular nature of RNA motifs and provides insight into how structured RNAs can arrange helices and contacts in multiple ways to achieve and stabilize functional structures. / text