Die Inositol-Pyrophosphate (PP-InsPs) sind eine ubiquitäre Gruppe hochphosphorylierter eukaryotischer Signalmoleküle. Sie werden mit einer Vielzahl zentraler zellulärer Prozesse in Verbindung gebracht, doch fehlt oft ein detailliertes Verständnis der einzelnen Signalereignisse, was zum Teil auf einen Mangel an chemischen Werkzeugen zurückzuführen ist. Diese Arbeit beschreibt die chemische Synthese, Validierung und Anwendung von PP-InsP-Affinitätsreagenzien zur Identifizierung von Proteinbindungspartnern von Inositolhexakisphosphat (InsP6) und 5-Diphosphoinositol-Pentakisphosphat (5PP-InsP5), zwei wichtigen eukaryotischen Metaboliten. Die Affinitätsreagenzien wurden entwickelt, um InsP6 und ein metabolisch stabiles 5PP-InsP5-Analogon auf drei verschiedene Arten darzustellen. Die Anwendung dieser triplexierten Reagenzien auf Säugetier-Lysate lieferte einen ersten umfassenden Datensatz in HCT116- und HEK293T-Zellen. Die Interaktome wurden mittels quantitativer Proteomik annotiert und enthüllten Hunderte von potenziellen Proteinbindungspartnern. Die quantitative Analyse der InsP6- und 5PP-InsP5-bindenden Proteine zeigte Beispiele für hochspezifische Protein-Ligand-Interaktionen auf. Biochemische Untersuchungen ergaben, dass Inositol-5-Phosphatasen, PRPS1 und spezifische Phosphatidyl-Inositolphosphat-Kinasen potenziell unentdeckte Zielproteine von PP-InsPs sind. Darüber hinaus wurde durch die Entwicklung einer neuen Strategie der Myo-Inositol-Desymmetrisierung erstmals die Synthese eines Affinitätsreagens auf der Basis von 1,5-Bisdiphosphoinositol-Tetrakisphosphat (1,5(PP)2-InsP4) beschrieben. Die Affinitätsreagenzien und die proteomischen Datensätze stellen für die Gemeinschaft leistungsstarke Ressourcen dar, um künftige Untersuchungen zu den vielfältigen Signalmodalitäten von Inositolpyrophosphaten einzuleiten. / Inositol pyrophosphates (PP-InsPs) are a ubiquitous group of highly phosphorylated eukaryotic messengers. They have been linked to a panoply of central cellular processes, but a detailed understanding of the discrete signaling events is often missing, which can partially be attributed to a lack of chemical tools. This thesis describes the chemical synthesis, validation and application of PP-InsP affinity reagents to identify protein binding partners of inositol hexakisphosphate (InsP6) and 5-diphosphoinositol pentakisphosphate (5PP-InsP5), two important eukaryotic metabolites. The affinity reagents were developed to display InsP6 and a metabolically stable 5PP-InsP5 analog in three different ways. Application of these triplexed reagents to mammalian lysates provided a first comprehensive data set in HCT116 and HEK293T cells. The interactomes were annotated using quantitative proteomics and uncovered hundreds of potential protein binding partners. Quantitative analysis of InsP6 versus 5PP-InsP5 binding proteins highlighted examples of highly specific protein-ligand interactions. Biochemical studies primed inositol 5-phosphatases, PRPS1 and specific phosphatidyl inositol phosphate kinases as potentially undiscovered targets of PP-InsPs. Moreover, by developing a novel strategy of myo-inositol desymmetrization, the synthesis of an affinity reagent based on 1,5-bisdiphosphoinositol tetrakisphosphate (1,5(PP)2-InsP4) was described for the first time. The affinity reagents and the proteomic data sets constitute powerful resources for the community, to help launching future investigations into the multiple signaling modalities of inositol pyrophosphates.

