No description available.

No description available.

The study of DNA templated events is not complete without considering the chromatin environment. Histone modifications help to regulate gene expression, chromatin compaction and DNA replication. Because DNA damage repair must occur within the context of chromatin, many remodeling enzymes and histone modifications work in concert to enable access to the DNA and aid in restoration of chromatin after repair is complete. CK2 has recently been identified as a histone modifying enzyme. In this study we identify CK2 as a histone H3 tail kinase in vitro, identify the phospho-acceptor site in vitro, and characterize the modification in vivo in S. cerevisiae. We also characterize the DNA damage phenotype of a strain lacking a single catalytic subunit of CK2. We further characterize the CK2- dependent phosphorylation of serine 1 of histone H4 in vivo. We find that it is recruited directly to the site of a DSB and this recruitment requires the SIN3/RPD3 histone deacetylase complex. We also characterize the contribution of H4 serine 1 phosphorylation in chromatin compaction by using reconstituted nucleosomal arrays to study folding in the analytical ultracentrifuge.

No description available.

Die LAMMER-Kinasen sind Dual-Spezifität-Proteinkinasen, die durch das namensgebende einzigartige LAMMER-Motiv gekennzeichnet sind. Sie sind evolutionär hoch konserviert und in den meisten Eukaryonten vorhanden. Die vorliegende Arbeit stellt die erste funktionelle Charakterisierung eines bisher kaum erforschten Vertreters der LAMMER-Proteinkinase Familie Kns1 aus der Bäckerhefe dar. Phänotypische Analysen belegten eine entscheidende Rolle für Kns1 in der Regulation der Toleranz gegenüber basischem pH-Stress. Das Entfernen des KNS1 Gens führte zu einer gesteigerten Empfindlichkeit der Zellen gegenüber basischen Wachstumsbedingungen. Weitere Analysen zeigten, dass Kns1 neben der katalytischen Aktivität auch nicht-katalytischen Mechanismen zur Förderung des Zellwachstums unter alkalischem pH-Stress nutzt. Die Reinigung des Kns1 Proteins in voller Länge aus E. coli ermöglichte die Identifizierung von neun in vitro-Autophosphorylierungsstellen mittels Massenspektrometrie. Die Mutation von Thr562, eine Autophosphorylierungsstelle innerhalb des LAMMER-Motivs, zu Alanin ergab in vitro eine Kinase mit intrinsischer katalytischer Aktivität, die sich jedoch in vivo hauptsächlich wie die katalytisch inaktive Kns1-Mutante verhielt. Die Calcium/Calmodulin-abhängige Proteinkinase II Cmk2, die konstitutiv autokatalytische Eigenschaften besitzt, wurde früher als mögliches in vitro Substrat von Kns1 vorgeschlagen. In dieser Arbeit beweise ich durch Verwendung einer katalytisch inaktiven Cmk2-Mutante als Substrat, dass Kns1 Cmk2 in vitro phosphoryliert. Darüber hinaus zeige ich, dass Cmk2 die basische pH-Toleranz der Zellen beschränkt. Gestützt durch genetische Hinweise agieren beide Proteine gemeinsam bei der Regulation der alkalischen Stresstoleranz, wobei Kns1 möglicherweise Cmk2 herabreguliert. Zusammenfassend beschreibt diese Arbeit eine neue und entscheidende Rolle von Kns1 und Cmk2 bei der Anpassung der Hefe an alkalisches Milieu. / The LAMMER protein kinases, termed after a unique signature motif found in their catalytic domains, are an evolutionary conserved family of dual-specificity kinases that are present in most eukaryotes. Here I report the first functional characterization of one of the most unexplored members of the LAMMER family, the budding yeast Kns1. Phenotypic analysis uncovered a crucial role for Kns1 in the control of the yeast tolerance to high pH stress. Deletion of the KNS1 gene conferred high sensitivity to alkaline pH, whereas its overexpression increased tolerance to this stress. Further analysis established that Kns1 promotes growth under alkaline pH stress using not only its catalytic activity but also non-catalytic mechanisms. Large-scale purification of full-length Kns1 from E. coli allowed for the identification of nine in vitro autophosphorylation sites on Kns1 by mass spectrometry. Mutation of the threonine residue at position 562, an autophosphorylation site located within the LAMMER motif, to a non-phosphorylatable residue yielded a kinase that preserves intrinsic catalytic activity in vitro but mostly behaves like the catalytically inactive mutant in vivo. This finding showed the physiological importance of autophosphorylation site Thr562 in the regulation of Kns1 function. The protein Cmk2, a calcium/calmodulin-dependent protein kinase II with autocatalytic properties, has been previously proposed as a possible in vitro substrate for Kns1. Here I demonstrate that Kns1 phosphorylates Cmk2 in vitro using a catalytically inactive Cmk2 mutant as substrate and show that Cmk2 restricts alkaline tolerance. Genetic evidence suggested that both proteins act in concert on a common pathway, in which Kns1 may downregulate Cmk2 to confer alkaline tolerance. In conclusion, this thesis describes a novel and crucial role for Kns1 and its in vitro substrate Cmk2 in the adaptation of yeast to alkaline stress.

