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The present work consists of four parts, containing experimental data obtained from analysis of 'Bacillus subtilis' specific and general defense strategies against reactive oxygen species. In the first part, the peroxide and superoxide stress stimulons ob 'B. subtilis' were analyzed by means of transcriptomics and proteomics. Oxidative stress responsive genes were classified into two groups: the gene expression pattern was either similar after both stresses or the genes primarily responded to one stimulus. The high induction observed for members of the PerR-regulon after both stimuli supported the assumption that activation of the peroxide specific PerR-regulon represented the primary stress response after superoxide and peroxide stress. The second part focuses on protein carbonylation in 'B. subtilis' wild-type and 'sigB' mutant cells. The introduction of carbonyl groups into amino acid side chains of proteins represents one possible form of protein modification after attack by reactive oxygen species. Carbonyl groups are readily detectable and the observed amounts can thus serve as an indicator for the severity of protein damage. The resultsdemonstrate clearly that 'B. subtilis' proteins are susceptible to hydrogen peroxide (H2O2) mediated carbonylation damage. The application of low concentrations of H2O2 prior to the exposure to otherwise lethal levels of peroxide reduced markedly the degree of protein carbonylation, which also held true for glucose starved cells. Artificial preloading with general stress proteins resulted in a lower level of protein carbonylation when cells were subjected to oxidative stress, but no differences were detected between wild-type and 'sigB' mutant cells. In the third part, strains with mutations in genes encoding general stress proteins were screenedfor decreased resistance after H2O2 challenge. It was demonstrated that resistance to H2O2 challenge. It was demonstrated that resistance to H2O2 after transient heat treatment, likewise to conditions of glucose starvation, was at least partly mediated by the sB-dependent general stress response. The screening of mutants in sB-controlled genes revealed an important role for the deoxyribonucleic acid (DNA)-binding protein Dps in the context of sB-mediated resistance to oxidative stress underlining previous reports. Therefore, the experimental strategy opens a global view on the importance of DNA integrity in 'B. subtilis' under conditions of oxidative stress. The fourth part includes analysis of a 'B. subtilis' thioredoxin conditional mutant. The thiol-disulfide oxidoreductase TrxA is an essential protein in 'B. subtilis' that is suggested to be involved in maintaining the cytoplasmic thiol-disulfide state even under conditions of oxidative stress. To investigate the physiological role of TrxA, growth experiments and two-dimensional gel electrophoresis were carried out with exponentially growing cells that were depleted of TrxA. The observations indicate that TrxA essentially involved in the re-reduction of phosphoadenosyl phosphosulfate reductase CysH within the sulfate assimilation pathway of 'B. subtilis'.
The toluene-degrading and solvent-tolerant strain Pseudomonas putida DOT-T1E was investigated with respect to its suitability and economic efficiency as biocatalyst in aqueous-organic two-phase systems with aliphatic solvents as organic phase (Rojas et al. 2004, chapter 4 and 5) and to its adaptive responses to the solvent decanol. The adaptive changes on the level of cell morphology (chapter 2), membrane fatty acids and permeability (chapter 3), as well as energetics and surface properties (chapter 5) of P. putida DOT-T1E have been investigated in order to ascertain information about the strain's suitability for two-phase biotransformation systems (chapter 4). The morphological adaptation to the presence of solvents was observable in changes of the cell size of P. putida DOT-T1E. Those changes were dependent on the cellular activity and occurred only after addition of non-lethal solvent concentrations. The cells reacted to the presence of organic solvents by decreasing the ratio between surface and volume of the cells and therefore reducing their relative surfaces (chapter 2). The cell surface and especially the cytoplasmic membrane are the major targets for toxic effects of membrane-active compounds like solvents. The mechanism of the cis-trans isomerisation of unsaturated fatty acids counteracts the fluidizing effect of solvents by increase the ordering of the membrane and therefore its rigidity. By comparing the responses of the cells to a series of stress factors (like solvents), a direct correlation between the activation of this mechanism and the well investigated K+-uptake pumps was observed (chapter 3). Huertas et al. (1998) reported that this strain tolerated concentrations of heptane, propylbenzene, octanol, and toluene of at least 10 % (vol/vol). 1-decanol is, in comparison to toluene, less hazardous and volatile, and it possesses good extraction properties for the desired fine chemical products. In further investigations of possible biotechnological processes, it was discovered that decanol is also a more suitable solvent as organic phase (chapter 4). Although the cells of P. putida DOT-T1E needed additional energy for their adaptation to the presence of the solvent decanol, they were able to maintain or activate their electron transport phosphorylation allowing homeostasis of ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities converging with more negative cell surface charges were observed in cells grown in the presence of 1-decanol (chapter 5). It is however important to note that all the cell’s properties observed are closely linked to each other since they are all part of the adaptive response of the cells. It can be concluded that the easy adaptability and good growth properties of Pseudomonas putida DOT-T1E in the presence of the organic solvent 1-decanol make this system an excellent candidate for two-phase fermentation processes. Moreover, the absence of differences in the energetics of the bacteria during exposure to 1-decanol as compared to bacteria that grew in the absence of 1-decanol, support that this organism can be used for the industrial production of fine chemicals in an economically sound manner.
