Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

<p>Abstract</p><p> Hfq is a pleiotropic posttranscriptional regulator and RNA chaperone that facilitates annealing of trans-encoded sRNA/mRNA pairs. It regulates many different cellular pathways including environmental stress responses, quorum sensing, virulence and maintenance of membrane integrity. Hfq is a member of the Sm/LSm family and forms a homohexamer that has two faces, termed proximal and distal. Hfq preferentially binds A/U rich regions that are near stem loop structures. Crystal structures have shown that poly-A sequences tend to bind the distal face while poly-U sequences bind the proximal face. Currently crystal structures reveal the binding mechanisms for short RNA sequences however; physiologically relevant RNA sequences are typically longer and more structured. To study how these more complex RNA sequences interact with Hfq, a tryptophan fluorescence quenching (TFQ) assay has been developed. Here it is presented that TFQ can correctly identify the binding face for two control sequences, A15 and U6, using the E. coli, S. aureus and L. monocytogenes Hfq homologues. Using fluorescence anisotropy and crystallography it is observed that Trp mutants necessary for TFQ may affect binding to some degree but do not affect the overall structure or RNA binding function of Hfq. TFQ is then used to examine the distal face binding motifs for both Gram-negative (E. coli) and Gram-positive (S. aureus/L. monocytogenes) Hfq, (A-R-N)n and (R-L)n respectively. Using sequences that either fulfilled just (A-R-N)n or both (A-R-N)n and (A-A-N)n motifs it is shown that the distal face motif for Gram-negative Hfq is the more specific (A-A-N)n motif. Using sequences that either fulfilled just (R-L)n or both (R-L)n and (A-L)n motifs it is shown that the Gram-positive distal face motif can be redefined to the (A-L)n motif. Finally TFQ is used to explore autoregulation of E. coli hfq. Two identified binding sites located in the 5'UTR of hfq mRNA, site A and site B, were used for TFQ, along with a longer RNA sequence that contains both sites and their native linker, 5' UTR. TFQ illustrates that the individual sites and the 5' UTR are capable of binding both faces. Each site appears to prefer binding to one face over the other, suggesting a model for hfq 5' UTR mRNA binding to Hfq where either one or two hfq mRNA bind a single Hfq hexamer. In conclusion, TFQ is a straightforward method for analyzing how RNA sequences interact with Hfq that can be utilized to study how longer, physiologically relevant RNA sequences bind Hfq.</p> / Dissertation

The Clp chaperones and proteases play a pivotal role in maintaining cellular homeostasis. They are highly conserved across prokaryotes and can also be found in the mitochondria of eukaryotes and chloroplast of plants. For my thesis, I provide an analysis of the Clp chaperones and protease in the human malaria parasite Plasmodium falciparum. The parasite contains four Clp ATPases, which I term PfClpB1, PfClpB2, PfClpC, and PfClpM. One PfClpP, the proteolytic protomer, and one PfClpR, an inactive isoform, were also identified. All proteins, with the exception of PfClpB2, were found to be localized to the apicoplast, a non-photosynthetic relic plastid in P. falciparum. Both PfClpP and PfClpR form mostly homoheptameric rings as observed by various techniques. Through X-ray crystallography, PfClpP assumed a compacted tetradecamer structure similar to that observed for other ClpPs. My data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum.

The AAA+ chaperone Hsp104 mediates the reactivation of aggregated proteins in Saccharomyces cerevisiae and is crucial for cell survival after exposure to stress. Protein disaggregation depends on cooperation between Hsp104 and a cognate Hsp70 chaperone system. Hsp104 forms a hexameric ring with a narrow axial channel penetrating the centre of the complex. In Chapter 2, I show that conserved loops in each AAA+ module that line this channel are required for disaggregation and that the position of these loops is likely determined by the nucleotide bound state of Hsp104. This evidence supports a common protein remodeling mechanism among Hsp100 members in which proteins are unfolded and threaded along the axial channel. In Chapter 3, I use a peptide-based substrate mimetic to reveal other novel features of Hsp104’s disaggregation mechanism. An Hsp104-binding peptide selected from solid phase arrays recapitulated several properties of an authentic Hsp104 substrate. Inactivation of the pore loops in either AAA+ module prevented stable peptide or protein binding. However, when the loop in the first AAA+ was inactivated, stimulation of ATPase turnover in the second AAA+ module of this mutant was abolished. Drawing on these data, I propose a detailed mechanistic model of protein unfolding by Hsp104 in which an initial unstable interaction involving the loop in the first AAA+ module simultaneously promotes penetration of the substrate into the second axial channel binding site and activates ATP turnover in the second AAA+ module. In Chapter 4, I explore the recognition elements within a model Hsp104-binding peptide that are required for rapid binding to Hsp104. Removal of bulky hydrophobic residues and lysines abrogated the ability of this peptide to function as a peptide-based substrate mimetic for Hsp104. Furthermore, rapid binding of a model unfolded protein to Hsp104 required an intact N-terminal domain and ATP binding at the first AAA+ module. Taken together, I have defined numerous structural features within Hsp104 and its model substrates that are crucial for substrate binding and processing by Hsp104. This work provides a theoretical framework that will encourage research in other protein remodeling AAA+ ATPases.

