Indiana University-Purdue University Indianapolis (IUPUI) / The Ca2+ pump or Ca2+-ATPase of cardiac sarcoplasmic reticulum, SERCA2a, is regulated by phospholamban (PLB), a small inhibitory phosphoprotein that decreases the apparent Ca2+ affinity of the enzyme. We propose that PLB decreases Ca2+ affinity by stabilizing the Ca2+-free, E2·ATP state of the enzyme, thus blocking the transition to E1, the high Ca2+ affinity state required for Ca2+ binding and ATP hydrolysis. The purpose of this dissertation research is to critically evaluate this idea using series of cross-linkable PLB mutants of increasing inhibitory strength (N30C-PLB < PLB3 < PLB4). Three hypotheses were tested; each specifically designed to address a fundamental point in the mechanism of PLB action. Hypothesis 1: SERCA2a with PLB bound is catalytically inactive. The catalytic activity of SERCA2a irreversibly cross-linked to PLB (PLB/SER) was assessed. Ca2+-ATPase activity, and formation of the phosphorylated intermediates were all completely inhibited. Thus, PLB/SER is entirely catalytically inactive. Hypothesis 2: PLB decreases the Ca2+ affinity of SERCA2a by competing with Ca2+ for binding to SERCA2a. The functional effects of N30C-PLB, PLB3, and PLB4 on Ca2+-ATPase activity and phosphoenzyme formation were measured, and correlated with their binding interactions with SERCA2a measured by chemical cross-linking. Successively higher Ca2+ concentrations were required to both activate the enzyme co-expressed with N30C-PLB, PLB3, and PLB4 and to dissociate N30C-PLB, PLB3, and PLB4 from SERCA2a, suggesting competition between PLB and Ca2+ for binding to SERCA2a. This was confirmed with the Ca2+ pump mutant, D351A, which is catalytically inactive but retains strong Ca2+ binding. Increasingly higher Ca2+ concentrations were also required to dissociate N30C-PLB, PLB3, and PLB4 from D351A, demonstrating directly that PLB competes with Ca2+ for binding to the Ca2+ pump. Hypothesis 3: PLB binds exclusively to the Ca2+-free E2 state with bound nucleotide (E2·ATP). Thapsigargin, vanadate, and nucleotide effects on PLB cross-linking to SERCA2a were determined. All three PLB mutants bound preferentially to E2 state with bound nucleotide (E2·ATP), and not at all to the thapsigargin or vanadate bound states. We conclude that PLB inhibits SERCA2a activity by stabilizing a unique E2·ATP conformation that cannot bind Ca2+.

PURPOSE: Muscle overuse is characterized by inflammation, reduced strength and muscle damage. It has been proposed that calcium (Ca2+) accumulation during muscle contraction, is responsible for muscle damage. Muscle contractile properties are regulated by calcium regulatory excitation contraction coupling mechanisms. Therefore, the main aim of the present study was to investigate the effects of voluntary repetitive tasks during six weeks on the rate of sarcoplasmic reticulum (SR) Ca2+-uptake, and Ca2+-release, in young female Sprague-Dawley rats. Secondly, this study aims to evaluate the effect of the training on muscular strength and the relationship between SR Ca2+-kinetics and grip strength test performance. METHODS: Six rats were trained (EXP), using a well-established model of reaching and handle pulling with the upper extremities (2 hr/day, 3days/week, 6 weeks), six control rats (KON) were included that were not exposed to the task. Grip strength were evaluated using a grip strength meter for rodents, two weeks prior the training was initiated, and two days after the training period was concluded. Tissue samples were obtained from the supraspinatus and trapezius muscle, and the rate of SR Ca2+-uptake and SR Ca2+-release were analysed using the fluorescent Ca2+ indicator indo 1. RESULTS: The analysis revealed that EXP had a significant higher rate of SR Ca2+-uptake, in both supraspinatus (33%, P &lt; 0,05) and trapezius (14%, P &lt; 0,05), compared to KON. However, no significant differences in SR Ca2+-release rate were found between groups, in neither of the muscles. A decline in grip strength were found in both EXP and KON, with no significant differences between groups. No significant correlation between grip strength and the Ca2+ release uptake variables could be found. CONCLUSION: The present results suggests that repetitive voluntary reaching and handle pulling with the upper extremities during six weeks, induce extant changes in SR Ca2+-uptake rate in rats.

published_or_final_version / abstract / Biochemistry / Master / Master of Philosophy

