<p>RNA localization provides the blueprint for compartmentalized protein synthesis in eukaryotic cells. Current paradigms indicate that RNAs encoding secretory and membrane proteins are recruited to the endoplasmic reticulum (ER), via positive selection of a `signal peptide' tag encoded in the protein. Thus RNA sorting to the ER follows protein sorting and the RNA is considered a passive player. However, RNAs have been shown to access the ER independent of the signal peptide and display a wide range of affinities to the ER that does not correlate with signal peptide strength. How and why mRNAs localize to the ER to varying extents and whether such localization serves a purpose besides protein sorting is poorly understood. To establish the cause and consequence of RNA binding to the ER membrane, I pose three primary questions: 1. How are mRNAs targeted to the ER? 2. Once targeted, how are mRNAs anchored to the ER membrane? 3. Are ER localized mRNAs subject to transcript-specific regulation? </p><p>I address cytosolic mRNA targeting to the ER by comparing the partitioning profiles of cytosolic/nuclear protein-encoding mRNA population (mRNACyto) to that of mRNAs encoding a signal peptide (mRNAER). I show that, at a population level, mRNACyto display a mean ER enrichment that is proportional to the amount of ER-bound ribosomes. Thus, I propose that targeting of mRNACyto to the ER is stochastic and over time, the specific interactions engaged by an individual mRNACyto with the ER determines its steady state partitioning profile between the cytoplasm and the ER. </p><p>To address the modes of direct binding of mRNA to the ER, I examined the association of various RNA populations with the ER after disrupting membrane-bound ribosome's interaction with its ER receptor. mRNACyto and most of mRNAs encoding secretory proteins (mRNACargo) are released upon disruption of ribosome-receptor interactions, indicating no direct mRNA-ER interactions. However, the population of mRNAs that encode resident proteins of the endomembrane organelles such as the ER, lysosome, endosome and the Golgi apparatus (mRNARes) maintain their association with the ER despite the disruption of ribosome-receptor interactions. These results indicate direct binding of mRNARes to the ER, further suggesting that the function of the encoded proteins dictates the mode of association of corresponding mRNA with the ER. </p><p>To uncover the mode of mRNARes binding directly to ER, I performed differential proteomic analysis of cytosolic and membrane bound RNA-protein complexes, which revealed a network of RNA binding proteins that interact uniquely with the ER-anchored mRNAs. The anchoring of endomembrane resident protein-encoding RNAs to the ER through these RNA binding proteins may reflect an imprinting of the ER with the information necessary for the continued biogenesis of the endomembrane organelle system even in situations where translation-dependent ER targeting of an mRNA is compromised. </p><p>Finally, I address whether ER-bound mRNAs can be regulated differentially by comparing the fates of two signal peptide-encoding RNAs, B2M and GRP94, during the unfolded protein response (UPR). I show that in response to ER stress, GRP94 mRNA, but not B2M, relocates to stress-induced RNA granules, thus escaping an RNA decay program that operates at the ER membrane during the UPR. Hence, I propose that the mode of RNA association to the ER is subject to regulation and influences the fate of RNAs during cellular stress. Thus, by demonstrating diverse modes of mRNA localization to the ER and differential regulation of ER bound mRNAs during cellular stress, my work has helped establish an emerging role for the ER as a post-transcriptional gene regulatory platform.</p> / Dissertation

When unfolded proteins accumulate in the endoplasmic reticulum (ER), the unfolded protein response (UPR) increases ER protein folding capacity to restore protein folding homeostasis. Unfolded proteins activate UPR signalling across the ER membrane to the nucleus by promoting oligomerisation of IRE1, a conserved transmembrane ER stress receptor. Despite significant research, the mechanism of coupling ER stress to IRE1 oligomerisation and activation has remained contested. There are two proposed mechanisms by which IRE1 may sense accumulating unfolded proteins. In the direct binding mechanism, unfolded proteins are able to bind directly to IRE1 to drive its oligomerisation. In the chaperone