This dissertation focuses on the spectroscopic and thermodynamic characterization of the unusual metal-RNA cluster found in the P5abc subdomain of the Tetrahymena group I intron. The P5abc subdomain is a part of the P4-P6 domain found in the Tetrahymena thermophila group I intron selfsplicing RNA. From both X-ray crystal structures of the P4-P6 domain, a remarkable cluster of Mg2+ or Mn2+ ions was found in the P5abc subdomain (Cate et al. 1996; Juneau et al. 2001). It is believed that the metal ion core in the P5abc subdomain stabilizes the active conformation of the RNA (Cate et al. 1996). An understanding of the role of these metal ions in facilitating the correct structure of the P5abc subdomain provides insight into how metal ions help overcome the folding barriers of complex RNA structures. Under solution conditions, the properties of this uncommon metal ion core and its influence on the truncated P5abc subdomain structure have been investigated. Both EPR spectroscopy and thermal denaturation experiments have been employed to search for a spectroscopic signature of metal ion core formation and also determine the thermodynamic contribution of the metal ion core on the stability of the folded P5abc structure. A spectroscopic signature of metal ion core formation was assigned for the P5abc subdomain by EPR microwave power saturation studies. Power saturation studies of the P5abc subdomain, P4-P6 domain and corresponding mutants reveal that the addition of 5 equivalents of Mn2+ are required for the wild type P5abc subdomain to form the metal ion core under solution conditions in 0.1 M NaCl. Results from both domain and subdomain microwave power saturation studies suggest that this technique can be applied for detecting clustering of Mn2+ ions in other RNA structures. The thermodynamic consequence of this metal ion core was probed by thermal denaturation techniques including UV-Vis spectroscopy and differential scanning calorimetry (DSC). DSC experiments were utilized to directly determine the thermodynamic contribution of the metal ion core. This value was determined to be an average of ∆∆G of -5.3 kcal/mol and is consistent with ∆∆G values obtained for other RNA tertiary structures.

The functions of many cellular RNAs require that they fold into specific three-dimensional native structures, which typically involves arranging secondary structure elements and stabilizing the folded structure with tertiary contacts. However, RNA folding is inherently complex, as most RNAs fold along pathways containing multiple intermediates, including some misfolded intermediates that can accumulate and persist. Our understanding of the origins and structures of misfolded forms and the resolution of misfolding remains limited. Here, we investigate folding of the Tetrahymena intron, an extensively studied RNA folding model system since its initial discovery decades ago. The ribozyme variant predominantly misfolds, and slow refolding to the native state requires extensive structural disruption. Paradoxically, the misfolded conformation contains extensive native structure and lacks incorrect secondary and tertiary contacts despite requiring displacement of a native helix, termed P3, with incorrect secondary structure to misfold. We propose a model for a new origin of RNA misfolding to resolve this paradox, wherein misfolded ribozyme contains within its core incorrect arrangement of two single-stranded segments, i.e. altered topology. This model predicts a requirement for P3 disruption to exchange the misfolded and native topologies. We mutated P3 to modulate its stability and used the ribozyme's catalytic activity to show that P3 is disrupted during the refolding transition. Furthermore, we demonstrate that unfolding of the peripheral tertiary contacts precedes disruption of P3 to allow the necessary structural transitions. We then explored the influence of topology on the pathways leading to the misfolded and native states. Our results suggest that P3 exists in an earlier pathway intermediate that resembles the misfolded conformation, and that P3 unfolds to allow a small yet significant fraction of ribozyme to avoid misfolding. Despite being on a path to misfolding, the decision to misfold depends upon the probability of disrupting P3 and exchanging topology at this intermediate. Additionally, we show that having a stable P3 in the unfolded ribozyme allows almost complete avoidance of misfolding. Together, these studies lead to a physical model for folding and misfolding of a large RNA that is unprecedented in its scope and detail. / text