Abstract ORIENTIA TSUTSUGAMUSHI ANKYRIN REPEAT-PROTEIN FAMILY TARGETING OF THE HOST ENDOPLASMIC RETICULUM By Lauren VieBrock, B.S. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University Virginia Commonwealth University, 2015 Director: Jason A. Carlyon, Ph.D. Professor Microbiology and Immunology Scrub typhus is an understudied, potentially fatal febrile illness, which poses threat to one billion people annually in the Asia-Pacific region. The host-pathogen interactions that facilitate the intracellular survival of the etiologic agent, Orientia tsutsugamushi, are not well understood. The Orientia tsutsugamushi genome encodes a large number of ankyrin repeat-containing proteins (Anks), key virulence factors for other intracellular pathogens, as well as components for Type I (T1SS) and Type 4 secretion systems (T4SS), commonly used to deliver them. We sought to characterize the roles of the Anks in O. tsutsugamushi infection. In this study, we demonstrated that O. tsutsugamushi expressed all 20 anks and the genes for the T1SS, for which they are substrates. Many ectopically expressed Anks displayed a tropism for the host endoplasmic reticulum (ER). These results suggest the importance of the Anks and the ER to Orientia tsutsugamushi pathobiology. We demonstrated that O. tsutsugamushi tightly associated with the ER and induced ER stress and defects in protein secretion of its host cells. Therefore, we hypothesized that the ER-tropic anks expressed during the initial hours of infection are critical for establishing infection and do so by interacting with specific host cell targets to modulate host cell function to benefit intracellular survival. ER-tropic Ank4 was detected as expressed early in infection and was further characterized for its contribution to the alterations of the ER during infection. Bat3 was identified as a target of Ank4, and Ank4 expression correlated with a decrease in Bat3 protein levels, induction of ER stress, and defects in protein secretion. These effects were Ank4 F-box dependent, implicating polyubiquitination and proteosomal degradation of Bat3. As Ank4 colocalized with Bat3, a chaperone component of ER-associated degradation (ERAD) of misfolded proteins, ERAD function was measured in cells expressing Ank4. In an F-box dependent manner, Ank4 expression resulted in decreased degradation of a model substrate and indicated inhibition of the ERAD pathway. Similarly, we demonstrated that in O. tsutsugamushi infection, Bat3 levels were significantly reduced early in infection and ERAD degradation was inhibited. After several days of infection however, Bat3 levels and ERAD degradation had both recovered, suggesting temporal modulation of ERAD in infection. Taken together, these data suggest that O. tsutsugamushi has a large capacity to disrupt the host ER, exemplified by Ank4 mediated ERAD dysfunction by depletion of host Bat3.