Phosphorus (P) is one of the three major macronutrients that plants need to grow and survive. When P is scarce, plants utilize a network of characterized responses known as the Phosphate Starvation Response (PSR) to remobilize internal stores of P as well as external P from soil. Emerging evidence shows the PSR is regulated by a specialized group of secondary messenger molecules, inositol pyrophosphates (PP-InsP). PP-InsPs and their precursors, inositol phosphates (InsPs), are important for plant abiotic stress responses, hormone signaling, and other stress responses. While PP-InsPs are critical for plant survival, much about the roles of PP-InsPs and how they are regulated remains to be understood. Further, the enzymes responsible for the synthesis of PP-InsPs in plants have been recently discovered; however, not much is known about the enzymes that degrade PP-InsPs in plants. The goal of the work presented herein is to understand critical aspects of the PP-InsP signaling in plants and leverage this information into a P phytoremediation strategy. To achieve this, I have investigated a group of PP-InsP phosphatases and assessed long-term impacts of depleting PP-InsPs in two plant species, Arabidopsis thaliana (Arabidopsis) and Thlaspi arvense (Pennycress). Exploring the impact of plant PP-InsP phosphatases has allowed me to explore critical aspects of PP-InsP sensing that show great promise for informing P remediation strategies. / Doctor of Philosophy / The Phosphorus (P) crisis presents a major challenge to food security. While Phosphorus (P) is critical for crop growth, P is a nonrenewable and increasingly limited resource. Our global population is fed at the expense of the remaining mineable P reserve, which may be depleted in as early as 30 years. Further, fertilizer runoff from farmland and urban areas poses a dangerous problem as increased nutrients in watersheds toxifies our water supply and aquatic ecosystems. Time is running out to preserve our P supply. New and innovative strategies that reduce fertilizer inputs and watershed pollution are key to securing the global food supply and protecting the environment. Emerging evidence shows plants sense and respond to P using signaling molecules known as inositol pyrophosphates (PP-InsPs). My work and that of others are key in showing that alteration of the levels of PP-InsPs can decrease plant P dependency or cause plants to hyperaccumulate P. Understanding how plants are able to sense, respond, and acquire P is crucial to inform future P phytoremediation strategies to secure global food security.

Phosphate (Pi) is an essential nutrient for plants, required for plant growth and seed viability. When Pi is limited, plants undergo dynamic morphological and metabolic changes to leverage available Pi, known as the Phosphate Starvation Response (PSR). The inositol phosphate (InsP) signaling pathway is a crucial element of the plant's ability to regulate the PSR and respond to changing energy conditions. InsPs are synthesized from the cyclic 6-carbon polyol scaffold, myo-inositol. Inositol hexakisphosphate (InsP6) is the most abundant InsP signaling molecule and can be phosphorylated by the multifunctional inositol tetrakisphosphate 1-kinase 1 (ITPK1) and diphosphoinositol pentakisphosphate (VIP) kinases, resulting in inositol pyrophosphates (PP-InsPs). PP-InsPs have high energy bonds and have been linked to Pi maintenance and energy homeostasis in yeast, plants, and mammals. However, the precise mechanism(s) by which PP-InsPs act within plant signaling pathways remains to be determined. Two approaches to understand the role of PP-InsPs in plants are described within this dissertation. The first approach analyzes genetic loss-of-function vip1/vip2 double mutants, and their responses to low Pi conditions. Specifically, vip1/vip2 double mutant gene expression and lipid remodeling patterns in response to low Pi were characterized. We found that vip1-2/vip2-2 had an impacted lipid remodeling response under low Pi conditions, whereas ipk1 had altered lipid composition under Pi-replete conditions. In a complementary approach, a gain-of-function in either the ITPK1 or the kinase domain of VIP (VIP2KD) were constructed in transgenic Arabidopsis thaliana plants. Both ITPK1 and VIP2KD transgenic plants contain elevated levels of the