inhibition mechanism, unfolded proteins compete for the repressive BiP bound to IRE1 leaving IRE1 free to oligomerise. Currently, these two mechanisms respectively lack compelling in vivo and in vitro evidence required to assess their validity. The work presented here first describes in vivo experiments that identify a role of the ER co-chaperone ERdj4 as an IRE1 repressor that promotes a complex between the luminal Hsp70 BiP and the luminal stress-sensing domain of IRE1α (IRE1LD). This is then built on by a series of in vitro experiments showing that ERdj4 catalyses formation of a repressive BiP-IRE1LD complex and that this complex can be disrupted by the presence of competing unfolded protein substrates to restore IRE1LD to its default, dimeric, and active state. The identification of ERdj4 and the in vitro reconstitution of chaperone inhibition establish BiP and its J-domain co-chaperones as key regulators of the UPR. This thesis also utilises the power of Cas9-CRISPR technology to introduce specific mutations into the endogenous IRE1α locus and to screen for derepressing IRE1α mutations. Via this methodology, two predicted unstructured regions of IRE1 are found to be important for IRE1 repression. Finally, this thesis challenges recent in vitro findings concerning the direct binding mechanism.

Orientador: Jorg Kobarg / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T01:48:42Z (GMT). No. of bitstreams: 1 Lanza_DanielCarlosFerreira_D.pdf: 39179290 bytes, checksum: cbd84a5b7ba74e985bc1fc48595debd6 (MD5) Previous issue date: 2009 / Resumo: A proteína FEZ1 foi caracterizada inicialmente como um ortólogo da proteína UNC76 de C. elegans, responsável pelo desenvolvimento e fasciculação neuronal nesse verme. Estudos subsequentes demonstraram sua atuação em processos de desenvolvimento neuronal, polarização celular, mecanismos de transporte associado à kinesinas e transporte de vesículas e mitocôndrias. Outros trabalhos demonstraram que a superexpressão de FEZ1 interfere no ciclo de vida de alguns tipos de vírus como HIV e JCV. FEZ1 é capaz de interagir com mais de 51 proteínas diferentes, e participa em muitos processos celulares. Observamos que FEZ1 apresenta ausência de estrutura molecular rígida, sendo pertencente à classe das natively unfolded proteins, e é capaz de formar dímeros em solução. Essa observação condiz com sua extrema capacidade de interagir com muitas proteínas diferentes. A capacidade de FEZ1 interagir com outras proteínas é influenciada pela fosforilação da sua região C-terminal por diferentes isoformas de PKC. FEZ1 interage e colocaliza com NEK1 e com CLASP2 em células de mamífero, em uma região candidata ao centrossomo. Essas interações são dependentes da região coiled-coil presente na parte C-terminal de FEZ1, e ocorrem em regiões coiled-coil de CLASP2 e NEK1. A interação com CLASP2 é rompida quando FEZ1 é fosforilada por PKC. A superexpressão de FEZ1 causa o fenótipo flower like observado em células de alguns tipos de leucemia. Nós observamos que FEZ1 interage e colocaliza com a e ?-tubulinas e que a formação desse fenótipo em células HEK293 ocorre devido a uma alteração na organização dos microtúbulos causada pelo excesso de FEZ1. A formação do fenótipo flower like é influenciada por ativação das vias de PKC e PI3K. Os dados obtidos durante o nosso trabalho indicam que FEZ1 é uma proteína intrinsecamente desenovelada, que atua em processos celulares associados ao citoesqueleto e centrossomo em conjunto com NEK1 e CLASP2, e que defeitos em sua regulação, possivelmente pelas vias de PKC ou PI3K, causam alteração da organização dos microtúbulos originando núcleos flower like. / Abstract: FEZ1 was identified first as a orthologue of C elegans UNC-76 protein, that plays functions related to neuronal development in this worm. Subsequent studies, shows FEZ1 functions in neuronal development process, cell polarization, transport mechanisms associated to kinesins and vesicular and mitochondrial transports. Other works showed that FEZ1 superexpression interfere in the life cycle of some viral types such as HIV and JCV. FEZ1 is able to interact with more than 51 different proteins and participates in several cellular processes. We observed that FEZ1 has a mobile molecular structure, is a member of the natively unfolded protein class, and can form dimers in solution. This observation is in agreement with its capacity to interact with a large number of different proteins. The capacity of FEZ1 