DsrA est un petit ARN régulateur que l'on retrouve chez plusieurs espèces bactériennes, notamment Escherichia coli non-pathogène et pathogène. DsrA est exprimé principalement lorsque la bactérie est dans un environnement température suboptimale (<37 [degrés Celsius]). En conditions d'expression de DsrA, on retrouve une forme pleine longueur de 85 nucléotides et une forme tronquée de 60 nucléotides. Il a été montré que DsrA, dans sa forme pleine longueur ou tronquée, peut diminuer l'initiation de la traduction de l'ARNm hns , codant pour la protéine H-NS, un régulateur majeur de la transcription qui module près de 5% des gènes chez E. coli . Toutefois, les mécanismes impliqués dans la répression traductionnelle d'hns par DsrA n'ont pas été caractérisés. Les travaux présentés dans ce mémoire démontrent que DsrA bloque l'initiation de la traduction d'hns en s'appariant immédiatement en aval du codon d'initiation de la traduction. De plus, DsrA provoque la dégradation de l'ARNm hns en recrutant le complexe dégradosome ARN. La RNase E, qui fait partie de ce complexe, va cliver l'ARNm au nucléotide 131 dans la région codante du gène, soit 80 nucléotides en aval de l'appariement entre hns et DsrA. Ce clivage va provoquer la dégradation rapide de l'ARNm hns par les exoribonucléases de E. coli . Mes travaux de maîtrise ont abouti à un modèle d'action de DsrA sur hns qui pourrait inclure les autres cibles négatives de DsrA. De plus, ils suggèrent que les sRNA semblent partager le même mécanisme général de dégradation des ARNm. Ces travaux démontrent également que l'extrémité 5' de DsrA tronqué est monophosphate ce qui suggère un clivage par une ribonucléase. Toutefois aucune ribonucléase connue d' E. coli ne semble produire la forme tronquée de DsrA, bien que l'exoribonucléase PNPase semble influencer sa dégradation. Ces travaux démontrent également l'impact des protéines RppH et CsdA dans la dégradation de l'ARNm hns à 25 [degrés Celsius], c'est-à-dire lorsque DsrA est naturellement exprimé. Ces protéines sont importantes pour la stabilité de hns et pour sa dégradation en présence de DsrA. Toutefois, le mécanisme d'action de ces protéines n'a pas été déterminé.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Aicardi-Goutières Syndrome (AGS) is a single gene, autoimmune disorder, with variable onset in the first year of life. Its clinical features exhibit similarities to several autoimmune diseases and congenital viral infections. AGS can result from mutations in ADAR1, TREX1 and SAMHD1 as well as any of the three genes that encode the protein subunits of the RNase H2 enzyme. It is hypothesised that impairment of nucleic acid metabolism results in abnormal nucleic acid species within the cell. This in turn is thought to cause the aberrant immune response that leads to AGS. The RNase H2 complex contains the catalytic RNASEH2A subunit and the auxiliary RNASEH2B and RNASEH2C subunits, which are thought to provide structural support and facilitate interactions with additional cellular proteins. RNase H2 can cleave the RNA strand of an RNA:DNA hybrid as well as 5’ of a single ribonucleotide embedded in dsDNA. Therefore, RNase H2 may have roles in several cellular processes, including DNA replication and repair, transcription, and viral infection. The aim of this PhD project was to investigate the physiological functions of RNase H2. The localisation of the RNase H2 proteins was investigated using EGFP-tagging and fluorescent microscopy. The interaction between the PIP-box of RNASEH2B and PCNA was found to localise RNase H2 and not RNase H1 to nuclear replication foci during S-phase. This suggests that RNase H2 is the dominant RNase H activity during DNA replication. Stable cell lines expressing EGFP-RNASEH2B and an alternative isoform, EGFP-RNASEH2Balt, were generated and used to perform a protein-protein interaction screen by GFP-Trap and mass spectrometry. The results indicate putative physical interactions between RNASEH2B and other factors involved in DNA replication and repair. Further evidence for a role in DNA repair was revealed when mammalian RNase H2 null cells were treated with hydroxyurea. Low doses of hydroxyurea increased ribonucleotide incorporation into genomic DNA and impaired S-phase progression. In contrast to wild-type cells, RNase H2 null cell proliferation also failed to recover from this replicative stress after HU withdrawal. However, the ribonucleotide content of genomic DNA from these cells did return to pre-hydroxyurea treatment levels. This suggests that an alternative repair pathway exists in mammalian cells, which can remove ribonucleotides from DNA in the absence of RNase H2, but that this pathway is also harmful to the cells. There is evidence that TREX1 facilitates viral infection while SAMHD1 has been shown to restrict viral infection. Therefore, experiments were performed to investigate if RNase H2 could be a viral facilitator or restriction factor. Ribonucleotides can be incorporated into viral DNA, so RNase H2 could act as a restriction factor by nicking and damaging the pre-integration complex. However, RNase H2 could also function as a facilitator of infection by processing viral RNA:DNA hybrid by-products and thus prevent the host immune response. The data obtained during this PhD project provides further evidence that RNase H2 is involved in DNA replication and repair and has contributed to the understanding of the function of RNase H2 in the cell. However, it is still unknown how mutations in RNase H2 lead to the pathology of AGS.

