Protein phosphorylation is a common post-translational protein modification used in almost all cellular processes. When a phosphate group is added to an amino acid side chain, it may alter the protein conformation and protein-protein interactions due to its size and its negative charge. It may also change the protein function, activity and even localization within the cell. Experimental detection of phosphorylation is still extremely labor demanding and very expensive, even when deploying protein mass spectrometry. For this very reason many bioinformatics scientific groups focus on the prediction of protein phosphorylation sites. Recent analyses of phosphorylation sites studied mainly non-phosphorylated phosphorylation sites and the distribution and representation of amino acids sequentially neighboring them. Since sequentially more distant, but structurally close amino acids can contribute to the recognition of protein substrate by protein kinase, structural environment of phosphorylation sites was studied in this thesis. Furthermore, 3D structures of phosphorylation sites were comprehensively studied for the first time in a phosphorylated state and the results were compared with the results obtained from the analysis of non- phosphorylated sites. Phosphorylation sites were found mostly within...

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Functional analysis of Spr1057 protein Streptococcus pneumoniae The genome of important human pathogen Streptococcus pneumoniae encodes a single gene of an eukaryotic type serine/threonine protein kinase StkP. Analysis of the global transcriptome of a mutant strain with inactivated stkP gene identified spr1057 gene whose expression was significantly repressed in ∆stkP strain. This gene is coding for Spr1057 protein which is a member of haloacid dehalogenase family. The analysis of the substrate specifity of the Spr1057 protein confirmed nucleotidase activity of this protein in vitro. To study the function of this protein in vivo we prepared several mutant S. pneumoniae strains. Growth characterictics of mutant strains were observed in the presence of modified nucleotides, 5-fluoro-2'-deoxyuridine (5-FdU) and 5-bromo-2'-deoxyuridine (5-BrdU). In addition, we monitored the rate of incorporation of 5-BrdU into the chromosomal DNA of the mutant strains in comparison with the wild type S. pneumoniae strain. The growth of the Δspr1057 strain was significantly inhibited in the presence of the modified nucleotides and increased incorporation of 5-BrdU in DNA was showed. Neither growth inhibition nor incorporation of 5-BrdU in DNA was observed for the wild type strain. The expression of an ectopic copy of spr1057...

<p>The proline-rich tyrosine kinase (Pyk2) together with focal adhesion kinase (FAK) define a family of non-receptor protein tyrosine kinases that are regulated by diverse stimuli. Activation of Pyk2 has been implicated in multiple signaling events, including modulation of ion channels, activation of MAP kinase cascades and apoptotic cell death. This thesis investigates the role of Pyk2 in the regulation of mitogenic signals and cell cytoskeleton.</p><p>We identified a hematopoietic isoform of Pyk2 (designated Pyk2-H)that is generated by alternative RNA splicing and is mainly expressed in thymocytes, B cells and natural killer cells. In addition, we demonstrated that engagement of antigen receptors in lymphocytes leads to rapid tyrosine phosphorylation of Pyk2-H suggesting a potential role in host immune responses. These findings were corroborated by defects in B cell-mediated immune responses of Pyk2-/- mice. </p><p>Several reports have previously indicated that Pyk2 acts as an upstream regulator of ERK and JNK MAP kinase cascades in response to numerous extracellular signals. Which MAP kinase pathway is activated by Pyk2 depends on arrays of effector proteins associated with Pyk2. We proposed a model where the formation of Pyk2-Src complexes results in phosphorylation of Shc, p130Cas and Pyk2. This creates binding sites for the SH2 domains of adaptor proteins Grb2 and Crk, which in turn recruit exchange factors for Ras and Rho GTPases that specifically activate ERK or JNK.</p><p>Integration of signaling pathways initiated by receptor tyrosine kinases and integrins is essential for growth factor-mediated biological responses. We described neuronal cellular models where activation of both growth factor receptors and integrins is required for neurite outgrowth. In these cells, Pyk2 and FAK associate with integrin-linked complexes containing EGF receptors via their C- and N-terminal domains. Inhibition of Pyk2/FAK functions was sufficient to block neurite outgrowth and effectors of the C-terminal domain of Pyk2/FAK, including paxillin, were shown to regulate neurite outgrowth independently of ERK/MAP kinase in these cells. We thus proposed that Pyk2 and FAK play important roles in signal integration proximal to the integrin-growth factor receptor complexes.</p>