specific inositol pyrophosphate, InsP8. Elevated InsP8 in both types of plants results in changes in growth and senescence phenotypes, delayed time to flowering, Pi accumulation, and altered PSR gene expression. The data from both approaches suggest new roles for PP-InsPs in the regulation of the PSR and other signaling pathways in plants. To enhance my teaching and leadership skills, I participated in the Graduate Teaching Scholars (GTS) program. As a GTS, I worked with the Virginia Tech Research and Extension Experiential Learning (VT-REEL) program where I developed a structured mentorship program for undergraduate and graduate students and created a professional development workshop series. During the COVID-19 pandemic, I developed an online version of the VT-REEL program. Using inclusive pedagogy practices and surveys from the participants, we compiled the best practices for moving a summer undergraduate research program online. These practices come from surveyed participants in the 2020 and provides strategies that can be tailored to various online research experiences and be implemented in both online and in-person formats. / Doctor of Philosophy / Phosphate (Pi) is crucial for plant development and crop yield, but is often limited in soils. Pi-containing fertilizers are often added to supplement soils. Overuse of Pi-containing fertilizers can lead to Pi runoff and can devastate aquatic ecosystems. In addition, Pi is a limited, nonrenewable resource, with U.S. stores projected to be depleted in as little as 30 years. It is now crucial to develop crops that can feed a growing population with less Pi input. Here, we describe how changing levels of plant messenger molecules known as inositol pyrophosphates (PP-InsPs) impact the ability of plants to sense and respond to Pi. This knowledge advances understanding f how mineral nutrient physiology affects many plants traits, and can be harnessed to develop novel strategies to reduce Pi-application and overuse.

The ability for an organism to sense and respond appropriately to its environment is often critical for survival. One mechanism for this is the inositol phosphate (InsP) signaling pathway. This work focuses on the role of InsP signaling in maintaining energy homeostasis in the plant. InsP signaling is connected to energy sensing in plants via a protein complex containing both the inositol polyphosphate 5-phosphatases (5PTase13) and the Sucrose non-Fermenting Related Kinase 1 (SnRK1). SnRK1 is considered a fuel gauge for the plant cell that senses energy status and reprograms growth appropriately. While the SnRK1.1 gene has been well studied, the role other SnRK1 isoforms play in energy or stress signaling is less well understood. This work examined the role of 3 SnRK1 isoforms in energy signaling, finding that SnRK1.1 and SnRK1.2 are regulated and function differently in Arabidopsis. The second part of this work focuses on the inositol pyrophosphates, which are a novel group of InsP signaling molecules containing diphosphate or triphosphate chains (i.e. PPx) attached to the inositol ring. These PPx-InsPs are emerging as critical players in the integration of cellular metabolism and stress signaling in non-plant eukaryotes. Most eukaryotes synthesize the precursor molecule, myo-inositol (1,2,3,4,5,6)-hexakisphosphate (InsP6), which can serve as a signaling molecule or as storage compound of inositol, phosphorus, and minerals. Even though plants produce huge amounts of InsP6 in seeds, almost no attention has been paid to whether PPx-InsPs exist in plants, and if so, what roles these molecules play. This work details the presence of PPx-InsPs in plants and delineates two Arabidopsis gene products (AtVip1 and AtVip2) capable of PP-InsP5 synthesis. We further examined the subcellular location of enzymes connected to PPx-InsP synthesis as well as the developmental and tissue specific patterns of expression of the genes that encode these enzymes. We localized the enzymes involved in InsP6 and PPx-InsP production to the nucleus and endoplasmic reticulum (ER). The subcellular compartmentalization of PPx-InsP signaling may be unique to plants. An increased understanding in the pathways involved in energy sensing and metabolic response may reveal novel strategies to improve crops for yield and viability in the future. / Ph. D.