One third of the world's population is infected with Mycobacterium tuberculosis, the bacterium that causes TB. During an infection, bacteria often survive host immune system attacks, which include oxidative stress conditions for bacteria growing inside macrophages. This makes treatment difficult and time-consuming. We hypothesize bacteria can adapt to environmental conditions by changing their mRNA maturation and degradation profiles. Using a model system, Mycobacteruim smegmatis, we focus on how mRNA expression is affected by oxidative stress. After construction and sequencing of RNA expression libraries, preliminary analysis showed that after three hours of H2O2 exposure most upregulated genes were related to DNA repair, while downregulated genes included transport proteins. After six hours of exposure, upregulated genes were similar to three hours and downregulated genes included tRNAs. 5' end mapping libraries were also constructed to access differential cleavage site abundance under oxidative stress conditions. We also investigated the roles RNase J may have in stress response and mRNA processing in Mycobacteria. RNase J and RNase E are thought to be the major RNases in bacteria. While most bacteria only have one of them, mycobacteria encode both in their genome, with RNase J being non-essential. We constructed a set of 4 strains (WT, RNase J overexpression, RNase J deletion, and complemented RNase J deletion) and tested their drug resistance and stress tolerance. Results suggests that RNase J deletion and overexpression alter drug sensitivity. Stress tolerance assays showed that WT is more tolerant to oxidative stress, followed by RNase J deletion strain and overexpression and complemented RNase J deletion strains, with the last two showing no growth when cultured with H2O2. Analysis of the expression profile of these strains was performed to help understand if gene expression differences are responsible for the phenotypes observed. For the complemented RNase J deletion, one operon had almost all its genes upregulated. This operon encodes a hydrogenase (Hyd3), suggesting that redox balance in the strain is perturbed.

Upon termination of translation, the fate of ribosomes is determined largely by the rate at which cells are growing. During periods of exponential growth, ribosomes are rapidly recycled, translation is re-initiated, and the ribosomes are extremely stable. However, when nutrient sources become limiting, and ribosomes are not actively translating, they may become substrates for degradation. While this phenomenon is well known, details of how the process is initiated and what are the signals for degradation have, until now, remained elusive. Here, I present in vitro and in vivo data showing that free ribosome subunits are the targets of degradative enzymes, whereas 70S particles that remain associated are protected from such degradation. Conditions that increase the formation of subunits both in vitro and in vivo lead to enhanced degradation. Thus, the simple presence of free 50S and 30S subunits is sufficient to serve as the mechanism that initiates ribosome degradation. In order to identify RNases involved in ribosome degradation, both in vitro and in vivo assays were developed. Together, they have provided evidence for a multi-step degradation process involving both endo- and exoribonucleases. Examination of extracts from strains deficient in known RNases revealed that the endoribonucleases, RNase E and RNase G, may be involved in the initial cleavages. The resulting fragments, some of which are small enough oligoribonucleotides that they remain part of the acid-soluble fraction are degraded to mononucleotides primarily by the 3'-5' exoribonucleases, RNase R and polynucleotide phosphorylase.

Replication of HIV-1 is inhibited by azidothymidine (AZT), which leads to chain termination and inhibition of DNA synthesis. Resistance to AZT is frequently the result of mutations that increase the ability of RT to remove the chain-terminating nucleotides after they have been incorporated. It has been proposed that RNase H cleavage of the RNA template can occur when RT is stalled near the site of chain termination and contributes to the inhibition by causing the dissociation of the primer-template before the chain terminator can be excised. Mutations in the connection and RNase H domains of RT have been shown to increase excision. It has long been known that resistance to thymidine analogs is conferred by the mutations M41L, D67N, K70R, L210W, T215F/Y and T219Q/E in RT and that this resistance is suppressed by the additional presence of the M184V mutation. Changes in excision activity on DNA templates have been observed with these mutant RTs, but effects on RNase H cleavage resulting in indirect effects on excision activity is also possible with RNA templates. We used a 5'-labeled -3'-chain-terminated DNA primer annealed to either a DNA or RNA template to evaluate primer rescue activities, a 5'-labeled RNA template to evaluate RNA cleavage activity and a biotin-tagged chain-terminated oligodeoxynucleotide to monitor primer-template dissociation. We first investigated differences between RNA and DNA templates when the primers were chain terminated and observed a correlation between RNase H activities and template/primer (T/P) dissociation. An inverse correlation was observed between excision rescue rates and RNase H cleavages leading to T/P dissociation. We observed that the chain terminator (i.e. AZTMP or ddAMP) affected RNase H cleavages and excision rates with RNA template and dNTPs. When we investigated mutations in the N-terminal domain of RT associated with nucleoside reverse transcriptase inhibitor (NRTI) resistance we found that primer rescue was decreased when M184V was present in combination with thymidine analog mutations (TAMs) and the template was RNA with either ATP or PPi as excision substrate. RNase H cleavage at secondary cleavage sites (-7, -8) was substantially reduced with M41L/T215Y RT in comparison with wild type RT, and primer-template dissociation was decreased. In contrast, when M184V was present, RNase H cleavage at the secondary cleavage sites and dissociation of the primer-template occurred at higher levels and excision rescue was decreased. The ability of RT to rescue an AZT terminated primer in the presence of the 184V mutation was restored when the RNase H activity was inactivated by the RNase H negative mutation E478Q. Electromobility shift assay (EMSA) analysis of AZT-resistant mutant RT with M184V showed an increased Kd for formation of the ternary complex. These results suggest that RNase H-mediated RNA-DNA template-primer dissociation is influenced by mutations associated with thymidine analog resistance, and that suppression of resistance to nucleoside RT inhibitors by M184V may be partly explained by effects on RNase H cleavage that decrease the time available for excision to occur. This is the first time that mutations in the polymerase domain are shown to affect excision rescue through an RNase H-dependent mechanism.