Le Réticulum endoplasmique (RE) est le premier compartiment intracellulaire traversé par les protéines sécrétées. Au sein de cet organite, les protéines acquièrent une conformation native, et subissent de nombreuses modifications post-traductionnelles telles que la N-glycosylation ou la formation de ponts disulfures. Dans certaines conditions (stress réducteurs, hypoxie, privation en glucose…) des protéines anormalement conformées s’accumulent au sein du RE ce qui conduit à l’induction de l'Unfolded Protein Response (UPR). Cette réponse va alors tout d’abord induire l’inhibition de la traduction, ce qui limite l’entrée de nouvelles protéines dans le RE. En parallèle, un programme transcriptionnel spécifique conduit à l’augmentation de l’expression de protéines impliquées dans le repliement et la dégradation des protéines accumulées dans la lumière du RE. Cette réponse adaptative intégrée est contrôlée principalement par 3 protéines transmembranaires du RE : PERK (PKR-related ER kinase), ATF6 (Activating transcription factor) et enfin IRE1 (Inositol requiring kinase 1) sur laquelle porte notre étude. Au cours de ma thèse, j’ai tout d’abord participé à une étude démontrant que l’activation des voies de signalisation dépendantes d’IRE1 contribuait à la surexpression du VEGF-A in vitro et régulait l’angiogenèse et la croissance tumorale in vivo dans un modèle de greffe orthotopique de cellules U87 dérivées de gliomes humains. Cette protéine pourrait donc constituer une cible thérapeutique potentielle. Ces résultats nous ont par conséquent amenés à identifier des modulateurs de l’activité de la protéine IRE1. Pour cela nous avons développé un test in vitro permettant d’évaluer l’étape essentielle dans l’activation de la protéine IRE1, sa dimérisation. Ce test nous a permis d’identifier un peptide capable d’interférer dans la formation des dimères de la protéine IRE1, mais aussi et de façon inattendue, d’accroître son activité endoribonucléase in vitro et in vivo. Ainsi, nous proposons que ce peptide interfacial issu du domaine kinase de la protéine IRE1 pourrait promouvoir un changement conformationnel du domaine cytosolique de la protéine entière et par conséquent, potentialiserait de façon significative son activité endoribonucléasique. Ce modulateur identifié pourrait donc représenter un nouvel outil à potentiel thérapeutique utilisable par exemple dans des maladies conformationnelles. / The endoplasmic Reticulum (ER) is the first intracellular compartment encountered by secretory proteins. In this organelle proteins acquire their correct conformation and undergo many post-translational modifications such as N-glycosylation or disulphide bond formation. Under specific environmental conditions (reductive stress, hypoxia, glucose deprivation …), protein folding is perturbed and uncorrectly folded proteins accumulate in the lumen of the ER. This leads to the activation of an adaptive response named the Unfolded Protein Response (UPR). The UPR consists in an attenuation of protein translation and an activation of a specific transcriptional program. This integrated adaptive response is mediated by 3 transmembrane ER resident proteins: PERK (PKR-related ER kinase), ATF6 (Activating transcription Factor) and IRE1 (Inositol requiring kinase 1) and we focused more particularly on IRE1. During my PhD thesis, I participated to a study that demonstrated the role of IRE1 signaling in the regulation of VEGF expression in vitro and tumor growth and angiogenesis in vivo. The latter was carried out using a ortotopic implantation model of human glioma-derived cells. As a consequence IRE1 could certainly constitute a potential therapeutic target. In an attempt to modulate IRE1 activity, we aimed at identifying artificial modulators of its activity. To this end, we designed an in vitro assay capable of monitoring the first essential step in IRE1 activation process, namely its dimerization. This assay allowed us to identify a peptide able to interfere with IRE1 dimer formation, but, unexpectedly, to also increase its RNAse activity in vitro and in vivo. We propose that this interfacial peptide, derived from IRE1 kinase domain could promote a conformational change in IRE1 cytosolic domain and consequently lead to an increase in its enzymatic activity. This modulator could represent a new tool with therapeutic potential that could then be used in protein misfolding diseases for instance.

Tumor cells often hijack endoplasmic reticulum (ER) mediated signaling to facilitate tumor progression by adapting to the cellular stress evoked by oncogene overexpression and adverse microenvironment. Despite the prevalence of MYC-driven cancers, how the MYC oncoprotein regulates ER stress response pathways during tumorigenesis remains incompletely understood. Here we show that MYC drives continuous upregulation of ubiquitin fusion degradation 1 (UFD1) during T-cell acute lymphoblastic leukemia (T-ALL) development. As the E2 component of an ER-associated degradation (ERAD) complex, UFD1 facilitates the elimination of misfolded/unfolded proteins from the ER. We found that genetic and pharmacological disruption of UFD1 function exacerbates ER stress and activates the unfolded protein response (UPR). Specifically, UFD1 knockdown in human T-ALL cells impairs ERAD and promotes the proapoptotic UPR through the PERK-CHOP-BCL2 axis. This effect is demonstrated by an upregulation of PERK, phospho-PERK and its downstream effector CHOP, as well as a downregulation of BCL2 and BCLxL. Indeed, CHOP inactivation or BCL2 overexpression is sufficient to rescue tumor-cell apoptosis induced by UFD1 knockdown. Allelic loss of ufd1 in zebrafish similarly induces tumor-cell apoptosis and impairs MYC-driven T-ALL progression without affecting general animal health. These studies establish the UFD1-mediated ER stress response as an important mediator of MYC-driven tumor progression and suggest strategies for targeted therapy in T-ALL, and perhaps other MYC-driven cancers. Although UFD1-specific inhibitors have yet to be developed, inhibitors that target the p97 co-factor in UFD1-mediated ERAD are readily available. Importantly, we show that treatment with CB-5083, a selective and oral bioactive inhibitor of p97, can effectively kill human MYC-overexpressing T-ALL patient cells ex vivo and inhibits tumor progression in zebrafish models of MYC-driven T-ALL. Thus, CB-5083 treatment may represent an effective targeted therapy for T-ALL, especially relapsed/refractory ones with gain-of-function NOTCH1 mutations and thus MYC-overexpression.

