The study of biological interaction networks is a central theme in systems biology. Here, we investigate common as well as differentiating principles of molecular interaction networks associated with different levels of molecular organization. They include metabolic pathway maps, protein-protein interaction networks as well as kinase interaction networks. First, we present an integrated analysis of metabolic pathway maps and protein-protein interaction networks (PIN). It has long been established that successive enzymatic steps are often catalyzed by physically interacting proteins forming permanent or transient multi-enzyme complexes. Inspecting high-throughput PIN data, it has been shown recently that, indeed, enzymes involved in successive reactions are generally more likely to interact than other protein pairs. In this study, we expanded this line of research to include comparisons of the respective underlying network topologies as well as to investigate whether the spatial organization of enzyme interactions correlates with metabolic efficiency. Analyzing yeast data, we detected long-range correlations between shortest paths between proteins in both network types suggesting a mutual correspondence of both network architectures. We discovered that the organizing principles of physical interactions between metabolic enzymes differ from the general PIN of all proteins. While physical interactions between proteins are generally dissortative, enzyme interactions were observed to be assortative. Thus, enzymes frequently interact with other enzymes of similar rather than different degree. Enzymes carrying high flux loads are more likely to physically interact than enzymes with lower metabolic throughput. In particular, enzymes associated with catabolic pathways as well as enzymes involved in the biosynthesis of complex molecules were found to exhibit high degrees of physical clustering. Single proteins were identified that connect major components of the cellular metabolism and hence might be essential for the structural integrity of several biosynthetic systems. Besides metabolic aspects of PINs, we investigated the characteristic topological properties of protein interactions involved in signaling and regulatory functions mediated by kinase interactions. Characteristic topological differences between PINs associated with metabolism, and those describing phosphorylation networks were revealed and shown to reflect the different modes of biological operation of both network types. The construction of phosphorylation networks is based on the identification of specific kinase-target relations including the determination of the actual phosphorylation sites (P-sites). The computational prediction of P-sites as well as the identification of involved kinases still suffers from insufficient accuracies and specificities of the underlying prediction algorithms, and the experimental identification in a genome-scale manner is not (yet) doable. Computational prediction methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding P-sites. However the recognition of such motifs by the respective kinases is a spatial event. Therefore, we characterized the spatial distributions of amino acid residue types around P-sites and extracted signature 3D-profiles. We then tested the added value of spatial information on the prediction performance. When compared to sequence-only based predictors, a consistent performance gain was obtained. The availability of reliable training data of experimentally determined P-sites is critical for the development of computational prediction methods. As part of this thesis, we provide an assessment of false-positive rates of phosphoproteomic data. / Ein zentrales Thema der Systembiologie ist die Untersuchung biologischer Interaktionsnetzwerke. In der vorliegenden Arbeit wurden gemeinsame sowie differenzierende Prinzipien molekularer Interaktionsnetzwerke untersucht, die sich durch unterschiedliche Ebenen der molekulareren Organisation