The function and evolution of introns have been topics of great interest since introns were discovered in the 1970s. Introns that interrupt protein-coding regions have the most obvious potential to affect coding sequences; therefore, their evolution have been studied most intensively. Splicing of introns within untranslated regions does not contribute directly to the diversity of proteins, yet ~35% of human transcripts contain introns within the 5' untranslated region (UTR). The evolution and possible functions of 5'UTR introns (5UIs) remain largely unexplored. Here we undertook a genome-wide functional analysis of 5UIs. Our main results are as follows: First, the distribution of these introns in the human genome is nonrandom. While genes with regulatory roles are enriched in having 5UIs, genes encoding proteins that are targeted to the endoplasmic reticulum and mitochondria are surprisingly depleted of these introns. Second, we offered and supported a model whereby gene encoding secretory and nuclear-encoded mitochondrial proteins share a common regulatory mechanism at the level of mRNA export, which is dependent on the absence of 5'UTR introns. Specifically, the upstream element in a given transcript, be it an intron or RNA elements near the 5' end of coding sequences (CDS), dictates the mRNA export pathway used. Finally, we discovered a strong correlation between existence of 5'UTR introns and sequence features near the 5' end of CDS. We developed an integrated machine-learning framework that can predict absence of 5UIs using solely the sequence near the 5' end of CDS. Our model achieved >80% accuracy when validated against nuclear-encoded mitochondrial transcripts. Specific RNA elements predictive of 5UI absence are found in ~40% of human transcripts spanning a wide spectrum of functions. By analyzing hundreds of large-scale datasets, we functionally characterized the transcripts with these RNA elements; revealing their association with translational regulation. These RNA elements were bound by proteins interacting with the Exon Junction Complex in vivo suggesting a molecular mechanism that links these elements to their downstream effects in mRNA export and translational regulation. While some 5'UTR introns might be evolving neutrally, our results, taken together, suggest that complex evolutionary forces are acting on this distinct class of introns.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

This dissertation details three studies dealing with the manipulation of nucleicacids. In the first investigation, each of the four natural nucleobases were analyzed for theability to serve as a universal template at the ligation junction of a T4 DNA ligasereaction. This resulted in the first instance of sequence-independent ligation catalyzed byany DNA ligase. Although all of the nucleobases display universal templatingcapabilities, thymidine and guanosine provided the most effective results. In addition,lowered MgCl2 and ATP concentrations, as well as the inclusion of DMSO, also aided inthe sequence-independent ligation reported here. In the course of these studies, currentmethods of removing urea from denaturing-gel purified nucleic acids provedcumbersome. Therefore, in the second study simple butanol extraction was examined as ameans to eliminate urea from nucleic acid solutions. Stepwise butanol extraction was themost effective approach to solving this problem and provided a much needed techniquefor nucleic acid purification. This type of extraction also does not result in significantlosses of nucleic acid sample. The third study exploits the molecular recognition andcatalytic properties inherent in an autocatalytic group I intron to develop a ribozyme thatcan replace the 5' end of an RNA substrate with a different RNA. This 5' replacementsplicing reaction can potentially repair mutations on the 5' ends of RNA transcripts thatlead to a variety of genetic mutations. The model system was a common mutation in asmall model mimic of the k-ras gene in vitro, which predisposes individuals to lungcancer. This 5' replacement splicing reaction occurred in vitro using this small modelsystem; the reaction was also enhanced by the alteration of the molecular interactionsinvolved. The results and implications of each of these studies are detailed in thisdissertation.