<p>Although it has been estimated that protein histidine phosphorylation account for about 6 % of the protein phosphorylation in eukaryotic cells; the knowledge of histidine phosphorylation and dephosphorylation is still limited. Lately, studies have appeared of a mammalian 14-kDa phospho- histidine phosphatase, also named protein histidine phosphatase and molecular cloning have provided some information of its physiological role. The object of the present study was to detect the protein expression of protein histidine phosphatase, PHPT1, in mouse tissue, by using immunohistochemistry. Tissue samples from a 4-week-old mouse (heart, liver, kidney, lung, muscle, and spleen), 5-month-old mouse (testis and intestinal), 8-month-old mouse (uterus) and an embryo from 14.5 days old mouse were obtained and processed for light microscopic examination. An absorption test was also made to confirm the specificity of the antibody. The results reveal that PHPT1 is mainly expressed in epithelium, heart- and skeletal muscle. These results provide new evidences for the understanding of the function of eukaryotic histidine phosphorylation and dephosphorylation.</p><p>KEYWORDS</p><p>Phosphohistidine, dephosphorylation, protein histidine phosphatase, phosphohistidine phosphatase, protein phosphorylation</p>

Die vakuoläre Protonen-ATPase, kurz V-ATPase, ist ein multimerer Enzymkomplex, der in fast jeder eukaryotischen Zelle zu finden ist und den aktiven elektrogenen Transport von Protonen über Membranen katalysiert. Die Aktivität der V-ATPase ist essentiell für eine Vielzahl physiologischer Prozesse. Ein grundlegender Mechanismus zur Regulation der V-ATPase-Aktivität ist die reversible Dissoziation des Holoenzyms in den integralen VO-Komplex, der als Protonenkanal dient, und den cytosolischen V1-Komplex, der ATP hydrolysiert und somit den Protonentransport energetisiert. Die Untereinheit C, die im dissoziierten Zustand der V-ATPase als einzige Untereinheit isoliert im Cytoplasma vorliegt, scheint bei der Bildung des aktiven Holoenzyms eine Schlüsselrolle zu übernehmen. In den Speicheldrüsen der Schmeißfliege Calliphora vicina ist die V-ATPase an der Speichelsekretion beteiligt. In den sekretorischen Zellen wird die Bildung des V-ATPase-Holoenzyms in der apikalen Plasmamembran durch das Neurohormon Serotonin (5-HT) stimuliert. Der Effekt von 5-HT auf die V-ATPase wird intrazellulär durch die Proteinkinase A (PKA) vermittelt und hält nur für die Dauer der Stimulierung an. In der vorliegenden Arbeit wurde mittels Phosphoproteinfärbungen und 2D-Elektrophorese nachgewiesen, dass infolge einer Stimulierung der Drüsenzellen mit 5-HT die Untereinheit C der V-ATPase durch die PKA reversibel phosphoryliert wird. Die Phosphorylierung geht einher mit einer Umverteilung der Untereinheit C aus dem Cytoplasma zur apikalen Plasmamembran und der Bildung des aktiven Holoenzyms. Immuncytochemische Untersuchungen zeigten, dass die katalytische Untereinheit der PKA ebenfalls umverteilt wird und in stimulierten Zellen im Bereich der apikalen Plasmamembran konzentriert vorliegt. Um herauszufinden welche Proteinphosphatase der PKA entgegenwirkt, wurden luminale pH-Messungen durchgeführt und der Effekt von spezifischen Proteinphosphatase-Inhibitoren und veresterten Komplexbildnern zweiwertiger Kationen auf die V-ATPase-Aktivität untersucht. Diese Messungen führten zu der Schlussfolgerung, dass eine Proteinphosphatase des Typs 2C an der Inaktivierung der V-ATPase beteiligt ist. Mit weiteren Phosphoproteinfärbungen konnte gezeigt werden, dass die Dephosphorylierung der Untereinheit C ebenfalls durch eine Proteinphosphatase 2C katalysiert wird und dies vermutlich die Dissoziation des VO- und V1-Komplexes begünstigt. Darüber hinaus konnte durch luminale pH-Messungen und ergänzende biochemische Untersuchungen eine Calcineurin-vermittelte Modulation des cAMP/PKA-Signalweges durch den parallel aktivierten IP3/Ca2+-Signalweg und damit einhergehend eine Beeinflussung der V-ATPase-Aktivität durch den [Ca2+]-Spiegel nachgewiesen