Inositolpyrophosphate (PP-InsP) sind eine Gruppe sekundärer Signalmoleküle, die in einer Vielzahl zellulärer Prozesse, von Phosphathomeostase über Insulinsignalisierung bis Apoptose eine Rolle spielen. Die Art und Weise, wie PP-InsPs ihre Funktion ausführen, noch weitgehend unbekannt. Deshalb wurden zwei neue analytische Methoden basierend auf Kernspinresonanzspektroskopie und Flüssigchromatographie mit Massenspektrometrie-Kopplung (LCMS) entwickelt. Um die limitierende Sensitivität der Kernresonanzspektroskopie zu umgehen, wurde die Synthese von kernspinresonanzaktivem, 13C-markiertem Inositol optimiert. Des Weiteren wurde eine chemoenzymatische Synthese für alle Säugetier-PP-InsP-Isomere entwickelt, die auf der skalierbaren Ausfällung mittels Mg2+ Ionen basiert. Menschliche Zellen wurden mit 13C-Inositol isotopenmarkiert und in den Spektren der Zellextrakte wurde, basierend auf den PP-InsP-Standards, Fingerabdrucksignale identifiziert mit denen die Konzentrationen der dazugehörigen Moleküle bestimmt werden konnte. Die LCMS basierte Methode wurde auf dem Prinzip der Umsetzung von hochgeladenen Inositolpyrophosphaten zu ihren korrespondieren Methylestern mittels Trimethylsilyldiazomethan geplant. Die ungeladenen, permethylierten PP-InsPs wären geeignet für LC-Auftrennungen und MS-Messungen und sollten eine von Kernspinresonanzspektroskopie nicht erreichbare Sensitivität ermöglichen. Die Methode wurde mittels Inositolhexakisphosphat (InsP6), einem einfacheren PP-InsP-Analog, etabliert und methyliertes InsP6 konnte in Mengen von 10 femtomol detektiert werden. Die Adaption der Methode für die PP-InsPs gestaltete sich jedoch herausfordernd, da der Analyt während der Reaktion zersetzt wurde. Ein Wechsel zu Diazomethan als Methylierungsagens zeigte vielversprechende Resultate. / Inositol pyrophosphates (PP-InsPs) are a well conserved group of second messengers that are involved in a plethora of cellular processes including phosphate homeostasis, insulin signaling, and apoptosis. Despite much effort, it is still mostly unknown how PP-InsPs exert their diverse functions. In order to decipher the mechanisms, researchers have relied either on metabolic labeling with radioactive inositol or on electrophoretic separation on polyacrylamide gels but these methods either lack ease of use or sensitivity. Therefore, two new analytical tools, based on nuclear magnetic resonance (NMR) spectroscopy, and liquid chromatography coupled mass spectrometry (LCMS), were developed. To overcome the limited sensitivity provided by NMR spectroscopy, a high yielding synthesis of NMR-active 13C-labeled inositol was designed and optimized. Furthermore, a chemoenzymatic synthesis of all mammalian PP-InsPs isomers was developed that relied on a scalable purification strategy utilizing precipitation with Mg2+ ions. Human cells were metabolically labeled with 13C-inositol and the prepared PP-InsPs were used as standards to identify peaks in the NMRspectra. These fingerprint signals enabled the quantification of the corresponding molecules. The LCMS-based method was based on the derivatization of the highly charged inositol pyrophosphates to their corresponding methyl esters by trimethylsilyldiazomethane. The permethylated InsPs and PP-InsPs were suitable for LC separation and MS measurement, and provide a sensitivity unmatched by NMR spectroscopy. The method was established using inositol hexakisphosphate, a simpler analog of PP-InsPs, and methylated InsP6 could be detected at quantities as low as 10 femtomole. However, the adaptation of the derivatization for PP-InsPs proved challenging as the reaction caused degradation of the analyte but strategies to circumvent the decay by changing the derivatization agent to diazomethane were promising.

Inositol phosphates play a fundamental role in many intracellular processes. Of particular importance is the role of phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] in the protein kinase B (PKB/Akt) signalling pathway. PtdIns(3,4,5)P3 recruits PKB to the cell membrane through binding interactions with its pleckstrin homology (PH) domain. In several human cancers, this signalling pathway is upregulated, resulting in increased cell growth and proliferation. In order to investigate the therapeutic potential of the PtdIns(3,4,5)P3–PH domain binding interaction, it is necessary to develop inositol phosphate-based probes. This DPhil dissertation highlights the synthesis of a number of derivatives of the PtdIns(3,4,5)P3 head group – inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P4]. These derivatives incorporated phosphate isosteres at both the 3- and 5-positions of Ins(1,3,4,5)P4, through the utilisation of novel protection and deprotection strategies. In addition, this dissertation highlights the efficient synthesis of the natural product inositol 1,3-bisphosphate [Ins(1,3)P2] and our work towards the synthesis of inositol pyrophosphate derivatives.