auszeichnen. Zu den untersuchten Interaktionsnetzwerken gehörten Netzwerke, die auf metabolischen Wechselwirkungen, physikalischen Wechselwirkungen zwischen Proteinen und Kinase-Interaktionen aufbauen. Zunächst wird eine integrativen Analyse der metabolischen Pfade und Protein Interaktionsnetzwerke vorgestellt. Es wird seit schon seit langem angenommen, dass aufeinander folgende enzymatische Schritte oft durch permanente oder transiente Multienzymkomplexe, die auf physikalischen Wechselwirkungen der involvierten Proteine basieren, katalysiert werden. Diese Annahme konnte durch die Auswertung von Ergebnissen aus Hochdurchsatz-Experimenten bestätigt werden. Demnach treten aufeinander folgende Enzyme häufiger in physikalische Wechselwirkung als zufällige Enzympaare. Die vorliegende Arbeit geht in ihrer Analyse weiter, in dem die Topologien der zugrundeliegenden Netzwerke, die auf metabolischen und physikalischen Wechselwirkungen basieren verglichen werden und der Zusammenhang zwischen der räumlichen Organisation der Enzyme und der metabolischen Effizienz gesucht wird. Ausgehend von Interaktionsdaten aus Hefe hat die Analyse der auf metabolischen und physikalischen Wechselwirkungen aufbauenden Interaktionswege eine weitgehende Korrelation der Distanzen aufgezeigt und somit eine wechselseitige Übereinstimmung der Architekturen nahegelegt. Allerdings folgen physikalische Wechselwirkungen zwischen metabolischen Enzymen anderen organisatorischen Regeln als Proteininteraktionen im allgemeinem PIN, das alle Proteininteraktionen enthält. Während Proteininteraktionen im allgemeinen PIN sich dissortativ verhalten, sind physikalische Enzyminteraktionen assortativ, d.h. dass die Anzahl der Interaktionen benachbarter Proteine im allgemeinem Netzwerk negativ und im metabolischen Netzwerk positiv korreliert. Ferner scheinen Enzyme von höherem metabolischen Durchsatz häufiger in Wechselwirkungen involviert zu sein. Enzyme der zentralen katabolischen Prozesse sowie der Biosynthese komplexer Membranlipide zeigen dabei einen besonders hohen Verknüpfungsgrad und eine dichte Clusterbildung. Einzelne Proteine wurden identifiziert, die die Hauptkomponenten des zellulären Metabolismus verbinden und so die Integrität verschiedener biosynthetischer Systeme essenziell beeinflussen könnten. Neben dem metabolischen Aspekt der PIN wurde auch der Aspekt der Regulation sowie der Signaltransduktion, der Kinase-Interaktionen, näher analysiert. Dabei wurden charakteristische topologische Unterschiede der mit dem Metabolismus und der Phosphorylierung assoziierten PIN gefunden, die die unterschiedlichen Aufgaben beider Netzwerke widerspiegeln. Die Rekonstruktion von Phosphorylierungs-Netzwerken basiert im Wesentlichen auf der Vorhersage von Kinase-Zielprotein Relationen und kann deshalb immer noch an der nicht genügenden Vorhersagegüte der angewandten Vorhersage-Algorithmen während der Bestimmung von Phosphorylierungsstellen (P-Stellen) und der dazugehörigen Kinasen leiden. Auch die experimentelle, genomweite Bestimmung der P-Stellen ist (noch) nicht durchführbar. Bisherige computergestützte Vorhersagemethoden beruhten für gewöhnlich auf der Auswertung charakteristischer Merkmale der lokalen, die P-Stelle umgebenden Proteinsequenz. Dieser Ansatz wird durch die Verwendung räumlicher 3D-Information in der vorliegenden Arbeit erweitert. Hierbei wird die Verteilung der Aminosäuren um die P-Stelle berechnet und spezifische 3D-Signaturen zur Vorhersage extrahiert. Beim Vergleich mit sequenz-basierten Vorhersagemethoden konnte eine konsistente Verbesserung der Vorhersage durch die Einbeziehung räumlicher Information gezeigt werden. Weiterhin wird in der vorliegenden Arbeit auch der Frage nach der Fehlerrate der experimentellen Phosphoprotein-Daten nachgegangen und ihre Verlässlichkeit bewertet. Die Verfügbarkeit eines verlässlichen Datensatzes ist bei der Entwicklung einer Vorhersagemethode ein entscheidendes Kriterium.

The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.