Proteomic signatures select the physiology state of the cell. By using 2-D technique, proteome signature of Bacillus subtilis under different stresses and starvations are analyzed. Consequently, a proteomic map of Bacillus subtilis in non-growing phase was created. The ammonium and tryptophan as well as phenol and catechol stress are analyzed using both of proteomics and transcriptomics. And the proteomic map represents a good application in the prediction of the mode of action of phenol and catechol stress.
The Gram-positive bacterium Bacillus licheniformis is an important industrial host for the production of enzymes. Genomic DNA arrays and proteomics are being used to investigate the physiology of this bacterium. A genome-wide transcriptional profiling analysis of the adaptation of B. licheniformis to phosphate starvation shows more than 100 induced genes. Most of strongly induced genes belong to the putative Pho regulon. The data of the transcriptome analysis have been verified by the analysis of the extracellular and cytoplasmic proteome. The main response of B. licheniformis to glucose starvation was a switch to the usage of alternative carbon sources. In addition, B. licheniformis seems to be using other organic substances like amino acids and lipids as carbon sources when subjected to glucose starvation. This was indicated by the induction of a high number of genes the proteins of which are involved in amino acid and lipid degradation. During nitrogen starvation genes necessary for the recruitment of nitrogen from alternative sources were induced, e.g. genes for nitrate and nitrite assimilation, several proteases and peptidases. Both starvation conditions led to a down-regulation of the transcription of most vegetative genes and subsequently to a reduced synthesis of the corresponding proteins. Only a few genes were induced by both starvation conditions like yvyD, citA and the methylcitrate shunt genes mmgD, mmgE and yqiQ. Data of this study use to better understand the physiology of this bacterium during fermentation processes and thus to identify and circumvent bottlenecks of B. licheniformis based bioprocesses. In addition, the phytase promoter was tested for the construction of an alternative phosphate regulated expression system for B. licheniformis.