A imunodeficiência comum variável (CVID) é caracterizada por hipogamaglobulinemia. Anteriormente identificou-se uma paciente com CVID que apresenta nível aumentado de estresse de retículo endoplasmático (ER), secundário a desregulação da via UPR. No presente trabalho, estendemos esta análise para outros pacientes e avaliamos o perfil de maturação de seus linfócitos B. Métodos: Western-blot, RT-PCR, Q-PCR, Citometria de Fluxo e cultura de células B ex vivo e imortalizadas. Resultados: A análise de 16 pacientes com CVID e 9 indivíduos saudáveis revelou três pacientes com porcentagens aumentadas de linfócitos B imaturos no sangue periférico. A análise da expressão de RNAm para BiP e XBP-1 em linfócitos B destes pacientes, após estímulo com LPS in vitro, identificou que os linfócitos B de um deles apresenta estresse de RE. Conclusão: Identificamos um subgrupo de pacientes com CVID que apresentam linfócitos B imaturos no sangue periférico. Um membro deste subgrupo apresenta estresse aumentado de ER. / Common Variable Immunodeficiency (CVID) is characterized by hypogammaglobulinemia. Previously a CVID patient was identified with increased levels of Endoplasmic Reticulum (ER) stress due to dysregulation of the UPR. In the present study these analyses were performed in other patients and healthy donors. Maturation markers of B lymphocytes were also characterized in these individuals. Methods: Western-blot, RT-PCR, Q-PCR, Flow cytometry and culturing of ex vivo and immortalized B cells. Results: The analysis of 16 CVID patients and 9 healthy donors revealed three patients that present higher percentage of immature B cells in peripheral blood. Analysis of expression of BiP and XBP1 induced by LPS treatment of B lymphocytes from these patients revealed that one patient present increased levels of ER stress.

Les bactéries intracellulaires Wolbachia ont développé une vaste gamme d’interactions symbiotiques, du parasitisme reproductif au mutualisme chez les arthropodes terrestres et les nématodes filaires, devenant ainsi les endosymbiotes les plus répandus sur terre. Bien qu’elles se développent lentement dans les cultures cellulaires d’insectes pour lesquelles les marqueurs sont limités et qu’elles ne sont génétiquement pas manipulables, il existe un intéret croissant de déchiffrer leur mode de vie intracellulaire pour 2 raisons. Premièrement, Wolbachia intervient dans le développement et la transmission des arbovirus et deuxièmement, les filarioses lymphatiques sont traitables grâce à la susceptibilité des Wolbachia qui infectent les nématodes filaires aux antibiotiques. Au début de ce projet, j’ai infecté 2 lignées cellulaires de Drosophila melanogaster qui sont transcriptomiquement divergentes par une même souche de Wolbachia pouvant naturellement infecter Drosophila melanogaster. J’ai utilisé ces 2 lignées cellulaires qui sont différentiellement permissive à l’infection pour explorer l’interaction de Wolbachia avec le réticulum endoplasmique. Les observations par microscopie à fluorescence en temps réel et par microscopie électronique prouvent que cet organite est une source de membranes pour Wolbachia et possiblement, une source de nutriments. Pourtant, les analyses d’expression génique et les approches d’immunofluorescence démontrent que Wolbachia n’induit ni un stress au niveau du réticulum endoplasmique ni une protéolyse via la voie de signalisation ERAD suggérant dès lors, que Wolbachia subvertissent d’autres mécanismes pour assurer leur besoin en acides aminés. Au cours de ce projet, j’ai commencé à mettre en place une technique pour transformer Wolbachia par biolistique. La validation de cette technique de transformation a ouvert la voie vers l’optimisation de la procédure de sélection des transformants pour enfin pouvoir génétiquement manipuler Wolbachia. / The intracellular bacteria Wolbachia have developed a wide range of symbiotic interactions, from being opportunistic reproductive parasites to mutualists with terrestrial arthropods and filarial nematode species, making them the most common endosymbionts on earth. The discovery that they interfere with arboviruses development and transmission by mosquito vectors and that filarial diseases can be cured by targeting Wolbachia, have created a strong interest in deciphering the mechanisms underlying their intracellular lifestyle. However, being obligate intracellular endosymbionts, Wolbachia remain genetically intractable. They grow slowly in insect cell cultures, for which markers are limited. Despite these obstacles, and to limit cell line-specific phenotypes, I chose to infect 2 Drosophila melanogaster cell lines presenting different sets of expressed genes, with a unique Wolbachia strain, naturally hosted by Drosophila melanogaster. Using these 2 cell lines that are differently permissive to the infection, I explored the interaction of Wolbachia with the endoplasmic reticulum (ER). Through fluorescence time-lapse confocal and electron microscopy observations, I provide strong evidence that this organelle is the source of membrane for Wolbachia, and possibly a source of nutrients. However, gene expression analyses and immunofluorescence approaches demonstrate that Wolbachia do not induce ER stress nor an increased ERAD- induced proteolysis, suggesting; unlike previously reported, that Wolbachia salvage amino acids by other subversion mechanisms. Additionally, I pioneered biolistic bombardement of Wolbachia-infected cells and the validation of this transformation technique has paved the way towards optimization of transformant selection steps and ultimately to the genetic engineering of Wolbachia.