Group I introns belong to a class of large RNAs that catalyze their own excision from precursor RNA through a two-step process called self-splicing reaction. These self-splicing introns have often been converted into ribozymes with the ability site specifically cleave RNA molecules. One such ribozyme, derived from a self-splicing Pneumocystis carinii group I intron, has subsequently been shown to sequence specifically excise a segment from an exogenous RNA transcript through trans excision-splicing reaction.The trans excision-splicing reaction requires that the substrate be cleaved at two positions called the 5' and 3' splice sites. The sequence requirements at these splice sites were studied. All sixteen possible base pair combinations at the 5' splice site and the four possible nucleotides at the 3' splice site were tested for reactivity. It was found that all base pair combinations at the 5' splice site allow the first reaction step and seven out of sixteen combinations allow the second step to occur. Moreover, it was also found that non-Watson-Crick base pairs are important for 5' splice site recognition and suppress cryptic splicing. In contrast to the 5' splice site, 3' splice site absolutely requires a guanosine.The pathway of the trans excision-splicing reaction is poorly understood. Therefore, as an initial approach, a kinetic framework for the first step (5' cleavage) was established. The framework revealed that substrate binds at a rate expected for RNA-RNA helix formation. The substrate dissociates with a rate constant (0.9 min-1), similar to that for substrate cleavage (3.9 min-1). Following cleavage, the product dissociation is slower than the cleavage, making this step rate limiting for multiple-turnover reactions. Furthermore, evidence suggests that P10 helix forms after the 5' cleavage step and a conformational change exists between the two reaction steps of trans excision-splicing reaction. Combining the data presented herein and the prior knowledge of RNA catalysis, provide a much more detailed view of the second step of the trans excision-splicing reaction.These studies further characterize trans excision-splicing reaction in vitro and provide an insight into its reaction pathway. In addition, the results describe the limits ofthe trans excision-splicing reaction and suggest how key steps can be targeted for improvement using rational ribozyme design approach.

Group I introns are catalytic RNAs capable of self-splicing out of RNA transcripts. Ribozymes derived from these group I introns are used to explore the molecular recognition properties involved in intron catalysis. New ribozyme reactions are designed based on the inherent ability of these ribozymes to perform site-specific nucleophilic attacks. This study explores the molecular recognition properties of group I intron-derived ribozyme reactions and describe a new ribozyme reaction involving molecular recognition properties previously not seen.We report the development, analysis, and use of a new combinatorial approach to analyze the substrate sequence dependence of suicide inhibition, cyclization, and reverse cyclization reactions catalyzed by a group I intron from the opportunistic pathogen Pneumocystis carinii. We demonstrate that the sequence specificity of these Internal Guide Sequence (IGS) mediated reactions is not high, suggesting that RNA targeting strategies which exploit tertiary interactions could have low specificity due to the tolerance of mismatched base pairs.A group I intron-derived ribozyme from P. carinii has been previously shown to bind an exogenous RNA substrate, splice-out an internal segment, and then ligate the two ends back together (the trans excision-splicing reaction). We now report that a group I intron derived ribozyme from the ciliate Tetrahymena thermophila can also perform the trans excision-splicing reaction, although not nearly as well as the P. carinii ribozyme.In addition, we discovered a new ribozyme reaction called trans insertion-splicing where the P. carinii ribozyme binds two exogenous RNA substrates and inserts one directly into the other. Although this reaction gives the reverse products of the trans excision-splicing reaction, the trans insertion-splicing reaction is not simply the reverse reaction. The ribozyme recognizes two exogenous substrates through more complex molecular recognition interactions than what has been previously seen in group I intron-derived ribozyme reactions. We give evidence for this new reaction mechanism composed of three steps, with intermediates attached to the ribozyme.