Higher plants cannot move to a more favorable place when the environmental conditions are changing. To adapt to changes in light, temperature and access to water the plants had to evolve special mechanisms at the molecular level. Post-translational modifications of proteins, like phosphorylation, often serve as “on-and-off” switches in regulation of cellular activity and may affect protein-protein interactions. Photosynthesis in higher plants is regulated by reversible protein phosphorylation events, in a unique light- and redox-controlled system. Several biochemical methods are effectively used for characterization of phosphorylated proteins in photosynthetic membranes. Nevertheless, mass spectrometry is the most effective technique when it comes to identification of exact phosphorylation site(s) in the protein sequence, which is the ultimate evidence of protein phosphorylation. The same tandem mass spectrometry analysis identifies other in vivo post-translational modifications as well, such as acetylation of the N-terminus of mature protein. To study membrane proteins is a challenging project. In the present work the “shaving” of surface-exposed part of the membrane proteins, where phosphorylation occur, is used. In combination with mass spectrometry, this technique does not require the use of radioactive labeling or antibodies. The present work in spinach and Arabidopsis thaliana has identified and characterized several known phosphoproteins, new phosphorylation sites in well-known photosynthetic proteins, as well as two phosphoproteins previously unknown to be present in the photosynthetic membrane. Several photosystem II (PSII) core proteins become phosphorylated in their N-termini (D1, D2, CP43, PsbH), process involved in the regulation of the repair cycle of photo-damaged PSII complexes. The protein-protein interactions between PSII and its light harvesting complex (LHCII) seem to be affected by phosphorylation events in the interface area. In higher plants, phosphorylation sites have been identified in LHCII polypeptides, in one of the proteins (CP29) present in the interface area, as well as in the peripheral TSP9 protein. The TSP9 protein is unique among photosynthetic phosphoproteins, since it is a plant-specific soluble protein that becomes triple-phosphorylated in the middle part of the protein. It is also shown that photosystem I (PSI) is subjected to protein phosphorylation. The extrinsic PSI subunit PsaD becomes phosphorylated in its N-terminus. In addition, the latest characterized subunit of PSI, PsaP, is identified as a phosphoprotein. PsaP is an intrinsic protein assembled on the same side of the PSI complex as LHCII attaches. Several kinases are involved in phosphorylation of photosynthetic proteins, some more specific to PSII core proteins whereas others recognize LHCII proteins better. The STN8 kinase does not phosphorylate LHCII proteins, but is involved in the phosphorylation of the PSII core proteins D1, D2, CP43 and PsbH. STN8 is light-activated and is also specific in phosphorylation of threonine-4 (Thr-4) in the PsbH protein, but only after another kinase has phosphorylated Thr-2 first. A common feature of all kinases in plant photosynthetic membranes is the specificity for Thr residues and that the phosphorylation reactions occur in the N-terminal sequence of the proteins, except for the TSP9 protein. Nowadays, research is on the way to solve the complex network of regulation of photosynthetic activity via protein phosphorylation, but far more efforts are needed to get a complete view of the importance of all phosphorylation events and enzymatic specificity.

The precise mechanism regulating focal adhesion disassembly has yet to be elucidated. Recently, we have implicated the Ste20-like kinase SLK in mediating efficient focal adhesion turnover and cell migration in a Rac-1 and FAK-dependent manner. Although an indirect association of this kinase with the microtubule network has been determined, the exact involvement of SLK in the disassembly of the adhesion complex remains unclear. With the identification of the focal adhesion protein paxillin as a substrate of SLK, we show that SLK regulates adhesion turnover through its phosphorylation at S250. Mutation of S250 to a threonine residue ablates SLK phosphorylation of paxillin in vitro and results in reduced adhesion turnover and migration in vivo. Additionally, our studies demonstrate that overexpression of the paxillin S250T mutation prevents the redistribution of paxillin to the membrane ruffle in migrating cells. The complete loss of polyubiquitylation in the S250T mutant, combined with no observed reduction in S250T protein expression, suggests that S250 phosphorylation is required for a ubiquitin-mediated modification that regulates paxillin redistribution within the cell. Moreover, we show that phosphorylation of S250 is required for paxillin to interact with FAK. An observed accumulation of phospho-FAKY397 in cells overexpressing the paxillin S250T mutant suggests that phosphorylation of S250 is involved in regulating FAK-dependent focal adhesion dynamics. Consequently, our data suggests that SLK regulates adhesion turnover through the phosphorylation of paxillin at S250.