werden. / The vacuolar-type H+-ATPase (V-ATPase) is a multimeric enzyme that can be found in nearly every eukaryotic cell. It catalyses the active electrogenic transport of protons across membranes and is essential for a multitude of physiological processes. A fundamental mechanism to regulate V-ATPase activity is the reversible dissociation of the holoenzyme into an integral proton conducting VO-complex and a cytosolic V1-complex that hydrolyses ATP and thus energises proton translocation. Subunit C occurs isolated in the cytoplasm upon dissociation of the V-ATPase complexes and seems to be critical for the formation of active holoenzymes. In the salivary glands of the blowfly Calliphora vicina the V-ATPase is involved in fluid secretion. In secretory cells, formation of the V-ATPase holoenzyme is stimulated by the hormone serotonin (5-HT). The effect of 5-HT on V-ATPase activity is mediated by protein kinase A (PKA) and persists for the duration of the 5-HT stimulus. In this study, it was shown by phosphoprotein stainings and two-dimensional electrophoresis that subunit C of the V-ATPase becomes phosphorylated by PKA upon exposure of blowfly salivary glands to 5-HT. Parallel to the phosphorylation event, subunit C translocates from the cytoplasm to the apical plasma membrane for the assembly of active V-ATPase holoenzymes. Using immunofluorescence staining, it could be shown that PKA catalytic subunit translocates as well to the apical membrane upon 5-HT stimulation. To examine which protein phosphatase counteracts PKA, luminal pH-measurements were carried out. Based on the results with protein phosphatase inhibitors and esterified chelating agents of bivalent cations, it may be concluded that a protein phosphatase 2C is involved in the process leading to V-ATPase inactivation. Phosphoprotein stainings revealed that dephosphorylation of subunit C is likewise catalysed by a protein phosphatase 2C. Therefore the dephosphorylation of subunit C seems to promote dissociation of VO- and V1-complexes. Finally, luminal pH-measurements and supplemental biochemical experiments revealed a Ca2+/calcineurin-mediated modulation of the cAMP/PKA signalling cascade and an influence of intracellular calcium on the V-ATPase activity.

The proline-rich tyrosine kinase (Pyk2) together with focal adhesion kinase (FAK) define a family of non-receptor protein tyrosine kinases that are regulated by diverse stimuli. Activation of Pyk2 has been implicated in multiple signaling events, including modulation of ion channels, activation of MAP kinase cascades and apoptotic cell death. This thesis investigates the role of Pyk2 in the regulation of mitogenic signals and cell cytoskeleton. We identified a hematopoietic isoform of Pyk2 (designated Pyk2-H)that is generated by alternative RNA splicing and is mainly expressed in thymocytes, B cells and natural killer cells. In addition, we demonstrated that engagement of antigen receptors in lymphocytes leads to rapid tyrosine phosphorylation of Pyk2-H suggesting a potential role in host immune responses. These findings were corroborated by defects in B cell-mediated immune responses of Pyk2-/- mice. Several reports have previously indicated that Pyk2 acts as an upstream regulator of ERK and JNK MAP kinase cascades in response to numerous extracellular signals. Which MAP kinase pathway is activated by Pyk2 depends on arrays of effector proteins associated with Pyk2. We proposed a model where the formation of Pyk2-Src complexes results in phosphorylation of Shc, p130Cas and Pyk2. This creates binding sites for the SH2 domains of adaptor proteins Grb2 and Crk, which in turn recruit exchange factors for Ras and Rho GTPases that specifically activate ERK or JNK. Integration of signaling pathways initiated by receptor tyrosine kinases and integrins is essential for growth factor-mediated biological responses. We described neuronal cellular models where activation of both growth factor receptors and integrins is required for neurite outgrowth. In these cells, Pyk2 and FAK associate with integrin-linked complexes containing EGF receptors via their C- and N-terminal domains. Inhibition of Pyk2/FAK functions was sufficient to block neurite outgrowth and effectors of the C-terminal domain of Pyk2/FAK, including paxillin, were shown to regulate neurite outgrowth independently of ERK/MAP kinase in these cells. We thus proposed that Pyk2 and FAK play important roles in signal integration proximal to the integrin-growth factor receptor complexes.

