Translation is a crucial factor in determining the rate of protein biosynthesis; for this reason, bacterial species typically evolve features to improve translation efficiency. Biosynthesis is a finely tuned cellular process aimed at providing the cell with an appropriate amount of proteins and RNAs to fulfill all of its metabolic functions. A key bacterial feature for faster recognition of the start codon on mRNA is the binding between the anti-Shine-Dalgarno (aSD) sequence on prokaryotic ribosomes at the 3’ end of the small subunit (SSU) 16S rRNA and Shine-Dalgarno (SD) sequence, a purine-rich sequence located upstream of the start codon in the mRNA. This binding helps to facilitate positioning of initiation codon at the ribosomal P site. This pairing, as well as factors such as the location of aSD binding relative to the start codon and the sequence of the aSD motif can heavily influence translation efficiency. The objective of this thesis is to understand the SD-aSD interactions and how changes in aSD sequences can affect SD sequences in addition to the underlying impact these changes have on the translational efficiency of prokaryotes. In chapter two, we hypothesized that differences in the prevalence of SD motifs between B. subtilis and E. coli arise as a result of changes in the free 3' end of 16S rRNA which may have led B. subtilis and E. coli to evolve differently. E. coli is expected to be more amenable to the acquisition of SD motifs that do not perfectly correspond with its free 3’ 16S rRNA end than B. subtilis. Further, we proposed that the evolutionary divergence of these upstream sequences may be exacerbated in B. subtilis by the absence of a functional S1 protein. Based on the differences between E. coli and B. subtilis, we were able to identify SD motifs that can only perfectly base pair in one of the two species and are expected to work well in one species, but not the other. Furthermore, we determine the frequency and proportion of these specific SD motifs that are expected to be preferentially present in one of the two species. Our motif detection is in keeping with the expectation that the predicted five categories of SD that are associated with B. subtilis and are expected to be less efficient in E. coli exhibit greater usage in the former than latter. Similarly, the predicted category of SD motifs associated with the E. coli 16S rRNA 3’ end is used more frequently in E. coli.Across prokaryote genomes, translation initiation efficiency varies due to codon usage differences whereas among genes, translation initiation varies because different genes vary in SD strength and location. In chapter 3 we hypothesized that there is differential translation initiation between 16 archaeal and 26 bacterial genomes. Translation initiation was found to be more efficient in Gram-positive than in Gram-negative bacteria and also more efficient in Euryarchaeota than in Crenarchaeota. We assessed the efficiency of translation initiation by measuring: i) the SD sequence’s strength and position and ii) the stability of the secondary structure flanking the start codon, which both affect accessibility of the start codon

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Se ist ein essentielles Spurenelement, das seine biologische Aktivität als Selenocystein in den katalytischen Untereinheiten von Selenoproteinen entfaltet. Es wird als Supplement in der Prävention und Therapie einiger Volkskrankheiten wie Autoimmunerkrankungen und Krebs eingesetzt. Die verfügbaren Ergebnisse der klinischen Studien deuten auf geschlechtsspezifische Unterschiede in der Wirksamkeit von Se. Aus diesem Grunde sollte in der vorliegenden Arbeit die Biosynthese von Selenoproteinen in männlichen und weiblichen Mäusen als Modellorganismus für höhere Säugetiere analysiert und verglichen werden. Die gewonnenen Ergebnisse belegen eindeutig, dass die mRNA Konzentrationen von Selenoprotein P, der 5''-Iodothyronin-Deiodase Typ 1 und der extrazellulären Glutathion-Peroxidase 3 geschlechtsspezifische Unterschiede aufweisen. Dieser Dimorphismus ist jedoch nicht konstant, sondern variiert von Gewebe zu Gewebe und zeigt überdies auch eine Abhängigkeit vom Se-Status der Tiere und dem untersuchten Mausstamm. Überraschenderweise korrelieren die resultierenden Proteinmengen nicht linear mit den Unterschieden der mRNA Konzentrationen. Besonders die 5''-Iodothyronin-Deiodase Typ 1 zeigt ausgeprägte Unterschiede in Leber und Niere, wobei sich die Geschlechtsdimorphismen auf mRNA- und Protein-Ebene unterschiedlich stark ausprägen und vom Se-Status beeinflusst werden. Zusammengenommen zeigt diese Arbeit, dass die Expression von Selenoproteinen auf zwei Kontrollebenen geschlechtsspezifisch reguliert wird: über steroidabhängige Gentranskription werden unterschiedliche mRNA Konzentrationen abhängig vom Mausstamm, Alter und Se-Status in den Geweben exprimiert, und über noch nicht eindeutig identifizierte Mechanismen wird die Effektivität, mit der diese Transkripte in die entsprechenden Selenoproteine übersetzt werden, geschlechtsspezifisch kontrolliert. Diese Se-abhängige Regulation der Biosyntheserate, die vermutlich über eine veränderte Translationseffizienz erfolgt, stellt ein sehr überraschendes Ergebnis dar. Sollte es sich in menschlichen Proben bestätigen, so könnten diese Ergebnisse helfen, die geschlechtsspezifischen Befunde in den klinischen Supplementationsstudien zu verstehen und entsprechend abgestimmte Empfehlungen für eine unterschiedliche Supplementation von Mann und Frau zu erarbeiten. / Selenium is an essential trace element and acts as Selenocystein in the catalytic entity of selenoproteins. It is currently in use as supplement in the prevention and therapy of a variety of diseases including autoimmune diseases and cancer. The epidemiological and clinical data indicate that the effectiveness of Se supplementations is sex-specific. Therefore, this thesis was initiated to analyse and compare the expression of selenoproteins in male and female mice as a suitable model organism for higher mammals. The experimental data clearly indicate that selenoprotein P, type I 5'' iodothyronine deiodinase and the secreted glutathione peroxidase 3 display sex-specific differences in mRNA concentrations. The sexual dimorphic expression patterns of these selenoproteins are not constant but depend on the tissue, the Se-status of the animals and the specific mouse strain analysed. Surprisingly, no direct correlation is observed when mRNA levels and expressed protein concentrations are compared. This becomes very obvious in the case of type I 5'' iodothyronine deiodinase in liver and kidney. Both mRNA and protein levels differ between the sexes in a discordant and Se-dependent manner. Taken together, this thesis indicates that selenoprotein expression is regulated in a sex-specific manner by two different mechanisms. First of all, steroid-dependent gene transcription gives rise to sexually dimorphic mRNA levels in the different tissues. Mouse strain, age and Se-status influence this process. Secondly, the sexes differ profoundly with respect to the efficiency of selenoprotein biosynthesis from a given number of transcripts. Presumably, this process involves Se-dependent translational control mechanisms that have not been described before. Under the assumption that these results can be verified with human samples, it is conceivable that this new mechanism might help to explain some of the enigmatic sex-specific effects observed in human supplementary studies and that sex-specific supplementation regimen need to be worked out in the long run.