to interact with other proteins is influenced by different PKC isoforms phosphorylation in its C-terminal region. FEZ1 interacts and co-localizes with NEK1 and CLASP2 in a centrossomal candidate region of mammalian cells. These interactions are dependent of a coiled coil inside the C-terminal region of FEZ1, and occur in dependence of coiled coil regions of NEK1 and CLASP2. The interaction between FEZ1 and CLASP2 is abolished after FEZ1 phosphorylation by PKC. The FEZ1 overexpression causes the flower like phenotype observed in cells of some leukemias. We observed that FEZ1 interacts and co-localizes with _ and _-tubulins and that the phenotype formation in HEK293 cells is mediated by an atypical organization of microtubule spindles, caused by overexpression of FEZ1. The flower like phenotype formation is influenced by activation of PKC and PI3K pathways. The data generated by our work indicate that FEZ1 is an intrinsically unfolded protein, that works in cellular processes associated to the cytoskeleton in conjunct with NEK1 and CLASP2, and that defects in its regulation, maybe via the PKC or PI3K pathways, causes alterations in microtubule organization and formation of the "flower like" nuclei. / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

Orientador: Gabriel Forato Anhê / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-27T14:26:05Z (GMT). No. of bitstreams: 1 Mesquita_CarolineCosta_D.pdf: 2692158 bytes, checksum: 5f07d43267a2e976f9b9818ec63ba452 (MD5) Previous issue date: 2015 / Resumo: Os ritmos circadianos de ingestão alimentar se estabelecem com objetivo de manter a homeostasia de nutrientes no meio celular, frente a variações intrínsecas ao ciclo claro/escuro. Neste sentido, a gliconeogênese de roedores é suprimida no período noturno, no qual há ocorrência de um surto alimentar bifásico que compreende aproximadamente 90% de todo o aporte calórico diário. Estes eventos apresentam, entre si, uma relação causal, onde o próprio aumento dos nutrientes circulantes, principalmente a glicose, controla a gliconeogênese. O padrão inverso é observado na fase clara do ciclo claro/escuro. Recentes estudos têm demonstrado que, a ativação farmacológica de vias da Unfolded Protein Response (UPR), no sistema nervoso central, resulta em resistência à ação anorexigênica da insulina e, consequentemente, aumento da ingestão alimentar através de um mecanismo não completamente esclarecido. A UPR é uma resposta celular adaptativa que atenua a taxa de tradução de mRNAs, aumenta a proteólise e, deste modo, recupera o fenótipo celular. Esta reposta, quando ativada cronicamente, pode resultar em morte celular programada e resistência à insulina. No entanto, ainda não estava claro se a via do ATF6 da UPR tem, de fato, uma relação com o ritmo alimentar. Para responder a esse questionamento, realizamos análises da variação circadiana das proteínas envolvidas na via da UPR, imunoprecipitações com animais adrenalectomizados, e aplicação de dexametasona subcutânea. Os resultados demonstram que o ATF6 teve um aumento noturno atingindo o máximo de transição da fase clara para fase escura. A partir desse fato, foram realizados ensaios de imunuprecipitações em ratos adrenalectomizados para evidenciar as associações dos complexos CRTC2/ATF6 e CRTC2/CREB1. Contudo, nossos dados suportam a hipótese que os níveis fisiológicos de glicocorticóides podem reprimir a expressão CRH e estimular a ingestão de alimentos, através de uma via dependente de ATF6. Estes eventos, por consequência, poderão reduzir a atividade transcricional do CREB1, sobre o CRH, corroborando com os dados da literatura que apontam que os glicocorticóides endógenos dos roedores (principalmente a corticosterona) exercem um conhecido papel no controle da ingestão alimentar, decorrente principalmente da modulação da expressão do neurotransmissor anorexigênico CRH / Abstract: The circadian cycles of food intake have an important role in the homeostasis of cellular environment, acting over intrinsic changes to the sleep/wake cycle. Therefore, mice gluconeogenesis is suppressed at night where a food outbreak, responsible by 90% of all daily caloric ingestion, occurs. These events are connected by a causal relation, where the current nutrient increasing, mostly glucose, controls gluconeogenesis. The oppose pattern is verified during the light stage of the sleep/wake cycle. Recent studies have indicated that pharmacological activation of Unfolded Protein Response (UPR) pathways, at central nervous system, implies in resistance to the anorectic insulin effect, and, consequently, increase of the food intake activity trough a not fully explained engine. UPR is an adaptive cellular response that reduces mRNA¿s transcriptional rate, increases proteolysis, and therefore, restores cellular phenotype. This response, when constantly enabled, may induce cellular death and insulin resistance. However, it was not clear yet if the UPR¿s ATF6 pathway has, indeed, a connection with the feed rhythm. To answer to this question, we did several analysis of the circadian variation of the proteins connected to the UPR¿s pathway, adrenalectomized animals immunopreciptations and subcutaneous dexamethasone applications. The results demonstrated that ATF6 has a nightly increase and has reached the maximum of transcription rate from the light to the dark cycle. From this point, it was made immunopreciptations tests in adrenalectomized mice to evidence the association between CRTC2/ATF6 and CRTC2/CREB1 complexes. However, our data support the hypothesis that the physiological levels of glucocorticoids may suppress CHR expression and stimulate food intake trough an ATF6 dependent pathway. Those events, therefore, may reduce CREB1¿s transcriptional activity, confirming other studies data that indicates that endogenous mice glucocorticoids (mainly corticosterone) play an well-known role in food intake control, mainly due from modulation of the expression of the anorectic neurotransmitter CRH / Doutorado / Farmacologia / Doutora em Farmacologia

The endoplasmic reticulum (ER) facilitates the synthesis, assembly and quality control of all secretory, transmembrane, and resident proteins of the endomembrane system. An accumulation of unfolded proteins or a disruption in the specialized folding environment within the organelle causes ER stress, thus impairing the folding capacity of the ER. In response to this stress, the ER initiates a signaling cascade called the unfolded protein response (UPR) in an attempt to restore ER homeostasis. The vertebrate UPR is propagated by three ER-resident transmembrane proteins (i.e., PERK, IRE1α, and ATF6α), each initiating a signaling cascade that ultimately culminates in production of a transcriptional activator. The UPR was originally characterized as a pathway for the upregulation of ER chaperones, and a comprehensive body of subsequent work has shown that protein synthesis, folding, oxidation, trafficking, and degradation are all transcriptionally enhanced by the UPR. However, UPR activation is also accompanied by extensive mRNA suppression. The mechanisms responsible for this suppression and its consequences for physiological processes beyond the realm of ER protein folding and processing are only now beginning to be described. The overall goal of my thesis work was to explore this process of UPR-mediated gene suppression by identifying the mechanisms involved and the cellular processes affected. As a result, I characterized a novel mechanism of UPR-mediated transcriptional repression involving the translational regulation of the transcription factor C/EBPβ resulting in the suppression of the gene Il4ra, encoding an essential subunit of the IL-4/IL-13 receptor. As a consequence of this suppression, a novel effect of ER stress was identified in the impairment of IL-4/IL-13 signaling, a finding of potential significance in the study of inflammatory disease. In addition to this mechanism, I validated a novel approach to the identification of UPR-regulated transcription factors using publically available bioinformatic software. Through this analysis, I identified the transcription factor HNF4α as a novel post-translational UPR-regulated transcription factor, the regulation of which, resulted in the suppression of a number of lipid metabolic genes. This analysis not only identified a novel UPR-regulated transcription factor, but also presented a new tool for the characterization of UPR-mediated gene suppression. My work represents an independent and original investigation into the process of UPR-mediated gene suppression; and reveals that the UPR facilitates transcriptional suppression through the transcriptional, translational, and post-translational regulation of multiple transcription factors, resulting in the coordinated attenuation of physiological pathways. This function of the UPR is likely to contribute to metabolic, inflammatory, and other chronic disease states.