Hereditary myopathy with lactic acidosis (HML, OMIM#255125) is an autosomal recessive disorder which originates from Västerbotten and Ångermanland in the Northern part of Sweden. HML is characterized by severe exercise intolerance which manifests with tachycardia, dyspnea, muscle pain, cramps, elevated lactate and pyruvate levels, weakness and myoglobinuria. The symptoms arise from malfunction of the energy metabolism in skeletal muscles with defects in several important enzymes involved in the TCA cycle and the electron transport chain. All affected proteins contain iron-sulfur (Fe-S) clusters, which led to the suggestion that the disease was caused by malfunctions in either the transportation, assembly or processing of Fe-S clusters. The aim of my thesis was to identify the disease causing gene of HML and to investigate the underlying disease-mechanisms. In paper I we identified a disease-critical region on chromosome 12; a region containing 16 genes. One of the genes coded for the Fe-S cluster assembly protein ISCU and an intronic base pair substitution (g.7044G>C) was identified in the last intron of this gene. The mutation gave rise to the insertion of intron sequence into the mRNA, leading to a protein containing 15 abberant amino acids and a premature stop. In paper II we investigated why a mutation in an evolutionary well conserved protein with a very important cellular role, which in addition is expressed in almost all tissues, gives rise to a muscle-restricted phenotype. Semi-quantitative RT-PCR analysis showed that the mutant transcript constituted almost 80% of total ISCU mRNA in muscle, while in both heart and liver the normal splice form was dominant. We could also show that, in mice, complete absence of Iscu protein was coupled with early embryonic death, further emphasizing the importance of the protein in all tissues. These data strongly suggested that tissue-specific splicing was the main mechanism responsible for the muscle-specific phenotype of HML. In paper III the splicing mechanisms that give rise to the mutant ISCU transcript was further investigated. We identified three proteins; PTBP1, IGF2BP1 and RBM39, that could bind to the region containing the mutation and could affect the splicing pattern of ISCU in an in vitro system. PTBP1 repressed the inclusion of the intronic sequence, while IGF2BP1 and RBM39 repressed the total ISCU mRNA level though the effect was more pronounced for the normal transcript. Moreover, IGF2BP1 and RBM39 were also able to reverse the effect of PTBP1. IGF2BP1, though not a splicing factor, had higher affinity for the mutant sequence. This suggested that the mutation enables IGF2BP1 binding, thereby preventing the PTBP1 induced repression seen in the normal case. In conclusion, we have determined the genetic cause of HML, identifying a base pair substitution in the last intron of the ISCU gene that gives rise to abnormally spliced transcript. The muscle-specific phenotype was also analyzed and tissue-specific splicing was identified as the main disease-mechanism. Furthermore, nuclear factors with ability to affect the splicing pattern of the mutant ISCU gene were identified. This work has thoroughly investigated the fundamental disease mechanisms, thus providing deeper understanding for this hereditary myopathy.

Techn. University, Diss., 2004--Dresden.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-06-02T22:15:26Z No. of bitstreams: 1 FelipeEmmanuelDoEspiritoSantoGomes_DISSERT.pdf: 3727906 bytes, checksum: 5ccaabce900c234137ecb8f5d64843dd (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-06-08T18:54:49Z (GMT) No. of bitstreams: 1 FelipeEmmanuelDoEspiritoSantoGomes_DISSERT.pdf: 3727906 bytes, checksum: 5ccaabce900c234137ecb8f5d64843dd (MD5) / Made available in DSpace on 2017-06-08T18:54:49Z (GMT). No. of bitstreams: 1 FelipeEmmanuelDoEspiritoSantoGomes_DISSERT.pdf: 3727906 bytes, checksum: 5ccaabce900c234137ecb8f5d64843dd (MD5) Previous issue date: 2017-03-16 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq) / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) / A criptococose, causada pelas esp?cies f?ngicas Cryptococcus neoformans e Cryptococcus gattii, ? uma das micoses oportun?sticas e/ou sist?micas mais importantes no mundo. Cada esp?cie possui quatro gen?tipos, usualmente definidos pelo PCR-RFLP do gene URA5, os quais apresentam diferen?as em sua ecologia, epidemiologia, distribui??o geogr?fica e