Degradation of branched chain aliphatic and aromatic petroleum hydrocarbons by microorganisms
(2008)
The overall aim of the work was to investigate the ability of several Gram-positive bacteria including Mycocbacterium neoaurum SBUG 109, Nocardia cyriacigeorgica SBUG 1472 and Rhodococcus ruber SBUG 82 and the yeast Trichosporon mucoides SBUG-Y 801 to degrade and transform branched chain hydrocarbons which occur in petroleum and its fraction products such as gasoline or gas oil and which are known as important and recalcitrant environmental pollutants. Pristane, iso-pentylbenzene and sec-octylbenzene were used in this work as model compounds. These compounds represent significant groups of petroleum constituents (branched chain alkanes and aromatic hydrocarbons). Three bacteria and the yeast T. mucoides SBUG-Y 801 were selected in a screen of 16 hydrocarbon-utilizing strains in the SBUG collection and from 21 isolated hydrocarbon-utilizing strains from oil-contaminated habitats of Saudi Arabian Desert and of Vietnam. The bacteria were identified in cooperation with DSZM (Deutsche Sammlung von Mikroorganismen und Zellkulturen) as M. neoaurum SBUG 109, N. cyriacigeorgica SBUG 1472, R. ruber SBUG 82. These bacterial and yeast strains were shown to possess high potential for degrading and transforming pristane, iso-pentylbenzene and sec-octylbenzene. The intermediates produced by these bacteria during incubation with pristane were analyzed by GC and GC/MS. The products 4-methyl pentanoic acid; methyl butanedioic acid; 2-methyl pentadioic acid; methyl propanedioic acid; 4-methyl heptanedioic acid and 2,6,10,14–tetramethyl-pentadecan–3–one were detected in M. neoaurum cultures. In R. ruber, methyl butanedioic acid; 2-methyl pentadioic acid; 4,8-dimethylnonanoic acid, 4-methyl heptanedioic acid; 2,6,10–trimethylundecanoic acid; 3,7-dimethyl decanedioic acid and 2,6,10,14–tetramethyl–pentadecan–3-one were identified. In N. cyriacigeorgica, 2-methylpentanedioic acid; 4,8-dimethylnonanedioic acid; 2,6-dimethylheptanedioic acid and pristanic acid were found. The detection of 11 intermediates during pristane degradation by the three Gram-positive bacteria provided sufficient information to elucidate in detail three degradative pathways of pristane involving mono-, di- and sub-terminal oxidations. The sub-terminal oxidation by M. neoaurum and R. ruber was demonstrated for the first time. This occurence of a sub-terminal oxidation in these strains was strengthened by further results of aromatic compounds transformation (see below). During this pathway, ketone mono-oxygenation reactions seem to be involved. Because of this it will be of interest to look more closely at the catalytic processes involved and their possible extension to the bio-degradation of other branched chain hydrocarbons. Since in the present study 59 %, 51 % and 84 % of pristane were degraded in 3 weeks by M. neoaurum, R. ruber and N. cyriacigeorgica, this illustrated that the degradation rates of this isoprenoid alkane were high. The bacteria we studied were not only effective degraders of multiple branched chain alkane but also useful transformers of aromatic hydrocarbons. The intermediates produced were analyzed by comparing the retention times and UV/Vis spectra of the HPLC elution profile as well as the retention times and mass spectra of the GC/MS with those of available standards. Using iso-pentylbenzene as a substrate, 8 metabolites were generated by M. neoaurum transformation including product A (phenylacetic acid), B (acetophenone), D (iso-valerophenone), E (succinic acid), F (benzoic acid), G [(2-hydroxy-phenyl)-acetic acid] and H (2-methyl-4-phenyl-butyric acid). We additionally identified an alkyl hydroxylated iso-pentylbenzene derivative as 2-methyl-4-phenyl-butan-2-ol or 2-methyl-4-phenyl-butan-1-ol. Two metabolites (C and D) were detected by N. cyriacigeorgica transformation and three metabolites (A, D and F) were identified by R. ruber transformation which led to the complete biotransformation of this substance. iso-Pentylbenzene transformation by M. neoaurum was initiated by attack on the alkyl side chain followed by ring cleavage. The appearance of iso-valeorophenone confirmed the occurrence of a sub-terminal oxidation mechanism in M. neoaurum and R. ruber. In addition to products A, C, D and G, the identification X-(3–methyl–butyl)-phenol (X means that position of the hydroxy group on the aromatic ring system, such as 2, 3 or 4 remained unclear) in T. mucoides cultivation demonstrated for the first time the capacity of alkyl side chain attack by this organism which was hitherto known only for its ability of ring cleavage. The detection of 15 degradation products of sec-octylbenzene (including 2-phenylpropionic acid, 3-phenylbutyric acid, ß-methylcinnamic acid, 5-phenylhexanoic acid, acetophenone, 2-hydroxy-acetophenone, 2,3-dihydroxy-benzoic acid, succinic acid, 7-phenyloctan-2-one, benzoic acid, phenylacetic acid, 7-phenyl-octan-2-ol, hydroxy-phenylacetic acid and 2-hydroxybenzoic acid), in the studied bacteria pointed to an effective sec-octylbenzene degradation pathway in which dehydrogenation of 3-phenylbutyric acid to form ß-methylcinnamic acid is a newly described option. The identification of 2-phenylpropionic acid and 3-phenylbutyric acid in sec-octylbenzene transformation experiments by T. mucoides confirmed the possibility of alkyl side chain attack by this yeast. Summarizing the results, we describe for the first time in detail the biotransformation of sec-octylbenzene by M. neoaurum, N. cyriacigeorgica, R. ruber and T. mucoides. Our results suggest that these microorganisms may be useful as potential strains for hydrocarbon degradation and it may be of interest to investigate their suitability to solve specific environmental pollutant problems associated with branched chain aliphatic and alkyl-branched compounds which contribute to the persistence of hydrocarbon fractions in the environment.
