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In many industrial sectors biotechnological production processes have replaced pure chemical methods and allowed new, ecologically friendly and enzyme-based processes. Microorganisms, such as modified Bacillus strains are used in particular for the industrial enzyme synthesis. The two organisms Bacillus licheniformis and Bacillus pumilus are of great industrial importance. B. licheniformis is able to secrete proteins in large amounts, while B. pumilus shows high resistance to oxidative stress. During production processes different conditions can occur that affect the physiology of the production hosts and may result in a quantitative, but also a qualitative impairment of the products. This influence is based on e.g. chemical processes, the setting of temperature, pH, or oxygen availability and can lead to various stress situations for the bacteria. Cells respond to changes in their environment by sensing stressors and initiate a response to the stress, which is usually implemented by an induction or derepression of various regulons. In order to conduct an optimal production process, the metabolism and stress responses of the utilized bacteria should be known exactly. The aim of this study was to analyze of the stress response of B. licheniformis to heat and salt stress, and the stress response of B. licheniformis and B. pumilus to oxidative stress. These analyses were performed at the level of transcriptomics using cDNA microarrays, which is the most direct and global method for the analysis of changes in the physiology of a cell. The identification of stress specific markers genes and their differentiation from the SigB regulated general stress response has been another purpose of this work. Knowledge of these marker genes enables a prompt analysis of the fermentation conditions and thus a possible optimization of the process. The transcriptome analyses of this work show that B. licheniformis responds to heat stress by the induction of heat shock genes belonging to different regulons. These include the htpG gene, the HrcA regulon or the CtsR regulon, encoding chaperones and proteases, which mainly contribute to the protein quality control. The heat stress response of B. licheniformis revealed no fundamental differences to the heat stress response of the Gram-positive model organism Bacillus subtilis. The general stress response (SigB regulon), which is activated by heat stress, could be analyzed in more detail by the study of a ΔsigB mutant of B. licheniformis. Salt stress also provokes a strong induction of the general stress response in B. licheniformis. Genes for the transport and synthesis of compatible solutes were strongly induced, as well as several genes for transport systems with more or less known functions. The synthesis of the osmoprotective metabolites proline and glycine betaine could be verified in more detail by a metabolomics approach. The response to oxidative stress showed differences between both B. licheniformis and B. pumilus, and also to the oxidative stress response of B. subtilis. In B. licheniformis, the genes of the glyoxylate cycle are induced during oxidative stress. An activation of the glyoxylate bypass under oxidative conditions could be confirmed by a metabolome analysis of B. licheniformis. In addition, the PerR regulon of B. licheniformis is extended to include another two genes compared to B. subtilis. In contrast, several genes of the PerR regulon lack in the genome of B. pumilus, such as katA (vegetative catalase) or ahpCF (alkyl hydroperoxide reductase). However, other genes were induced in B. pumilus that were upregulated under oxidative stress conditions neither in B. subtilis nor in B. licheniformis. In addition, known regulons, regulated by e.g. Spx, CtsR or SOS were induced in both organisms. In summary, this dissertation transcriptionally analyzes the stress responses of B. licheniformis to heat, salt and oxidative stress, and in addition the oxidative stress response of B. pumilus. Several stress-specific regulons were identified in both, B. pumilus and B. licheniformis, which also correspond to the stress response of B. subtilis. However, it was possible to additionally assign genes to the stress specific responses of both organisms and to find differences, such as the absence of parts of the PerR regulon of B. pumilus, or the activation of the glyoxylate pathway in B. licheniformis during oxidative stress.
Reversible posttranslational modifications play an important role during the regulation of many central processes in bacterial cells. Protein phosphorylation, in particular, can influence signal transduction processes and thus enables a distinct reaction of the cell to different stress and environmental conditions. In the case of the human pathogen Staphylococcus aureus, protein phosphorylation is involved in the adaptation to changing conditions during colonisation of human hosts. For this reason, the investigation of phosphorylations in S. aureus allows a better understanding of pathophysiology and virulence of this organism. Apart from stable phosphorylations at the amino acids serine, threonine and tyrosine, insights into energy-rich phosphorylations, for instance at arginine residues, gain more and more scientific attention. For this reason, one purpose of this study was the investigation of incidence and physiological relevance of this protein modification at a global scale. Firstly, the analysis of this modification was methodically optimised resulting in the identification of eight arginine phosphorylations in wild type cells of S. aureus COL. Secondly, the deletion mutant ΔptpB missing the gene that codes for an arginine phosphatase, was analysed. The characterisation of PtpB in vitro proved its activity and specificity towards arginine phosphorylations. This enabled the global analysis of the phosphoproteome with a focus on arginine phosphorylations. In addition to the optimisation of the phosphopeptide enrichment as part of the sample preparation, the data analysis process was adapted to the special challenges of energy-rich phosphorylations. Here, classical database search was extended by spectral library based analyses. In addition, synthetic peptides allow the generation of high quality mass spectra and the verification of database based evaluation strategies to ensure the quality of the spectral library. Next, S. aureus COL was cultivated under various conditions and several subcellular fractions were analysed with the aim to cover a broad part of the proteome. The combination of the spectra of synthetic peptides, the spectra of non-phosphorylated peptides from extensive cultivation experiments and the spectra of enriched phosphopeptides rendered the construction of a spectral library possible. This contained 2,270 proteins out of which 392 were found to be phosphorylated. A comparison of the database based analysis with spectral library based analysis showed the advantages of the latter when comparing the reproducibility of biological replicates. Thereby a permanent issue in phosphoproteomics was investigated. Hence, spectral libraries were used for the analysis of the phosphoproteome of S. aureus under control and stress conditions. 215 arginine phosphosites were identified within the mutant under control conditions and 117 under oxidative stress conditions. Oxidative stress was chosen because phenotypic characterisation of the mutant revealed that the most distinct growth changes in comparison with the wild type occurred after oxidative stress. These phenotypic changes were quantitatively approached in the last part of this work. Total proteome quantification of the wild type and mutant under control and stress conditions revealed an influence of the ptpB deletion on amino acid metabolism, oxidative stress response and virulence. The quantification of phosphopeptides by means of a combination of spectral library with Census based analysis finally confirmed the observations made during total proteome quantification.