Inositolpyrophosphate (PP-InsPs) sind eine wichtige Gruppe eukaryotischer Botenstoffe, die mit verschiedenen Prozessen wie Apoptose, Phosphathomeostase und Insulinsignalkaskaden verknüpft sind. Trotz ihrer Entdeckung vor mehr als 20 Jahren bleibt es eine Herausforderung, die Signalmechanismen dieser Moleküle zu verstehen. Ursachen dafür sind der limitierte Zugang zu synthetischen PP-InsPs und ein Mangel an allgemein zugänglichen analytischen Methoden. Daher wurden in dieser Arbeit chemische und analytische Verfahren entwickelt, um unser Verständnis von diesen Molekülen sowohl auf ein biochemischer als auch auf zelluläre Ebene zu verbessern. Um der Knappheit an synthetischen PP-InsPs entgegen zu wirken, wurde eine hocheffiziente chemoenzymatische Synthese entwickelt, bei der mehr als 100 mg aller wesentlichen PP-InsPs aus Säugern hergestellt werden konnten. Parallel wurde ein neues analytisches Werkzeug entwickelt, dass Konzentrationen von PP-InsPs in komplexen Proben quantifizieren konnte. Mittels Enzymkatalyse konnten 13C-markiertes myo-inositol und 13C-markierte PP-InsPs hergestellt werden und niedrige Konzentrationen mit nuklearer Magnetresonanzspektroskopie detektiert werden. In vitro waren diese Verbindungen sehr nützlich, um PP-InsP Kinasen von Pflanzen und Säugern zu charakterisieren. Endogene Konzentrationen von PP-InsPs konnten durch metabolisches Markieren mit 13C-markiertem myo-inositol in humanen Zelllinien quantifiziert werden. Letztendlich wurde mittels eines neuen entwickelten proteomischen Ansatzes endogene Proteinpyrophosphorilierung, eine von PP-InsP eingebaute posttranslationale Proteinmodifikation, in menschlichen Zelllinien zum ersten Mal nachgewiesen. Zusammenfassend haben die aufgelisteten chemischen und analytischen Werkzeuge ein hohes Potenzial unser Verständnis der Signalmechanismen hinter den diversen Phänotypen der PP-InsPs zu stärken und Forschungsarbeit in dieser Richtung zu beschleunigen. / Inositol pyrophosphates (PP-InsPs) are an important group of second messengers that intersect with a wide range of processes in eukaryotic cells including phosphate homeostasis, insulin signaling and apoptosis. Despite their discovery more than two decades ago, elucidating the underlying signaling mechanisms remains a significant challenge. Therefore, a new set of chemical and analytical methods was developed here to improve our understanding of these intriguing molecules on the biochemical and cellular level. To overcome the shortage of synthetic PP-InsPs, a highly efficient and scalable chemoenzymatic approach was designed and the major mammalian PP-InsPs could be obtained in hundreds of milligram quantities and in high purity. In parallel, a new analytical tool was developed to quantify levels of PP-InsPs in complex samples. Chemoenzymatic access to 13C-labeled myo-inositol and 13C-labeled PP-InsPs enabled the detection of low concentrations of PP-InsPs using nuclear magnetic resonance spectroscopy. In vitro, these compounds were of great use for the biochemical characterization of PP-InsPs kinases from mammals and plants. Endogenous pools of PP-InsPs from human cell lines were identified and quantified by metabolic labeling with 13C-labeled myo-inositol. Finally, a new proteomics workflow towards the detection of protein pyrophosphorylation, a posttranslational modification mediated by PP-InsPs, using mass spectrometry was optimized and endogenously modified mammalian proteins could be identified for the first time and with high confidence. Taken together, the chemical and analytical tools presented here have great potential to accelerate the understanding of PP-InsP signaling and metabolism. Access to large amounts of PP-InsPs together with a reliable quantification method and the detection of endogenous protein pyrophosphorylation sites will be essential to unravel the signaling mechanisms underlying the diverse phenotypes associated with these metabolites.