Understanding of the regulatory mechanisms controlling stress gene expression of S.aureus in response to environmental stress is very essential in studying its fitness and virulence. In this work, the changes in protein expression profiles as well as the gene transcription of S.aureus after heat exposure, osmotic stress and in response to the antibiotic puromycin were studied in order to provide detailed insights into the response of S.aureus to various kinds of environmental stress under in vitro conditions, namely: (1) to investigate the global response of S.aureus to heat stress conditions using transcriptomic and proteomic analyses. (2) to study the transcriptome and proteome of S.aureus in response to antibiotic substance puromycin. (3) to define the proteome signatures of S.aureus under NaCl stress condition. (4) to complete the proteome map of cytoplasmic proteins of S.aureus by identifying proteins exclusively synthesized during the exposure to stress. Firstly, the high resolution 2-D protein gel electrophoresis technique combined with MALDI-TOF-MS and a DNA array approach were used to investigate the cellular response of S.aureus to heat stress. A switch from normal growth temperature to high temperature condition revealed complex changes in the protein expression pattern as well as the genes expression profile. The effect of puromycin stress on S.aureus cells was analyzed, using a gel-based proteomic approach and transcriptomic analyses with DNA microarrays. We compared the protein synthesis pattern as well as the transcription data of S.aureus in response to puromycin stress with that in response to heat shock. The results demonstrated that both stress conditions induced specific, overlapping and general responses. Finally, the protein expression profile of S.aureus in response to NaCl stress was analyzed with 2D gel based proteomic approach. Our proteome analyses revealed the repression of the synthesis of many enzymes belong to different metabolism pathways . In summary, the signatures for stress or starvation stimuli can be used as diagnostic tools for the prediction of the mode of action of new antibiotics or for studying the physiological state of cells grown. Expression of the respective genes under in vivo conditions could provide some ideas on the environmental signals that specifically influence the survival of S.aureus within and outside the host.