Protein phosphorylation is one of the major post-translational modifications to allow for signal transmission and fine tuning of metabolism on the cellular proteomic level. As such it is “one of the last instances” to modulate the activity of enzymes and hence to impact the cellular life irrespective of the basic conditions provided by the genome – and epigenome– controlled gene expression. The evolutionary increase in cellular complexity is reflected by highly sophisticated regulatory networks in multicellular eukaryotes based on the transfer of phosphate mostly onto the side chains of serine, threonine and tyrosine residues. Nature has chosen phosphate for inter- and intracellular communication, which is also an integral component of nucleic acids and can be regarded as the molecule of choice for life. Currently, life science is interested to unravel the network of reversible protein phosphorylation that is catalyzed by two antagonistic enzyme classes: the protein kinases and protein phosphatases. We are currently in the era of proteomics and enormously benefit from the progress of mass-spectrometry methods. This is documented by a huge number of “proteomic studies” that mostly provide a simple inventory of the existence of proteins – and/or their phosphorylated forms – under more or less defined conditions. So far, the physiological correlations could be established only in a few cases, e.g. by comparing two physiological conditions. Another strategy, which was addressed in this work, is the systematic screening of mutants defective in genes encoding either protein kinases or protein phosphatases. This approach benefits from the ease to predict these enzymes due to the presence of characteristic protein motifs. In combination with the major goal of this work – to shed light on the impact of protein phosphorylation in the mitochondrial (mt) compartment – the yeast Saccharomyces cerevisiae was chosen as a model system because of its respiro-fermentative metabolism, that allows for the maintenance of respiratory defective mutants. Indeed, this reverse genetic approach successfully revealed two kinases (Pkp1p, Pkp2p) and two phosphatases (Ppp1p, Ppp2p) as the key components regulating the pyruvate dehydrogenase complex by phosphorylation of serine 313 of its α- subunit Pda1p. In addition, evidence is provided that Pkp1p has an additional role in the assembly process of the PDH complex. Also, the effect of the deletion of the COQ8 gene (gene engaged in coenzyme Q synthesis; originally named ABC1) leading to respiratory deficiency, could be correlated with the phosphorylation of subunit Coq3p of the mitochondrial ubiquinone biosynthesis complex. Finally, in the case of the kinase Sat4p (protein involved in salt tolerance), overexpression of the enzyme was used as an alternative approach to unravel the molecular basis of the originally observed salt sensitivity of sat4 mutants. The data suggest that Sat4p has a direct or indirect role in the late steps of iron-sulfur (Fe/S) cluster assembly of the so-called “aconitase-type” enzymes in mitochondria, accompanied by a strongly reduced steady state concentration of the Fe/S-cluster protein aconitase. Interestingly, a secondary phenotype became apparent upon overexpression of Sat4p: the abundance of the lipoic acid containing mitochondrial proteome was markedly reduced. Most likely this phenotype is due to the fact that the synthesis and/or attachment of lipoic acid depend on a Fe/S-cluster bearing enzyme. In the course of the work it became clear that the regulatory (mt) protein phosphorylation network of yeast evolved to meet the criteria of a life adapted to the ecological niche on temporarily available sugar rich sources. Clearly, the transfer of the respective data to higher eukaryotes is limited. However, it shows that yeast is primarily an excellent model system for the principal molecular reactions shared with higher eukaryotes. / Phosphorylierungen von Aminosäuren ist eine der verbreitetsten post-translationalen Modifikationen für zelluläre Signalübertragungswege und zur Regulation des Metabolismus auf Proteom-Ebene. Mit der reversiblen Protein-Phosphorylierung