Organelles sequester biological phenomena within the cell, and allow an additional layer of complexity to life. The presence and maintenance of these organelles is crucial for cellular function. Two of the most expansive and complex organelles are the mitochondria and endoplasmic reticulum. These organelles contribute energy, protein folding and secretion, lipids, calcium regulation, and various other metabolites to the biology of the cell. Importantly, these organelles accumulate damage and cannot be derived de novo, therefore must be inherited and maintained in a functioning state. The study of these organelle quality control processes serves as the basis for my thesis. We use the budding yeast as a model organism to uncover conserved pathways affecting organelle, and ultimately cellular homeostasis. In yeast we find mitochondrial inheritance is critical for cell survival. Furthermore, not only is inheritance critical, but inheritance of a certain threshold of functional mitochondria appears critical in maintaining normal lifespan in yeast, identifying mitochondria as an aging determinant. By examining mutants that negatively affect mitochondrial inheritance in yeast, we established a role for phosphatidylcholine biosynthesis in organelle maintenance and inheritance. Glycerophospholipid biosynthesis plays a clear role not only in mitochondrial inheritance but also in that of the endoplasmic reticulum. We use insights gained from yeast to guide research into a human disease caused by similar glycerophospholipid biosynthetic deficiency.

In eukaryotic cells, proteins continuously flux through the organelles of the secretory pathway in an essential cellular process called protein secretion. This dynamic process originates at the endoplasmic reticulum (ER), where translating ribosomes push linear peptides into the ER membrane and lumen. ER chaperones assist in folding nascent peptides into three-dimensional conformations and proteins are concentrated into membrane-encapsulated vesicles bound for the Golgi apparatus. ER to Golgi transport is mediated by a set of cytosolic coat proteins called COPII. The COPII coat polymerizes into a lattice on the ER membrane that is able to bend the membrane around secretory cargo and bud off a spherical vesicle. Protein secretion is subject to rapid changes as a cell responds to its environment and requirements for viability alter. In addition to accommodating short-term demands, such as translational up-regulation, evolved complexity of secretory proteins over time, has also required that secretory components adapt. In both cases changes in secretory demands require that the COPII proteins have an inherent flexibility to navigate these changes without disrupting secretory flux. In this work I have examined a family of quintessential secretory cargo, p24 proteins, that challenge protein secretion. This family of proteins forms a hetero-tetrameric complex that cycles between the ER and the Golgi and mediates transport of glycosylphosphatidylinositol-anchored proteins (GPI-APs). Here I present evidence that suggests, when present in vesicles, both p24 proteins and their GPI-AP cargo present a challenge to vesicle formation. I posit that three attributes of these proteins present a local barrier to membrane bending: Lumenal asymmetric distribution across the membrane, high cellular abundance and affinity for ceramide rich membranes. I have also elucidated mechanisms that the coat has evolved to accommodate troublesome cargo such as p24 proteins, which enhance structural scaffolding and increase average vesicle size. Finally I present preliminary findings indicating that p24s also contribute to ER homeostasis by preventing aberrant incorporation of proteins into vesicles. Comprehensively, these findings have shed light on the role of p24 proteins in vesicles. Traditionally thought to be canonical ER cargo receptors, these proteins also appear capable of contributing to the composition of the vesicles in which they reside, and impacting trafficking efficiency in two ways: First by directly mediating transport of GPI-APs and second by uniformly packing vesicles to avoid wasteful secretion. My work has contributed to a growing notion in the field that secretory cargo are not inert passengers but active participants in vesicle mediated secretion.