Synaptic long-term modifications following neuronal activation are believed to be at the origin of learning and long-term memory. Recent experiments suggest that these long-term synaptic changes are all-or-none switch-like events between discrete states of a single synapse. The biochemical network involving calcium/calmodulin-dependent protein kinase II (CaMKII) and its regulating protein signaling cascade has been hypothesized to durably maintain the synaptic state in form of a bistable switch. Furthermore, it has been shown experimentally that CaMKII and associated proteins such as protein kinase A and calcineurin are necessary for the induction of long-lasting increases (long-term potentiation, LTP) and/or long-lasting decreases (long-term depression, LTD) of synaptic efficacy. However, the biochemical mechanisms by which experimental LTP/LTD protocols lead to corresponding transitions between the two states in realistic models of such networks are still unknown. We present a detailed biochemical model of the calcium/calmodulin-dependent autophosphorylation of CaMKII and the protein signaling cascade governing the dephosphorylation of CaMKII. As previously shown, two stable states of the CaMKII phosphorylation level exist at resting intracellular calcium concentrations. Repetitive high calcium levels switch the system from a weakly- to a highly phosphorylated state (LTP). We show that the reverse transition (LTD) can be mediated by elevated phosphatase activity at intermediate calcium levels. It is shown that the CaMKII kinase-phosphatase system can qualitatively reproduce plasticity results in response to spike-timing dependent plasticity (STDP) and presynaptic stimulation protocols. A reduced model based on the CaMKII system is used to elucidate which parameters control the synaptic plasticity outcomes in response to STDP protocols, and in particular how the plasticity results depend on the differential activation of phosphatase and kinase pathways and the level of noise in the calcium transients. Our results show that the protein network including CaMKII can account for (i) induction - through LTP/LTD-like transitions - and (ii) storage - due to its bistability - of synaptic changes. The model allows to link biochemical properties of the synapse with phenomenological 'learning rules' used by theoreticians in neural network studies.

No description available.

Synaptic long-term modifications following neuronal activation are believed to be at the origin of learning and long-term memory. Recent experiments suggest that these long-term synaptic changes are all-or-none switch-like events between discrete states of a single synapse. The biochemical network involving calcium/calmodulin-dependent protein kinase II (CaMKII) and its regulating protein signaling cascade has been hypothesized to durably maintain the synaptic state in form of a bistable switch. Furthermore, it has been shown experimentally that CaMKII and associated proteins such as protein kinase A and calcineurin are necessary for the induction of long-lasting increases (long-term potentiation, LTP) and/or long-lasting decreases (long-term depression, LTD) of synaptic efficacy. However, the biochemical mechanisms by which experimental LTP/LTD protocols lead to corresponding transitions between the two states in realistic models of such networks are still unknown. We present a detailed biochemical model of the calcium/calmodulin-dependent autophosphorylation of CaMKII and the protein signaling cascade governing the dephosphorylation of CaMKII. As previously shown, two stable states of the CaMKII phosphorylation level exist at resting intracellular calcium concentrations. Repetitive high calcium levels switch the system from a weakly- to a highly phosphorylated state (LTP). We show that the reverse transition (LTD) can be mediated by elevated phosphatase activity at intermediate calcium levels. It is shown that the CaMKII kinase-phosphatase system can qualitatively reproduce plasticity results in response to spike-timing dependent plasticity (STDP) and presynaptic stimulation protocols. A reduced model based on the CaMKII system is used to elucidate which parameters control the synaptic plasticity outcomes in response to STDP protocols, and in particular how the plasticity results depend on the differential activation of phosphatase and kinase pathways and the level of noise in the calcium transients. Our results show that the protein network including CaMKII can account for (i) induction - through LTP/LTD-like transitions - and (ii) storage - due to its bistability - of synaptic changes. The model allows to link biochemical properties of the synapse with phenomenological 'learning rules' used by theoreticians in neural network studies.