Triacylglycerols are the predominant molecules of energy storage in eukaryotes. Triacylglycerol synthesis is catalyzed by acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes, DGAT1 and DGAT2. Although the use of molecular tools, including targeted disruption of either DGAT enzyme, has shed light on their metabolic functions, little is known about the mechanisms responsible for regulating DGAT activity. Several lines of evidence from previous studies have suggested that DGAT1, but not DGAT2, is subject to regulation by phosphorylation and that protein kinase A (PKA)-dependent pathways are likely involved. In this study, the role of PKA in regulating DGAT activity and triacylglycerol synthesis during lipolysis was investigated. By using 3T3-L1 adipocytes, in vitro DGAT activity was shown to increase 2 fold during lipolysis. This data suggests that PKA might phosphorylate and activate DGAT1 during lipolysis to promote the recycling/re-esterification of excessive free fatty acids into triacylglycerols before they reach toxic levels within the cell. Additionally, high-performance liquid chromatography electrospray ionization mass spectrometry/mass spectrometry was exploited to identify PKA phosphorylation sites of DGAT1, and serine-17, -20 and -25 were identified as potential PKA phosphorylation sites using this methodology. The functional importance of these three potential phosphorylation sites was examined. Mutations of these sites to alanines (to prevent phosphorylation) or aspartates (to mimic phosphorylation) gave rise to enzymes functioning similarly to wild-type DGAT1. These phosphorylation sites appeared to be functionally silent as they were not involved in regulating DGAT1 activity, multimer formation, or enzyme stability. However, PKA phosphorylation at these three sites seemed to play a role in affinity of DGAT1 for its diacylglycerol substrate. These results indicate the existence of other unidentified, functionally active PKA phosphorylation sites or phosphorylation sites of other kinases, which are involved in regulating DGAT1.

DNA double-strand breaks (DSBs) are a threat to cell survival and genome integrity. In addition to canonical DNA repair systems, DSBs can be converted to telomeres by telomerase. This process, herein termed telomere healing, endangers genome stability since it usually results in chromosome arm loss. Therefore, cells possess mechanisms that prevent the untimely action of telomerase on DSBs. In this work, I reported the completion of a transposon mutagenesis screen in budding yeast and the identification of five novel genes (RRD1, CIK1, CTF18, RTS1, and IRC6) critical for telomere healing. The characterization of Rrd1 led to the surprising finding that Rrd1 facilitates telomere healing at DSBs with little or no TG-rich sequences but not at DSBs with long tracts of telomeric sequences. Pph3, a PP4 phosphatase, acts in conjunction with Rrd1 to promote telomere healing. Conversely, Mec1, the ATR ortholog, phosphorylates Cdc13 on its S306 residue to suppress its accumulation at DSBs. Rrd1 and Pph3 oppose Cdc13 S306 phosphorylation and are necessary for the efficient accumulation of Cdc13 at DSBs. Next, I found that Cik1 and its kinesin partner Kar3 are both important for telomere healing. Importantly, Kar3 contributes to telomere healing through its motor function. In contrast to Rrd1, Kar3 contributes to telomere healing regardless of telomeric sequence lengths adjacent to the break. Finally, Cik1 and Kar3 have a general role in DNA repair and physically associate with DSBs, which is dependent on the process of anchoring DSBs to nuclear periphery. In conclusion, I identified a mechanism by which the ATR family of kinases enforces genome integrity, a phosphoregulatory loop that underscores the contribution of Cdc13 to the fate of DNA ends, and a kinesin complex critical for the spatial organization of DNA repair.