susceptibilidade a antif?ngicos. Marcadores moleculares de acesso mais direto s?o atrativos para um r?pido reconhecimento de gen?tipos ou de carater?sticas relevantes como virul?ncia e susceptibilidade antif?ngica. Neste sentido, introns autocatal?ticos do grupo I, no rRNA LSU mitocondrial foram aqui avaliados como potencial marcador molecular para os gen?tipos de C. neoformans e C. gattii, bem como quanto a sua rela??o com a susceptibilidade a antif?ngicos. Foram utilizados 77 isolados brasileiros, sendo a maioria do gen?tipo VNI (39 cepas), seguido de 20 VGII, 5 VNIV, 4 VNII, 3 VNIII, 2 VGI, 2 VGIII e 2 VGIV. Os introns Cne.mL2449 e Cne.mL2504 foram amplificados em um s? PCR com primers complementares a regi?o do gene rRNA LSU flanqueadora dos introns. Os produtos de PCR mostraram um polimorfismo de comprimento significativo entre gen?tipos de C. neoformans e C. gattii. O sequenciamento destes produtos indicou que algumas cepas apresentaram nenhum, um, dois, tr?s ou quatro introns em s?rie. Estes dois novos introns, n?o descritos anteriormente, foram nomeados de Cne.mL2439 e Cne.mL2584 em C. neoformans e Cga.mL2439 e Cga.mL2584 em C. gattii. Os introns Cne.mL2439/Cga.mL2439 foram classificados como pertences a subclasse IB2 ao passo que Cne.mL2584/Cga.mL2584, pertencentes a subclasse IA1. Curiosamente, os gen?tipos com isolados sem introns, VNI, VGII, VGI e VNIV, s?o aqueles conhecidos como mais virulentos e menos suscept?veis a agentes antif?ngicos. De fato, tais isolados apresentaram MICs significativamente superiores para 5-flucitosina. Estes achados sugerem que estes elementos podem ser utilizados como potenciais marcadores moleculares para a resist?ncia deste antif?ngico. Por fim, an?lises filogen?ticas sugeriram alta similaridade de sequ?ncia entre os introns Cne.mL2449, Cne.mL2504, Cne.mL2439/Cga.mL2439 e Cne.mL2584/Cga.mL2584 com outros introns mitocondriais presentes nos genes COX1, COX2, COX3, NAD5, ATP9, COB, LSU de fungos distintos, sustentando a hip?tese de origem antiga dos introns (hip?tese ?introns early?), al?m da dispers?o destes elementos em s?tios heter?logos, via splicing reverso. / Cryptococcosis, caused by the fungal species Cryptococcus neoformans or Cryptococcus gattii, is one of the most important systemic and/or opportunistic diseases in the world. Each species has four genotypes, usually accessed by PCR-RFLP of the URA5 gene, which present differences in their ecology, epidemiology, geographical distribution and antifungal susceptibility. Easier accessible molecular markers are attractive for rapid recognition of genotypes or relevant characteristics such as virulence and antifungal susceptibility. In this way, group I autocatalytic introns in the mitochondrial LSU rRNA were evaluated as potential molecular marker for the genotypes of C. neoformans and C. gatti, as well as their relationship to antifungal susceptibility. Seventy-seven Brazilian isolates were used, most of the genotype VNI (39 strains) followed by 20 VGII, 5 VNIV, 4 VNII, 3 VNIII, 2 VGI, 2 VGIII and 2 VGIV. The introns Cne.mL2449 and Cne.mL2504 were amplified in a single PCR with complementary primers to the flanking region of the introns LSU rRNA gene. PCR products showed a significant polymorphism between C. neoformans and C. gattii genotypes. Sequencing of the PCR products indicated that some strains had none, one, two, three or four introns followed. This new two introns, not previously described in the mitochondrial genome of Cryptococcus, were named Cne.mL2439 and Cne.mL2584 in C. neoformans and Cga.mL2439 and Cga.mL2584 in C. gattii. Cne.mL2439/Cga.mL2439 introns were classified as belonging to IB2, whereas Cne.mL2584/Cga.mL2584, as belonging IA1 subclass. Interestingly, genotypes with some intronless strains, VNI, VGII, VGI and VNIV, are those known to be more virulent and less susceptible to antifungal agents. Here, we observed that those intronless isolates had significant higher MICs values for 5-flucytosine. The findings suggest that these elements can be used as potential molecular markers for antifungal resistance. Finally, phylogenetic analyzes suggested high sequence similarity between the introns Cne.mL2449, Cne.mL2504, Cne.mL2439/Cga.mL2439 and Cne.mL2584/Cga.mL2584 with other mitochondrial introns present in the genes COX1, COX2, COX3, NAD5, ATP9, COB, LSU of fungi supporting the ?introns early? hypothesis, as well as its dispersion to heterologous sites by reverse splicing.