eng verbunden ist die unabhängige Modulation der Aktivität von Enzymen ungeachtet der Genom- und Epigenom-basierten Genexpression. Die evolutionäre Zunahme der zellularen Komplexität äußert sich in zunehmend komplexeren Regulations-Netzwerken in mehrzelligen eukaryotischen Organismen basierend auf dem Transfer von Phosphatgruppen vorzugsweise auf die Aminosäuren Serin, Threonin und Tyrosin. Die Natur hat evolutionär als Baustein der inter- und intrazellulären Kommunikation Phosphat gewählt, welches auch ein integraler Bestandteil der Nukleinsäuren ist und somit als das „Molekül der Wahl“ für das Leben bezeichnet werden darf. Die Lebenswissenschaften sind gegenwärtig daran interessiert das Netzwerk der Proteinphosphorylierung aufzuklären, welches durch zwei antagonistisch wirkende Enzymklassen, die Proteinkinasen und Proteinphosphatasen charakterisiert ist. Dabei profitieren wir gegenwärtig von den Fortschritten der „Proteomics-Ära“ auf dem Gebiet der massenspektrometrischen Proteinidentifizierung. Ausdruck dessen ist eine Vielzahl von Proteom-Studien, die jedoch meist nur eine einfache Inventarisierung der unter mehr oder weniger gut definierten zellulären Bedingungen existierenden Proteine in ihrer Phosphat-modifizierten oder unphosphorylierten Form darstellen. Die beteiligten Enzyme werden dabei kaum berücksichtigt. Insbesondere gilt dies für extra-cytoplasmatische Ereignisse. Bisher gelang es nur in wenigen Fällen eine Korrelation der physiologischen Rolle dieser Proteinmodifikation, z.B. durch den Vergleich der Phospho-Proteome unter zwei unterschiedlichen physiologischen Bedingungen, herzustellen. Eine andere Strategie, die auch Gegenstand dieser Arbeit ist, sieht ein Screening von Mutanten vor, die durch Deletionen von Genen, die für Proteinkinasen bzw. –phosphatasen kodieren, gekennzeichnet sind. Dieser Ansatz profitiert von der Existenz und leichten bioinformatischen Vorhersagbarkeit charakteristischer Kinase- bzw. Phosphatase- Sequenzmotive. In Kombination mit dem Hauptziel der Arbeit – Licht ins Dunkel der Proteinphosphorylierung im mitochondrialen Kompartiment zu bringen – wurde die Hefe Saccharomyces cerevisiae als Modellsystem gewählt, insbesondere vor dem Hintergrund ihres fermentativen Metabolismus. Als Beleg der prinzipiellen Funktionalität des vorgeschlagenen Ansatzes konnten zwei Kinasen (Pkp1p, Pkp2p) und zwei Phosphatasen (Ppp1p, Ppp2p) als Schlüsselkomponenten der Regulation des Pyruvatdehydrogenase (PDH) Komplexes identifiziert und charakterisiert werden. Darüber hinaus konnte sowohl das Zielprotein der Phosphorylierung, Pda1p, die α-Untereinheit des Komplexes, als auch die modifizierte Aminosäure (Serin 313) experimentell bestätigt werden. Ferner konnte der Atmungsdefekt von Stämmen mit einer nicht-funktionellen Abc1p-Kinase mit dem Phosphorylierungszustand der Untereinheit Coq3p des Ubiquinon-Biosynthese Komplexes und dem Ausfall der Ubiquinonsynthese korreliert werden. Eine alternative Herangehensweise, die Überexpression einer Kinase, führte zur Identifizierung möglicher Zielproteine von Sat4p. Vergleichende Analysen des 2D-gelelektrophoretisch separierten mitochondrialen Genoms mit dem des Wildtyps legen die Vermutung nahe, dass Sat4p eine direkte oder indirekte Rolle bei der Regulation der „Aconitase-Typ“ Eisen-Schwefel (Fe/S) Proteine besitzt. Der darüber hinaus beobachtete Effekt einer Abnahme von Liponsäure-tragenden mitochondrialen Enzymen, ist wahrscheinlich sekundärer Natur und kann durch die Zugehörigkeit der Liponsäure-Synthase zur oben erwähnten Gruppe der „Aconitase-Typ“ -Fe/S-Proteine erklärt werden. Im Verlauf der Arbeit wurde deutlich, dass das regulatorische Netzwerk der Proteinphosphorylierung der Hefe eher den Kriterien einer evolutionären Adaptation an eine spezifische ökologische Nische – der temporären Verfügbarkeit zuckerreicher Substanzen – entsprechen. Das schränkt die Übertragbarkeit der gewonnen Einsichten in die Regulation des mitochondrialen Metabolismus auf höhere Eukaryonten ein. Es zeigt jedoch, dass Hefe in erster Linie ein exzellentes Modellsystem für die prinzipiellen molekulare Mechanismen ist, die sie mit den höheren Eukaryonten teilt.