The research was designed to investigate the effects of AIT-082, a derivative of the purine hypoxanthine containing a para-amino benzoic acid moiety, on neural cells. AIT-082 has been shown to possess a number of neurotrophic and neuroprotective properties and to enhance memory. Furthermore, AIT-082 is undergoing clinical trials as a potential treatment for Alzheimers disease.<p>The first part of the study investigated the ability of AIT-082 to influence cellular ATP levels in cortical neurons. Decreased energy metabolism is a key point in Yings (Ying, 1996a) theory of the development of Alzheimers disease. Previous work with AIT-082 had shown that it could protect hippocampal neurons from cellular damage caused by sublethal doses of glutamate. Specifically, AIT-082 prevented neurite degeneration. Also, AIT-082 was shown to increase mitochondrial membrane potential, especially at the distal tips of the neurites, in hippocampal neurons. I hypothesized that AIT-082 was protecting the neurons by increasing the ability of the mitochondria to generate ATP and thereby increasing the amount of ATP available to the cell. ATP was collected and measured from cortical neuron cultures that were exposed to glutamate, AIT-082, glutamate and AIT-082. The ATP levels were compared to the ATP levels from cortical neuron cultures that were exposed to vehicle for glutamate and AIT-082. The results did not significantly increase ATP levels in cortical neurons following glutamate exposure. <p>The next set of experiments involved investigations into the ability of AIT-082 to influence phosphorylation events in neural cells. AIT-082 shares some neurotrophic and neuroprotective properties with a group of drugs called the immunophilin ligands. The neuroprotective properties of the immunophilin ligands are mainly due to their ability to influence protein phosphorylation by inhibiting the activity of calcineurin a protein phosphatase. The first set of experiments used western blot techniques to measure serine peptide and threonine peptide phosphorylation levels in proteins from whole brain homogenates that were incubated with vehicle, AIT-082, and GMP. Both AIT-082 and GMP caused an increase in the level of serine peptide phosphorylation compared to vehicle but only the increase caused by GMP treatment proved to be significant. Further, threonine phosphorylation levels were significantly increased by GMP but not AIT-082. Phosphorylation levels of short peptide sequences containing either a phosphorylated serine or threonine residue were also measured in neuronal and astrocytic cultures. The neuronal cultures were exposed to 4 h of hypoxia to mimic the conditions of reduced energy availability observed in Alzheimers disease brains. Astrocyte cultures were exposed to 4 h of hypoxia/ischemia for the same reason. Both cell types were allowed to recover for 0, 1, 4, 12 and 24 hours with or without AIT-082 following the insult. AIT-082 treatment did not significantly affect phosphorylation levels of proteins harvested from either neuron or astrocyte cultures at any time period. I conclude therefore, that AIT-082 is not able to influence phosphorylation of the short amino acid sequences containing phosphorylated serine or threonine residues that could be detected by the primary antibodies used in my experiments.

The research was designed to investigate the effects of AIT-082, a derivative of the purine hypoxanthine containing a para-amino benzoic acid moiety, on neural cells. AIT-082 has been shown to possess a number of neurotrophic and neuroprotective properties and to enhance memory. Furthermore, AIT-082 is undergoing clinical trials as a potential treatment for Alzheimers disease.<p>The first part of the study investigated the ability of AIT-082 to influence cellular ATP levels in cortical neurons. Decreased energy metabolism is a key point in Yings (Ying, 1996a) theory of the development of Alzheimers disease. Previous work with AIT-082 had shown that it could protect hippocampal neurons from cellular damage caused by sublethal doses of glutamate. Specifically, AIT-082 prevented neurite degeneration. Also, AIT-082 was shown to increase mitochondrial membrane potential, especially at the distal tips of the neurites, in hippocampal neurons. I hypothesized that AIT-082 was protecting the neurons by increasing the ability of the mitochondria to generate ATP and thereby increasing the amount of ATP available to the cell. ATP was collected and measured from cortical neuron cultures that were exposed to glutamate, AIT-082, glutamate and AIT-082. The ATP levels were compared to the ATP levels from cortical neuron cultures that were exposed to vehicle for glutamate and AIT-082. The results did not significantly increase ATP levels in cortical neurons following glutamate exposure. <p>The next set of experiments involved investigations into the ability of AIT-082 to influence phosphorylation events in neural cells. AIT-082 shares some neurotrophic and neuroprotective properties with a group of drugs called the immunophilin ligands. The neuroprotective properties of the immunophilin ligands are mainly due to their ability to influence protein phosphorylation by inhibiting the activity of calcineurin a protein phosphatase. The first set of experiments used western blot techniques to measure serine peptide and threonine peptide phosphorylation levels in proteins from whole brain homogenates that were incubated with vehicle, AIT-082, and GMP. Both AIT-082 and GMP caused an increase in the level of serine peptide phosphorylation compared to vehicle but only the increase caused by GMP treatment proved to be significant. Further, threonine phosphorylation levels were significantly increased by GMP but not AIT-082. Phosphorylation levels of short peptide sequences containing either a phosphorylated serine or threonine residue were also measured in neuronal and astrocytic cultures. The neuronal cultures were exposed to 4 h of hypoxia to mimic the conditions of reduced energy availability observed in Alzheimers disease brains. Astrocyte cultures were exposed to 4 h of hypoxia/ischemia for the same reason. Both cell types were allowed to recover for 0, 1, 4, 12 and 24 hours with or without AIT-082 following the insult. AIT-082 treatment did not significantly affect phosphorylation levels of proteins harvested from either neuron or astrocyte cultures at any time period. I conclude therefore, that AIT-082 is not able to influence phosphorylation of the short amino acid sequences containing phosphorylated serine or threonine residues that could be detected by the primary antibodies used in my experiments.