La localisation de l'ARNm est un mécanisme post-transcriptionnel régulant l'expression des gènes qui donne un contrôle précis sur la production spatiale et temporelle des protéines. Des milliers de transcrits dans un large éventail d'organismes ou de types cellulaires se sont avérés localisés dans un compartiment sous-cellulaire spécifique. La levure bourgeonnante Saccharomyces cerevisiae est l'un des organismes modèle les plus étudiés pour comprendre le processus de localisation de l'ARNm. Plus de trente ARNm sont activement transportés et localisés à l'extrémité du bourgeon de la levure bourgeonnante. Dans cet organisme, la localisation des transcrits à l'extrémité du bourgeon, tels que l'ARNm ASH1, dépend de la protéine de liaison à l'ARN She2, qui interagit directement avec les éléments de localisation dans ces ARNm durant leur transcription. She2 est une protéine liant l’ARN non-canonique, qui s’assemble en tétramère pour pouvoir lier l’ARN. Lorsque le complexe ARNm-She2 est exporté vers le cytoplasme, celui-ci interagit avec la protéine She3 et la myosine Myo4, qui transportent le complexe vers le bourgeon. Une fois qu'un ARNm est correctement localisé, sa traduction est activée pour permettre la synthèse locale de sa protéine. Les mécanismes régulant la localisation des ARNm sont encore très peu connus. Cependant, plusieurs évidences suggèrent que la machinerie de localisation peut être régulée par des modifications post-traductionnelles. Dans notre étude, en utilisant une colonne de purification de phosphoprotéines, nous avons constaté que She2 est une phosphoprotéine. Nous avons utilisé une approche de phosphoprotéomique pour identifier les résidus phosphorylés dans She2 in vivo. Nous avons identifié plusieurs nouveaux phosphosites qui affectent la capacité de She2 à favoriser l'accumulation asymétrique de la protéine Ash1. Fait intéressant, plusieurs phosphosites sont présents aux interfaces de dimérisation et de tétramérisation de She2. En nous concentrant sur la position T109, nous montrons qu'un mutant phosphomimétique T109D inhibe l'interaction She2-She2 et diminue l'interaction de She2 avec ses cofacteurs Srp1, She3 et l’ARNm ASH1. Fait intéressant, la mutation T109D réduit considérablement l'expression de She2 et perturbe la localisation de l'ARNm ASH1. Nos résultats montrent que le contrôle de l'oligomérisation de She2 par phosphorylation représente un mécanisme qui régule la localisation de l'ARNm dans la levure bourgeonnante. Dans le but d’identifier la ou les kinases impliquées dans la phosphorylation de She2, nous avons recherché des motifs de reconnaissance de kinases connues parmi les phosphosites que nous avons identifiés. Nous avons trouvé que les résidus T109, S217 et S224 font partie de sites putatifs de la Caséine kinase II (CKII), suggérant que ces positions seraient susceptibles d'être phosphorylés par cette kinase. Un essai de phosphorylation in vitro a révélé que She2 est phosphorylée par CKII au niveau des résidus S217 et S224, mais pas au résidu T109. Nous avons montré que la phosphorylation de la forme monomérique de She2 par CKII in vitro est augmentée par rapport à la forme sauvage tétramérique. De plus, nous avons observé que le domaine C-terminal de She2, qui contient sa séquence de localisation nucléaire (NLS) est phosphorylé par CKII. Cependant, le rôle de la phosphorylation dans le NLS de She2 demeure inconnu. Dans l'ensemble, nos résultats montrent que les modifications post-traductionnelles sur She2 régulent la localisation de l'ARNm chez la levure. Cette étude permettra d'élucider les mécanismes de contrôle de la localisation de l'ARNm chez la levure et comment des modifications post-traductionnelles sur She2 régulent ce processus. / mRNA localization is a post-transcriptional mechanism regulating gene expression that gives precise control over the spatial and temporal production of proteins. Thousands of transcripts in a wide array of organisms or cell types were shown to localize to specific subcellular compartments. The budding yeast Saccharomyces cerevisiae serves as one of the best model organisms to study the mechanisms of mRNA localization. Over thirty transcripts are actively transported and localized at the bud tip of the budding yeast. In this organism, localization of transcripts to the bud tip, such as the ASH1 mRNA, depends on the RNA-binding protein She2, which is responsible for recognizing localization elements in these mRNAs during transcription. She2 is a non-canonical RNA-binding protein which assembles as a tetramer in order to bind RNA. When the mRNA-She2 complex is exported to the cytoplasm, the protein She3 and myosin Myo4 join the complex to transport it to the bud. Once an mRNA is properly localized, its translation is generally activated to allow the local synthesis of its protein. The mechanisms regulating the localization of mRNAs are still poorly known. Still, several pieces of evidence suggest that post-translational modifications may regulate the localization machinery. Using a phosphoprotein purification column, we found that She2 is a phosphoprotein. We used a phosphoproteomic analysis to identify the phosphorylated residues in She2 in vivo. We identified several new phosphosites that impact the capacity of She2 to promote the asymmetric accumulation of Ash1. Interestingly, several of these phosphosites are present at the dimerization and tetramerization interfaces of She2. Focusing on T109, we show that a phosphomimetic mutant T109D inhibits She2-She2 interaction and decreases the interaction of She2 with its co-interactors Srp1, She3 and ASH1 mRNA. Interestingly, the T109D mutation significantly reduces the expression of She2 and disrupts ASH1 mRNA localization. Altogether, our results show that the control of She2 oligomerization by phosphorylation represents a mechanism that regulates mRNA localization in budding yeast. In order to identify which kinase(s) are involved in She2 phosphorylation, we searched for known kinases recognition motifs among the identified phosphosites. We found that T109, S217 and S224 are putative Casein kinase II (CKII) sites, suggesting that this kinase may phosphorylate these residues. Indeed, an in vitro phosphorylation assay revealed that She2 is phosphorylated by CKII at S217 and S224 but not at T109. We found that the phosphorylation of a monomeric She2 mutant by CKII in vitro is increased compared to the wild-type tetrameric protein. Furthermore, we found that the C-terminal domain of She2, which contains its nuclear localization signal (NLS), is phosphorylated by CKII. However, the biological function of the phosphorylation in the NLS is still unknown. Altogether, our results show that post-translational modifications in She2 regulate mRNA localization in yeast. This study will help elucidate the mechanisms that control mRNA localization in yeast and how post-translational modifications in She2 regulate this process.

