Killer strains of the yeast Kluyveromyces lactis secrete a heterotrimeric protein toxin (zymocin) to inhibit the growth of sensitive yeasts. The cytotoxicity of zymocin resides in the γ subunit (γ-toxin), however the mechanism of cytotoxicity caused by γ-toxin was previously unknown. This thesis aimed to unravel the mode of γ-toxin action and characterize the interaction between γ-toxin and its substrates. Previous studies suggested a link between the action of γ-toxin and a distinct set of transfer RNAs. In paper I, we show that γ-toxin is a tRNA anticodon endonuclease which cleaves tRNA carrying modified nucleoside 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at position 34 (wobble position). The cleavage occurs 3’ to the wobble uridine and yields 2’, 3’-cyclic phosphate and 5´-hydroxyl termini. In paper II, we identified the determinants in tRNA important for efficient γ-toxin cleavage. The modifications present on the wobble uridines have different effects on tRNA cleavage by γ-toxin. The Saccharomyces cerevisiae wobble modification mcm5 group has a strong positive effect, whereas the Escherichia coli wobble modification 5-methylaminomethyl group has a strong inhibitory effect on tRNA cleavage. The s2 group present in both S. cerevisiae and E. coli tRNAs has a weaker positive effect on the cleavage. The anticodon stem loop (ASL) of tRNA represents the minimal structural requirement for γ-toxin action. Nucleotides U34U35C36A37C38 in the ASL are required for optimal cleavage by γ-toxin, whereas a purine at position 32 or a G at position 33 dramatically reduces the reactivity of ASL. Screening for S. cerevisiae mutants resistant to zymocin led to the identification of novel proteins important for mcm5s2U formation (paper III). Sit4p (a protein phosphatase), Sap185p and Sap190p (two of the Sit4 associated proteins), and Kti14p (a protein kinase) are required for the formation of mcm5 side chain. Ncs2p, Ncs6p, Urm1p, and Uba4p, the latter two function in a protein modification (urmylation) pathway, are required for the formation of s2 group. The gene product of YOR251C is also involved in the formation of s2 group. The involvement of multiple proteins suggests that the biogenesis of mcm5s2U is very complex.

In chronic inflammatory diseases like asthma or rheumatoid arthritis, erroneous and exaggerated accumulation of leukocytes in a tissue inadvertently causes the body harm. Several efficient anti-inflammatory drugs exist, for example corticosteroids and cyclo-oxygenase inhibitors. However, these drugs have potent and diverse effects and often act by inhibiting events subsequent to initiation of the inflammatory response, leading to more or less severe side-effects, especially when used in high doses for long periods of time. For this reason, strategies aimed at early inhibition of recruitment and activation of leukocytes have been suggested as safer and more specific approaches to reduce inflammation. Leukocyte adhesion to activated endothelium is a prerequisite to the following activation and extravasation, and takes place in the initial phase of inflammation. By using a model that allows leukocytes to adhere to tumour necrosis factor (TNF)-activated endothelial cells, thus mimicking aspects of an inflammatory reaction, we found that uridine, 4-thiouridine and isomaltitol could all reduce adhesion. This suggested that they may have anti-inflammatory potential. We therefore tried the three substances in a Sephadex-induced lung inflammation model and found that uridine and 4-thiouridine have several anti-inflammatory effects, such as being able to reduce leukocyte accumulation, decrease TNF protein levels and partly inhibit the oedema induced by Sephadex. Isomaltitol turned out to have immunomodulating, rather than anti-inflammatory, effects, which could be of interest in diseases where inadequate inflammatory responses are a problem.

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Der erste Teil der Arbeit beschreibt die Etablierung einer modifizierten Form des klassichen SILAC-Verfahrens, das in der quantitativen Massenspektrometrie zur Bestimmung von relativen Änderungen in Proteinmengen benutzt wird. Im sog. „pulsed SILAC (pSILAC)“ Verfahren werden Zellen im Zuge einer differentiellen Behandlung in Kulturmedien transferiert, die unterschiedlich Isotop-markierte Aminosäuren enthalten. Da hier die Quantifizierung auf dem Verhältnis der neusynthetisierten Proteinmengen beruht, können gezielt Unterschiede in der Proteinproduktion bestimmt werden. Mit Hilfe von pSILAC konnte im zweiten Teil der Arbeit erstmals quantitativ erfasst werden, welchen Einfluss microRNAs auf die Proteinsynthese ausüben. So konnte gezeigt werden, dass sowohl die Überexpression als auch die Repression einzelner microRNAs die Produktion hunderter Proteine beeinflussen kann. Außerdem konnten Genprodukte identifiziert werden, die ausschließlich translational reguliert werden. Die Messung von Proteinneusynthese ermöglichte auch die Bestimmung von Proteinumsatzraten, dargestellt im dritten Teil der Arbeit. Zusammen mit mRNA-Umsatzraten sowie Protein- und mRNA-Mengen bilden sie die Grundlage für eine dynamische Beschreibung zelluärer Genexpression. Durch den gleichzeitigen Einsatz des Nukleosidanalogons 4-Thiouridin (4sU) und von schweren Aminosäuren (SILAC) konnte eine metabolische Markierung neusynthetiserter mRNAs und Proteine in murinen Fibroblasten erreicht und damit eine Berechnung von Protein- und mRNA-Halbwertszeiten und absoluten Mengen für ca. 5,000 Gene ermöglicht werden. Während mRNA- und Proteinenmengen deutlich korrelierten, war zwischen mRNA- und Proteinhalbwertszeiten nur eine äußerste schwache Korrelation zu erkennen. Dennoch stehen mRNA- und Proteinumsatzraten nicht einem willkürlichen Zusammhang zu einander, da bestimmte Kombinationen von mRNA- und Proteinhalbwertszeiten eine Optimierung von Genen hinsichtlich ihrer biologischen Funktionen erkennen ließen. / The first part of the thesis describes the establishment of a modified version of the classic SILAC approach routinely used in quantitative mass spectrometry (MS) to assay relative changes in protein levels. In the newly-devised approach termed pulsed SILAC (pSILAC) differentially treated cells are transferred to culture medium supplemented with different versions of stable-isotope labeled heavy amino acids. As MS-based relative quantification is exclusively based on the newly-synthesized heavy protein amounts the method enables the detection of differences in protein production resulting from the treatment. The second part of the thesis shows the use of pSILAC to globally quantify the impact of microRNAs onto the proteome. Ectopic over-expression or knock-down of a single microRNA both affected protein production of hundreds of proteins. pSILAC identified several target genes as exclusively translationally regulated as changes in corresponding transcript levels were virtually absent. Measuring newly-synthesized protein amounts with heavy amino acids in a pulsed-labeling fashion has also been used to determine turnover rates of individual proteins, described in the third part of the present work. Along with transcript turnover as well as mRNA and protein levels they are essential for a dynamic description of gene expression. Simultaneous application of the nucleoside analogue 4-thiouridine (4sU) and heavy amino acids (SILAC) to metabolically label newly-produced mRNAs and proteins in mouse fibroblasts resulted in the calculation of mRNA and protein lifetimes and absolute levels for approximately 5,000 genes. While mRNA and protein levels were overall well correlated, a correlation between mRNA and protein half-lives was virtually absent. Yet this seemingly chaotic distribution of mRNA and protein half-lives was highly instructive since specific gene subsets have obviously evolved distinct combinations of half-lives that relate to their biological functions.