京都大学 / 0048 / 新制・課程博士 / 博士(薬科学) / 甲第20059号 / 薬科博第66号 / 新制||薬科||8(附属図書館) / 京都大学大学院薬学研究科薬科学専攻 / (主査)教授 竹島 浩, 教授 中山 和久, 教授 根岸 学 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

Combining the nematode Caenorhabditis elegans with novel microfluidic technology has produced a phenotypic movement assay that is at once rapid, sensitive, and low-cost. The method is based on the neurophysiologic phenomenon of worms exhibiting robust, continuous, directed locomotion in response to mild electric fields inside a microchannel. As we demonstrate with the studies reported herein, our microfluidic electrotaxis platform is a unique tool for studying the effects of environmental and genetic manipulations on C. elegans’ movement behaviour, which in turn indicates the state of the organism’s neuronal and muscular systems. In one initiative to develop an inexpensive biosensor, we use the setup to measure the response of worms to common environmental pollutants. Results indicate that worms’ electrotactic swimming behaviour is particularly susceptible to metal salts. A comparison with traditional assays measuring fecundity, growth, and lifespan reveals that electrotactic speed shows a comparable level of sensitivity as a toxicity endpoint. Another study demonstrates that worms expressing a mutant form of α-synuclein, a familial Parkinson’s disease-related protein, show deficits in electrotactic swimming speed that coincide with dopaminergic neuron damage. We further show that both the electrotaxis and neuronal phenotypes can be ameliorated by treatment with curcumin, a putative neuroprotective agent. We have also used the platform to investigate the effects of other environmental and genetic stresses on electrotactic behaviour. Our findings indicate that the response can withstand many different insults but is affected by stresses that induce the mitochondrial and ER unfolded protein responses, which themselves play roles in preserving electrotactic swimming behaviour alongside the heat shock response. These data expand our knowledge of how the motor output component of C. elegans’ electrotactic response is perturbed by environmental and genetic manipulations, and also support the utility of microfluidic electrotaxis as a functional output of nematode locomotory circuits in a multitude of contexts. / Thesis / Doctor of Science (PhD)

Cholera toxin (CT) is a bacterial protein toxin responsible for the gastrointestinal disease known as cholera. CT stimulates its own entry into intestinal cells after binding to cell surface receptors. Once internalized, CT is delivered via vesicle-mediated transport to the endoplasmic reticulum (ER), where the CTA1 subunit dissociates from the rest of the toxin and is exported (or translocated) into the cytosol. CTA1 translocates from the ER lumen into the host cytosol by exploiting a host quality control mechanism called ER-associated degradation (ERAD) that facilitates the translocation of misfolded proteins into the cytosol for degradation. Cytosolic CTA1, however, escapes this fate and is then free to activate its target, heterotrimeric G-protein subunit alpha (Gsα), leading to adenlyate cyclase (AC) hyperactivation and increased cAMP concentrations. This causes the secretion of chloride ions and water into the intestinal lumen. The result is severe diarrhea and dehydration which are the major symptoms of cholera. CTA1’s ability to exploit vesicle-mediated transport and ERAD for cytosolic entry demonstrates a potential link between cholera intoxication and a separate quality control mechanism called the unfolded protein response (UPR), which up-regulates vesicle-mediated transport and ERAD during ER stress. Other toxins in the same family such as ricin and Shiga toxin were shown to regulate the UPR, resulting in enhanced intoxication. Here, we show UPR activation by CT, which coincides with a marked increase in cytosolic CTA1 after 4 hours of toxin exposure. Drug induced-UPR activation also increases CTA1 delivery to the cytosol and increases cAMP concentrations during intoxication. We investigated whether CT stimulated UPR activation through Gsα or AC. Chemical activation of Gsα induced the UPR and increased CTA1 delivery to the cytosol. However, AC activation did iv not increase cytosolic CTA1 nor did it activate the UPR. These data provide further insight into the molecular mechanisms that cause cholera intoxication and suggest a novel role for Gsα during intoxication, which is UPR activation via an AC-independent mechanism