The Clp chaperones and proteases play a pivotal role in maintaining cellular homeostasis. They are highly conserved across prokaryotes and can also be found in the mitochondria of eukaryotes and chloroplast of plants. For my thesis, I provide an analysis of the Clp chaperones and protease in the human malaria parasite Plasmodium falciparum. The parasite contains four Clp ATPases, which I term PfClpB1, PfClpB2, PfClpC, and PfClpM. One PfClpP, the proteolytic protomer, and one PfClpR, an inactive isoform, were also identified. All proteins, with the exception of PfClpB2, were found to be localized to the apicoplast, a non-photosynthetic relic plastid in P. falciparum. Both PfClpP and PfClpR form mostly homoheptameric rings as observed by various techniques. Through X-ray crystallography, PfClpP assumed a compacted tetradecamer structure similar to that observed for other ClpPs. My data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum.

O gene humano KIAA0090 mapeia uma região cromossômica (1p36.13) com freqüentes aberrações em cânceres humanos e é superexpresso em muitos tipos de tumores. É um gene altamente complexo cujas seqüências de cDNA oriundas de bases de dados públicas apóiam a existência de mais de 20 transcritos alternativos. Sua RefSeq prediz a codificação de uma proteína altamente conservada com 993aa, cujo ortólogo em S. cerevisae (ECM1) foi proposto recentemente atuar no enovelamento de proteínas transmembrana no retículo endoplasmático (RE). O objetivo deste trabalho foi adquirir conhecimento sobre a localização e função da proteína KIAA0090, em células e tecidos normais e tumorais, bem como em células expostas a estresse. Geramos anticorpos policlonais (anti-K2) contra a metade C-terminal da proteína e comparamos seu padrão ao tratamento obtido com o anticorpo (anti-K1), previamente gerado contra a metade N-terminal. A proteína endógena foi localizada primariamente no Golgi e na mitocôndria, dependendo se o anticorpo utilizado foi contra a região N- ou C-terminal, respectivamente. Observamos também, embora menos notável, uma marcação sobreposta com a rede do RE e na margem celular, e variáveis graus de marcação dentro do núcleo e associada a pequenas partículas citoplasmáticas. A análise imunohistoquímica forneceu evidências que a KIAA0090 é ubiquamente epressa. O anti-K2 marcou estruturas semelhantes a Golgi em todo tipo celular, predominando assim naquelas com Golgi mais visíveis, como células secretórias. Observamos para a maioria dos tecidos uma marcação leve a moderada para o anti-K1, mas uma forte marcação foi encontrada em grupos restritos de células, como as células reticulares do timo, epitélio ductal das glândulas da língua e na lâmina basal do epitélio escamoso na zona de transição esôfago-gástrica. Em cortes histológicos de melanoma primário, observamos uma forte marcação para o anti-K1, principalmente em vasos e em células invasoras na margem do tumor, enquanto o anti-K2 mostrou um padrão sugestivo de infiltrado inflamatório e/ou células mesenquimais. Em tecidos de câncer de mama, vimos uma forte marcação nas células de carcinoma ductal em comparação ao epitélio ductal normal para o anti-K2, ao passo que o anti-K1, marcou fortemente vasos e células basais no epitélio de revestimento glandular, tanto no tecido normal como no tumoral. Utilizando uma matriz com amostras teciduais de câncer de mama obtidas de 96 pacientes, observamos uma marcação forte a moderada para o anti-K1 em 84% dos casos, enquanto 16% dos casos não apresentaram marcação. Notamos que os casos positivos para o anti-K1 estavam 100, 85 e 71% entre os casos de grade 1, 2 e 3, respectivamente, sugerindo uma tendência de perda da KIAA0090 associada à progressão do câncer de mama. Foi interessante notar que a brefeldina A e MG132 alteraram os níveis de RNAm da KIAA0090 e levaram à redistribuição da proteína endógena. Outros tratamentos de estresse, incluindo tunicamicina, complexo de rutênio doador de óxido nítrico e etoposídeo, também alteraram o padrão de distribuição da proteína. Este estudo fornece evidências preliminares que corroboram os resultados obtidos de estudos de expressão gênica em larga escala, fortalecendo os indícios de que a KIAA0090 desenvolve um papel na homeostase celular e está envolvida no câncer. / Human KIAA0090 gene maps to a chromosomal region (1p36.13) with frequent aberrations in cancer and is overexpressed in many tumor types. It is a highly complex gene with cDNA sequences in databases supporting the occurrence of more than 20 alternative transcripts. The RefSeq transcript is predicted to encode a highly conserved 993 aa transmembrane protein whose S. cerevisiae ortolog (EMC1) was recently proposed to function on transmembrane protein folding in the endoplasmic reticulum (ER). The aim of this work was to gain insight into the localization and function of KIAA0090 protein, in normal and tumor cells and tissues, as well as in cells exposed to stress treatments. We raised a polyclonal antibody (anti-K2) to the C-terminal half of the protein and compared its pattern of staining with an antibody (anti-K1) previously generated in our laboratory to the N-terminal half. The endogenous protein was primarily localized either to mitochondria or Golgi, depending whether the antibody used was to the N- or C-terminal, respectively. Also, less conspicuous staining overlapped with the ER network and cell margin, and variable degrees of labeling was observed within the nucleus and associated to small cytoplasmic particles. Immunohistochemistry survey provided evidence that the KIAA0090 protein is ubiquitously expressed. Anti-K2 labeled in a Golgi-like pattern in every cell type, predominating in those with more conspicuous Golgi, such as secretory cells. Faint to moderate anti-K1 staining was found in most tissues, but very strong staining was seen in restricted groups of cells, such as thymus reticular cells, ductal epithelium of salivary lingual glands and the basal layer of the squamous epithelium in the esophagus-gastric transition zone. In histological sections of primary melanomas, we observed a strong staining for the anti-K1, mostly in vessels and at the invasive tumor margin, while the anti-K2 showed a staining pattern suggestive of infiltrating inflammatory and mesenchymal cells. In breast tissues, stronger staining was seen in ductal carcinoma cells in comparison to normal ductal epithelium for anti-K2 antibody, whereas anti-K1 strongly marked vessels and basal cells in epithelia lining glandular ducts both in normal and tumor tissues. Using a tissue array of breast cancer samples obtained from 96 patients, we observed strong to moderate staining for anti-K1 in 84% of the samples and lack of staining in 16%, interestingly anti-K1 positive cases were 100, 85 and 71% among cases of grades 1, 2 and 3, respectively, suggesting a tendency of KIAA0090 loss associated with breast cancer progression. A positive correlation was found with estrogen receptor expression and the opposite for HER2. Interestingly, Brefeldin A and MG132 altered KIAA0090 mRNA levels and caused endogenous KIAA0090 protein to redistribute. Other stress treatments, including tunicamycin, a ruthenium complex nitric oxide donor and etoposide, also altered KIAA0090 distribution. This study supports the notion that KIAA0090 play a role in cellular homeostasis and is involved in cancer.