DNA double-strand breaks (DSBs) are a threat to cell survival and genome integrity. In addition to canonical DNA repair systems, DSBs can be converted to telomeres by telomerase. This process, herein termed telomere healing, endangers genome stability since it usually results in chromosome arm loss. Therefore, cells possess mechanisms that prevent the untimely action of telomerase on DSBs. In this work, I reported the completion of a transposon mutagenesis screen in budding yeast and the identification of five novel genes (RRD1, CIK1, CTF18, RTS1, and IRC6) critical for telomere healing. The characterization of Rrd1 led to the surprising finding that Rrd1 facilitates telomere healing at DSBs with little or no TG-rich sequences but not at DSBs with long tracts of telomeric sequences. Pph3, a PP4 phosphatase, acts in conjunction with Rrd1 to promote telomere healing. Conversely, Mec1, the ATR ortholog, phosphorylates Cdc13 on its S306 residue to suppress its accumulation at DSBs. Rrd1 and Pph3 oppose Cdc13 S306 phosphorylation and are necessary for the efficient accumulation of Cdc13 at DSBs. Next, I found that Cik1 and its kinesin partner Kar3 are both important for telomere healing. Importantly, Kar3 contributes to telomere healing through its motor function. In contrast to Rrd1, Kar3 contributes to telomere healing regardless of telomeric sequence lengths adjacent to the break. Finally, Cik1 and Kar3 have a general role in DNA repair and physically associate with DSBs, which is dependent on the process of anchoring DSBs to nuclear periphery. In conclusion, I identified a mechanism by which the ATR family of kinases enforces genome integrity, a phosphoregulatory loop that underscores the contribution of Cdc13 to the fate of DNA ends, and a kinesin complex critical for the spatial organization of DNA repair.

The precise mechanism regulating focal adhesion disassembly has yet to be elucidated. Recently, we have implicated the Ste20-like kinase SLK in mediating efficient focal adhesion turnover and cell migration in a Rac-1 and FAK-dependent manner. Although an indirect association of this kinase with the microtubule network has been determined, the exact involvement of SLK in the disassembly of the adhesion complex remains unclear. With the identification of the focal adhesion protein paxillin as a substrate of SLK, we show that SLK regulates adhesion turnover through its phosphorylation at S250. Mutation of S250 to a threonine residue ablates SLK phosphorylation of paxillin in vitro and results in reduced adhesion turnover and migration in vivo. Additionally, our studies demonstrate that overexpression of the paxillin S250T mutation prevents the redistribution of paxillin to the membrane ruffle in migrating cells. The complete loss of polyubiquitylation in the S250T mutant, combined with no observed reduction in S250T protein expression, suggests that S250 phosphorylation is required for a ubiquitin-mediated modification that regulates paxillin redistribution within the cell. Moreover, we show that phosphorylation of S250 is required for paxillin to interact with FAK. An observed accumulation of phospho-FAKY397 in cells overexpressing the paxillin S250T mutant suggests that phosphorylation of S250 is involved in regulating FAK-dependent focal adhesion dynamics. Consequently, our data suggests that SLK regulates adhesion turnover through the phosphorylation of paxillin at S250.