Storage starch is synthesized in sub-cellular organelles called amyloplasts in higher plants. The synthesis of the starch granule is a result of the coordinated activity of several groups of starch biosynthetic enzymes. There are four major groups of these enzymes, ADP-glucose pyrophosphorylase (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDE). Starch phosphorylase (SP) exists as both dimeric and tetrameric forms in plastids in developing cereal endosperm and catalyses the reversible transfer of glucosyl units from glucose-1-phosphate to the non-reducing end of α-1-4 linked glucan chains, although the precise role in the pathway remains unclear. The present study was conducted to investigate the role and regulation of SP and SSIV in starch biosynthesis in developing maize endosperm. The results of this study showed that the tetrameric form of SP accounts for the majority of measurable catalytic activity, with the dimeric form being barely active and the monomer catalytically inactive. A catalytically active recombinant maize SP was heterologously expressed and used as an affinity ligand with amyloplast lysates to test protein-protein interactions in vitro. Results showed that the different multimeric status of SP influenced interactions with other enzymes of starch synthesis. Tetrameric SP interacted with SBEI and SSIIa, whilst the dimeric form of the enzyme interacted with SBEI, SBEIIb. All of these interactions were enhanced when amyloplasts were pre-treated with ATP, and broken following treatment with alkaline phosphatase (APase), indicating these interactions are regulated by protein phosphorylation. In addition, the catalytic activity of SSIV was reduced following treatment with APase, indicating a role for protein phosphorylation in the regulation of SSIV activity. Protein-protein interaction experiments also suggested a weak interaction between SSIV and SP. Multimeric forms of SP regulated by protein-protein interactions and protein phosphorylation suggested a role for SP in starch biosynthesis in maize endosperm.

Aerobic exercise (AE) may interfere with muscle adaptations induced by resistance exercise (RE). Three experimental campaigns were conducted to explore the influence of AE on molecular, functional and muscular adaptations to acute and chronic RE. Twenty-nine men performed unilateral knee extensor RE preceded by AE (AE+RE). The contralateral leg did RE only. First, the influence of acute AE on muscle molecular responses to RE performed 6 h later was studied. Subsequently, this exercise regimen was implemented over 5 weeks training. The relationships between acute and chronic outcomes were examined and molecular responses to acute exercise were assessed in untrained and trained muscle. Finally, acute and chronic responses to AE+RE, interspersed by only 15 min recovery, were investigated.Phosphorylation of mTOR and p70S6K was greater after AE+RE than after RE. In parallel, myostatin was suppressed for a longer time after AE+RE. These results suggest that AE+RE enhance skeletal muscle anabolic environment more than RE alone (Paper I). After 5 weeks training, improvements in muscle strength and power were similar across legs. However, AE+RE prompted a greater increase in muscle size than RE, suggesting that AE potentiates the hypertrophic stimulus to RE training without altering muscle function progress (Paper II). Consistent with changes in whole-muscle size, AE+RE showed greater anabolic molecular responses than RE. As chronic training blunted this effect, it appears that AE offers a synergistic hypertrophic stimulus to RE only during short-term training (Paper III). Although putative regulators of hypertrophy such as p70S6K, myostatin and PGC-1a4 were examined, no molecular marker correlated with changes in muscle size, strength or power induced by training. Hence, this study challenges the concept that single molecular markers are viable predictors of training-induced muscle adaptations (Paper III–IV). When recovery time between exercise bouts was reduced to 15 min, AE+RE still produced a more substantial increase in muscle size than RE. However, progression of concentric strength was blunted. Thus, while restored muscle function between exercise bouts is a prerequisite for achieving maximal gains in strength and power, incomplete recovery appears not to compromise muscle hypertrophy (Paper V).Collectively, the results suggest that outcomes of AE+RE are impacted by chronic training and time allowed for recovery between exercise modes. Yet, the current study offers no support to the view that AE interferes with muscle hypertrophy induced by RE.