Le génome des cellules eucaryotes est empaqueté dans la chromatine, dont l’établissement et la maintenance nécessitent des processus d’assemblage et de remodelage. Ce travail de thèse a été consacré à la caractérisation de deux facteurs de la machinerie d’assemblage de la chromatine. Le premier facteur étudié dans ce travail était HIRIP3, un homologue mammifère de la levure H2A.Z chaperon Chz1. Nous voulions vérifier si HIRIP3 est une chaperon d'histone par elle-même. Pour commencer, nous avons décrit l'interaction de HIRIP3 avec les histones in vivo. Ensuite, nous avons étudié la spécificité structurale de cette interaction in vitro. Nous avons caractérisé HIRIP3 comme une nouvelle chaperon d'histone H2A qui utilise le motif CHZ pour sa fonction. La deuxième partie de ce travail a été axée sur le complexe de remodelage de la chromatine SRCAP. Nous avons cherché à décoder son réseau d'interaction et à décrire ses sous-complexes. Nous avons reconstitué le complexe de base YL1, SRCAP, TIP49A, TIP49B et H2A.Z / H2B en utilisant le système d'expression chez baculovirus. Notre protocole nous a permis de purifier un complexe de base adapté aux futures études structurelles par microscopie cryo-électronique. / The genome of eukaryotic cells is packaged into chromatin, which establishment and maintenance require mechanisms of assembly and remodelling. This thesis work was dedicated to the characterization of two factors of chromatin assembly machinery. The first factor studied in this work was HIRIP3, a mammalian homologue of yeast H2A.Z chaperone Chz1. We aimed to test whether HIRIP3 is a histone chaperone by itself. At first, we established HIRIP3 interaction with histones in vivo. After then, we studied the structural specificity of this interaction in vitro. We have characterized HIRIP3 as a novel H2A histone chaperone that utilizes the CHZ motif for its function. The second part of this work was focused on SRCAP chromatin remodelling complex. We aimed to decipher its interaction network and to describe its sub-complexes. We have reconstituted YL1, SRCAP, TIP49A, TIP49B and H2A.Z/H2B core complex using baculovirus expression system. Our protocol allowed us to purify core complex suitable for future structural studies by cryo-electron microscopy.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22660号 / 工博第4744号 / 新制||工||1741(附属図書館) / 京都大学大学院工学研究科高分子化学専攻 / (主査)教授 秋吉 一成, 教授 大内 誠, 准教授 佐々木 善浩 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Indiana University-Purdue University Indianapolis (IUPUI)

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