Hintergrund: LOX-1, ein Rezeptor für oxidiertes Low-Density Lipoprotein, wird von Endothelzellen, Makrophagen, vaskulären glatten Muskelzellen und anderen Zellen exprimiert. Seine Expression kann durch oxidiertes LDL (oxLDL), Angiotensin II, inflammatorische Zytokine (zum Beispiel Tumornekrose-Faktor alpha), Scherkräfte am Endothel und andere Faktoren induziert werden. LOX-1 ist bei der Entstehung von oxidativem Stress und der endothelialen Dysfunktion beteiligt und trägt vermutlich zur Instabilität von atherosklerotischen Plaques bei, was bei Patienten mit einer koronaren Herzkrankheit zum akuten Koronarsyndrom führen kann. Material und Methoden: Untersucht wurden Atherektomieproben von 37 Patienten (Alter 62,5 ± 9,7 Jahre, Body-Mass-Index 28,6 ± 5,3 kg/m2), die sich zwischen Juli 2001 und April 2005 wegen Brustschmerzen/Angina pectoris einer medizinisch indizierten Koronarangiographie mit in gleicher Sitzung durchgeführter Direktionaler koronarer Atherektomie (DCA) in der Klinik für Innere Medizin B der Universitätsmedizin Greifswald unterzogen hatten. Die in der DCA gewonnenen Atherektomieproben wurden sofort in flüssigem Stickstoff schockgefroren, am Kryotom (Leica C19) ohne aufzutauen geschnitten (Schnittdicke 5 Mikrometer) und mit Hämatoxylin/Eosin (H.E.), Ölrot O (für Lipide), Elastica-van Gieson (für Kollagen) und von-Kossa (für Verkalkungen) gefärbt. Die LOX-1 Expression wurde durch ein Immunfluoreszenz-Verfahren mit einem polyklonalen Kaninchenantikörper, der gegen die Aminosäuren 143 bis 273 des humanen LOX-1 Proteins gerichtet war, und einem FITC-markierten Sekundärantikörper nach dem ELISA-Prinzip (Enzyme-linked immunosorbent Assay) nachgewiesen. Die digitalen Aufnahmen wurden mit Corel PHOTO-PAINT 12, Scion Image und SigmaPlot 11 analysiert. Die LOX-1 Signalintensitäten wurden mit dem in der Koronarangiographie ermittelten Stenosegrad der betreffenden Plaques, dem Lipidgehalt in der Plaque und anderen Patientenparametern (z.B. Vorliegen eines akuten Koronarsyndroms) verglichen. Zur statistischen Analyse wurde der Rangkorrelationskoeffizient nach Spearman bestimmt und der Mann-Whitney-Rank-Test durchgeführt. Ergebnisse: Die LOX-1 Expression korrelierte mit dem Lipidgehalt der humanen koronaren Atherektomieproben, jedoch im Mittel statistisch nicht signifikant (p=0,056). Im Trend war die LOX-1 Expression in den Proben von Patienten mit einem akuten Koronarsyndrom (n=11), bei Männern (n=26) und Rauchern (n=15) höher und in Patienten, die HMG-CoA-Reduktase-Hemmer einnahmen (zum Beispiel Simvastatin), niedriger (n=16). Keine Korrelationen fanden sich zwischen LOX-1 Expression und Stenosegrad, Plaquelokalisation, Alter, Body-Mass-Index, Arterieller Hypertonie (n=31), Diabetes mellitus Typ II (n=9) und Dyslipoproteinämie (n=32). Schlussfolgerungen: Die LOX-1 Expression in atherosklerotischen Plaques ist positiv mit dem Lipidgehalt der Plaques assoziiert und ist im Trend höher in Patienten mit einem akuten Koronarsyndrom. Eine hohe LOX-1 Expression in atherosklerotischen Plaques könnte zu deren Instabilität somit zum Auftreten eines akuten Koronarsyndroms beitragen. Die Senkung des LDL-Angebots in der Arterienwand und Wege zur Plaquestabilisierung bei manifester Atherosklerose bleiben wichtigste Therapieziele.