Inositolpolyphosphate (InsPs) bilden eine ubiquitäre Gruppe an hochphosphorylierten, intrazellulären Signalmolekülen in eukaryotischen Zellen. Trotz deren Beteiligung an unzähligen biologischen Prozessen bleibt die Detektion von InsPs (insb. einzelner Enantiomere) eine Herausforderung, da die momentan verfügbaren Analysemethoden immer noch limitiert sind. In der vorliegenden Arbeit wird die stabile Isotopenmarkierung von myo-Inositol (Ins) und InsPs in Kombination mit Kernspinresonanzspektroskopie (engl. Nuclear Magnetic Resonance spectroscopy, NMR) erkundet, um diese Lücke zu schließen. Die Abhängigkeit von NMR-Daten und chemischer Struktur erlaubte die Analyse komplexer Mixturen aus InsPs aus in vitro-Experimenten und biologischen Proben. Durch stereospezifische 13C-Markierung konnten sogar Enantiomere voneinander unterschieden werden. Mit Hilfe dieser Methode wurden mehrere InsP-Stoffwechselwege untersucht. Als Erstes wurde das menschliche, Phytase-artige Enzym MINPP1 (engl. Multiple Inositol Polyphosphate Phosphatase 1) detailliert in vitro und in lebenden Zellen charakterisiert. Dabei wurde ein bisher unbeschriebener InsP-Stoffwechselweg in menschlichen Zellen erstmals beschrieben. Als Zweites wurden InsP verdauende Bakterien aus der menschlichen Darmflora untersucht, sodass der Abbauweg von Inositolhexakisphosphat beleuchtet werden konnte. Als Drittes wurden DUSP-Enzyme (engl. Dual-Specificity Phosphatases) identifiziert und in vitro charakterisiert, die in der Lage sind, die Phosphoanhydrid-Bindung von Inositolpyrophosphaten (PP-InsPs) zu spalten. Die vorliegende Arbeit demonstriert, dass 13C-Markierung in Verbindung mit NMR ein mächtiges Werkzeug darstellt, um InsP-Stoffwechselvorgänge zu untersuchen. / Inositol polyphosphates (InsPs) comprise a ubiquitous group of densely phosphorylated intracellular messengers in eukaryotic cells. Despite their contributions to a myriad of biological processes the detection of InsPs remains challenging to this day, especially with regards to differentiating enantiomers, as the available analytical toolset is still limited. In this thesis the use of stable isotope labelling of myo-inositol (Ins) and InsPs is explored to address this shortcoming. Combining 13C-labelling and nuclear magnetic resonance spectroscopy (NMR) provides both enhanced sensitivity and makes use of NMR’s strong structure-data dependency. This enabled the deconvolution of complex mixtures of InsPs from in vitro experiments or biological samples. With stereo-specific 13C-labels InsP mixtures could be resolved to individual enantiomers. Using this technique several InsP metabolic pathways were examined. Firstly, the human phytase-like enzyme Multiple Inositol Polyphosphate Phosphatase (MINPP1) was characterized in depth in vitro and in living cells, establishing a hitherto undescribed inositol polyphosphate metabolic path in humans. Secondly, inositol phosphate digesting bacteria isolated from the human gut microbiome were investigated, shedding light on the metabolic fate of inositol hexakisphosphate in the digestive track. Thirdly, a set of Dual-Specificity Phosphatases (DUSPs) were identified to be able to hydrolyze the phosphoanhydride bond of inositol pyrophosphates (PP-InsPs) and characterized in vitro. The 13C-labelling approach of InsPs in junction with NMR represents a powerful tool for the study of inositol polyphosphate metabolism. In the thesis at hand, this method has facilitated our understanding of inositol polyphosphate pathways and it will be continuing doing so in the future in several biological contexts.