<p> Cellular cholesterol homeostasis is a fundamental and highly regulated process. Transcription factors known as sterol regulatory element binding proteins (SREBP) are responsible for the expression of many genes involved in the uptake and biosynthesis of cholesterol. SREBP activation and lipid dysregulation has been associated with cellular endoplasmic reticulum (ER) stress and the activation of the unfolded protein response (UPR). Our lab has previously reported a relationship between ER stress and SREBP activation causing lipid dysregulation and hepatic steatosis. This project was designed to elucidate the mechanism of ER stress-induced SREBP activation and determine its relationship with cellular pathologies associated with ER stress and lipid accumulation. My research has examined the mechanism by which ER stress activates SREBP-2 in various cell lines, including epithelial and macrophage cells. This research revealed that (1) ER stress-induced SREBP-2 activation is not dependent on caspases and occurs through the conventional sterol-mediated proteolytic pathway; (2) the mechanism of ER stress-induced SREBP-2 activation is sensitive to changes in ER calcium; (3) ER stress is associated with SREBP-2 activation and lipid dysregulation in a model of renal injury; and ( 4) ER stress-induced SREBP activation in vitro is not associated with lipid accumulation in macrophage foam cells. </P> <p> This project has also offered me the opportunity to further enhance our understanding of the mechanism by which ER stress causes SREBP activation in a sterolindependent manner. </P> / Thesis / Doctor of Philosophy (PhD)

<p>Atherosclerosis is a chronic inflammatory disease of the arterial wall and is the primary cause of coronary artery disease, the most common cause of death in western societies. Risk factors for cardiovascular disease include dyslipidemia, diabetes, smoking, and obesity. These risk factors have also been shown to promote vascular endoplasmic reticulum (ER) stress; a cellular response characterized by the accumulation of misfolded proteins in the ER. Thickening and decreased stability of arterial plaque can lead to thrombosis and subsequent clinical complications of myocardial infarction and stroke. However, the exact mechanisms that lead to the development of atherosclerosis remain unclear. Here we show that inhibition, as well as a deficiency of glycogen synthase kinase (GSK)-3α, can protect against accelerated atherosclerosis in a low-density lipoprotein receptor (LDLR) knockout mouse model. Compared to LDLR^-/- controls, mice deficient in GSK-3α showed a decrease in lesion volume in the aortic root as well as protection against diet-induced hepatic steatosis. In addition, necrotic core volume was significantly reduced in LDLR^-/-GSK-3α^-/- mice compared to controls, a characteristic indicative of advanced plaque formation. Furthermore, hepatic and vascular ER stress levels were unaffected by the deletion of GSK-3α, a result that is consistent with the hypothesis that GSK-3α functions downstream of ER stress. Macrophages isolated from GSK-3α deficient mice had a reduction in unesterified cholesterol accumulation as well as a significant increase in the expression of the anti-inflammatory cytokine IL-10. Finally, BMT experiments showed a significant decrease in plaque size in the aortic sinus of LDLR^-/-GSK-3α^+/+ mice transplanted with GSK-3α deficient bone marrow. These results demonstrate a possible link between ER stress-induced activation of GSK-3α and the downstream effects leading to atherogenic initiation and progression.</p> / Master of Science (MSc)