Indiana University-Purdue University Indianapolis (IUPUI). / Calcium/calmodulin-dependent protein kinase II (CaMKII) is a critical modulator of synaptic function, plasticity, and learning and memory. In neurons and astrocytes, CaMKII regulates cellular excitability, cytoskeletal structure, and cell metabolism. A rapid increase in CaMKII activity is observed within the first few minutes of ischemic stroke in vivo; this calcium-dependent process is also observed following glutamate stimulation in vitro. Activation of CaMKII during pathological conditions is immediately followed by inactivation and aggregation of the kinase. The extent of CaMKII inactivation is directly correlated with the extent of neuronal damage. The studies presented here show that these fluctuations in CaMKII activity are not correlated with neuronal death; rather, they play a causal role in neuronal death. Pharmacological inhibition of CaMKII in the time immediately surrounding glutamate insult protects cultured cortical neurons from excitotoxicity. Interestingly, pharmacological inhibition of CaMKII during excitotoxic insult also prevents the aggregation and prolonged inactivation of the kinase, suggesting that CaMKII activity during excitotoxic glutamate signaling is detrimental to neuronal viability because it leads to a prolonged loss of CaMKII activity, culminating in neuronal death. In support of this, CaMKII inhibition in the absence of excitotoxic insult induces cortical neuron apoptosis by dysregulating intracellular calcium homeostasis and increasing excitatory glutamate signaling. Blockade of the NMDA-receptors and enzymatic degradation of the extracellular glutamate signal affords neuroprotection from CaMKII inhibition-induced toxicity. Co-cultures of neurons and glutamate-buffering astrocytes also exhibit this slow-induced excitotoxicity, as CaMKII inhibitors reduce glutamate uptake within the astrocytes. CaMKII inhibition also dysregulates calcium homeostasis in astrocytes and leads to increased ATP release, which was neurotoxic when applied to naïve cortical neurons. Together, these findings indicate that during aberrant calcium signaling, the activation of CaMKII is toxic because it supports aggregation and prolonged inactivation of the kinase. Without CaMKII activity, neurons and astrocytes release stores of transmitters that further exacerbate neuronal toxicity.