Properly folded proteins are necessary for all living organisms. Incorrectly folded proteins can lead to a variety of diseases such as Alzheimer’s Disease or Bovine Spongiform Encephalitis (Mad Cow Disease). Understanding the forces involved in protein folding is essential to the understanding and treatment of protein misfolding diseases. When proteins fold, a significant amount of surface area is buried in the protein interior. It has long been known that burial of hydrophobic surface area was important to the stability of the folded structure. However, the impact of burying polar surface area is not well understood. Theoretical results suggest that burying polar groups decreases the stability, but experimental evidence supports the belief that polar group burial increases the stability. Studies of tyrosine to phenylalanine mutations have shown the removal of the tyrosine OH group generally decreases stability. Through computational investigations into the effect of buried tyrosine on protein stability, favorable van der Waals interactions are shown to correlate with the change in stability caused by replacing the tyrosine with phenylalanine to remove the polar OH group. Two large-scale studies on nearly 1000 high-resolution x-ray structures are presented. The first investigates the electrostatic and van der Waals interactions, analyzing the energetics of burying various atom groups in the protein interior. The second large-scale study analyzes the packing differences in the interior of the protein and shows that hydrogen bonding increases packing, decreasing the volume of a hydrogen bonded backbone by about 1.5 Å3 per hydrogen bond. Finally, a structural comparison between RNase Sa and a variant in which five lysines replaced five acidic groups to reverse the net charge is presented. It is shown that these mutations have a marginal impact on the structure, with only small changes in some loop regions.

RNA editing in trypanosomes is the post-transcriptional insertion or deletion of uridylates at specific sites in mitochondrial mRNAs. This process is catalyzed by a multienzyme, multisubunit complex through a series of enzymatic cycles directed by small, trans-acting RNA molecules. Despite impressive progress in our understanding of the mechanism of RNA editing and the composition of the editing complex, fundamental questions regarding RNP assembly and the regulation of catalysis remain. This dissertation presents studies of RNA-protein interactions between RNA editing complexes and substrate RNAs and the determination of substrate secondary structural determinants that govern them. Our results suggest that substrate association, cleavage and full-round editing by RNA editing complexes in vitro obey hierarchical determinants that increase in complexity as editing progresses and we propose a model for substrate recognition by RNA editing complexes. In addition, this dissertation also presents the characterization of a novel mitochondrial RNA helicase, named REH2 and its macromolecular interactions. Our data suggest that REH2 is intimately involved in interactions with macromolecular complexes that integrate diverse processes mediating mitochondrial gene expression. These results have implications for the mechanism of substrate RNA recognition by RNA editing complexes as well as for the integration of RNA editing to other facets of mitochondrial RNA metabolism.

Properly folded proteins are necessary for all living organisms. Incorrectly folded proteins can lead to a variety of diseases such as Alzheimer’s Disease or Bovine Spongiform Encephalitis (Mad Cow Disease). Understanding the forces involved in protein folding is essential to the understanding and treatment of protein misfolding diseases. When proteins fold, a significant amount of surface area is buried in the protein interior. It has long been known that burial of hydrophobic surface area was important to the stability of the folded structure. However, the impact of burying polar surface area is not well understood. Theoretical results suggest that burying polar groups decreases the stability, but experimental evidence supports the belief that polar group burial increases the stability. Studies of tyrosine to phenylalanine mutations have shown the removal of the tyrosine OH group generally decreases stability. Through computational investigations into the effect of buried tyrosine on protein stability, favorable van der Waals interactions are shown to correlate with the change in stability caused by replacing the tyrosine with phenylalanine to remove the polar OH group. Two large-scale studies on nearly 1000 high-resolution x-ray structures are presented. The first investigates the electrostatic and van der Waals interactions, analyzing the energetics of burying various atom groups in the protein interior. The second large-scale study analyzes the packing differences in the interior of the protein and shows that hydrogen bonding increases packing, decreasing the volume of a hydrogen bonded backbone by about 1.5 Å3 per hydrogen bond. Finally, a structural comparison between RNase Sa and a variant in which five lysines replaced five acidic groups to reverse the net charge is presented. It is shown that these mutations have a marginal impact on the structure, with only small changes in some loop regions.