The introduction of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) enabled the separation and visualization of a substantial fraction of an organism’s entire proteome, and when mass spectrometry entered protein science, these proteins became even amenable to identification on a grand scale. Nevertheless, important classes of proteins elude a separation on classical 2 D gels, as the ones showing extremes in isoelectric point or molecular weight, and foremost very hydrophobic proteins naturally embedded in lipid membranes. This thesis aimed at the establishment and adaptation of alternatives to 2-D PAGE. New techniques allowing for an identification and quantification of critical protein classes were designed and adopted to physiological questions in the Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus. In a comprehensive study on cytoplasmic proteins of S. aureus COL the number of proteins identified by a 2-D gel based approach could be extended by 650 proteins employing gel free technologies. Application of these complementary methods resulted in the establishment of a comprehensive reference map of the cytosolic proteome in growing and non-growing S. aureus cells which can serve as basis for further physiological investigations. Gel free separation of complex protein digests was likewise used in a quantitative study on heat stress in B. subtilis. By implementation of the iTRAQ® technology four different physiological states could be relatively quantified in one experiment. A parallel generation of 2-D gel based data enabled the depiction of strengths and weaknesses of protein quantitation by both, spot intensities on 2-D gels and iTRAQ® signal intensities in MS/MS spectra. Furthermore, new insights into heat sensitivity of pivotal enzymes involved in amino acid biosynthesis could be delivered. The institution of gel free approaches and advancements in 2-D PAGE provide the tools to penetrate into yet unamenable scopes of proteomes. A review on proteome coverage in B. subtilis gives an overview on the strategies which have been explored for most comprehensive protein identification in various sub-proteomes. Although more than one third of B. subtilis’ open reading frames could be demonstrated on protein level, one has to be aware of the fact that it still is a long way to achieve complete coverage of its proteome. Integral membrane proteins make up about one quarter of the entirety of proteins in a cell. Despite their large portion they are clearly understudied due to the intricacy of identification. Their low abundance and non-accessibility of membrane-spanning domains represent major experimental difficulties. The establishment of a protocol efficiently depleting cytosolic proteins by membrane shaving and targeting trans-membrane peptides by novel digestion strategies essentially facilitated identification of highly hydrophobic integral membrane proteins. This protocol was not only successfully applied to the membrane proteome of growing S. aureus cells, but was shown to be applicable in B. subtilis as well. Both studies displayed the novel membrane shaving approach to be highly complementary to a previously established separation of membrane proteins via 1 D PAGE. A combination of the two techniques resulted in identification of about half of the theoretical membrane proteome in both bacteria, and hence layed the foundation for advanced and quantitative analyses. In this regard, 14N/15N metabolically labeled membrane samples of growing and non-growing cells of S. aureus COL were relatively quantified revealing a significant difference in amount for more than one third of the proteins. A corresponding experimental setup was used to compare the membrane proteomes of S. aureus SA113 and its mutant deficient in the lysylphosphatidylglycerol synthetase MprF. Interesting quantitative differences were obtained for proteins most likely involved in the regulation of cellular surface net charge as well as for virulence-associated proteins.
Deciphering the entire protein complement of a living cell together with the elucidation of dynamic processes on protein level are the main goals of proteomics as it is used today. To achieve this goal, namely the elucidation of dynamic processes of the entire bacterial cell, we have developed strategies and distinct workflows to cover the most proteins in different subcellular localizations in bacteria together with a stable isotopes labeling approach to follow temporal and spatial changes in different proteomic subfractions. In this work, it has been shown that the use of mass spectrometry based in vivo quantitation techniques and the application of subcellular and chromatographic fractionation has lead to a new level of qualitative and quantitative proteomics data. Emphasizing on the studies revealing the dynamics of the bacterial physiology on a time resolved base, both spatial and temporal processes can be monitored to obtain knowledge on physiological processes in a depth that has not been reached before in comparable global studies.
Protein quality control systems are essential for the viability and growth of all living organisms. They protect the cell from irreversible protein aggregation. Because the frequency of protein misfolding, which ultimately results in protein aggregation, varies with the environmental conditions, the amount and activity of protein quality systems have to be accurately adapted to the rate of protein misfolding. The main goal of this thesis was to gain detailed molecular insights into the transcriptional and post-translational regulation of these protein quality control networks in the ecologically, medically and industrially important phylum of low GC, Gram-positive bacteria. In these bacteria the core protein quality control systems are under the transcriptional control of the global repressor CtsR. In a first study it was demonstrated that the arginine kinase McsB is not responsible for the regulation of CtsR activity during heat stress, as was concluded by others on the basis of previous in vitro data. Rather, it was demonstrated that CtsR acts as an intrinsic thermosensor that adapts its activity to the surrounding temperature. CtsR displays a decreased DNA binding at higher temperatures, which leads to induction of transcription of the protein quality control systems under these conditions. This CtsR feature is conserved in all low GC, Gram-positive bacteria. However, the CtsR proteins of various low GC, Gram-positive species do not have the same temperature optima. CtsR responds to heat in a species-specific manner according to their corresponding growth temperature. Detailed analysis revealed that a highly conserved tetra-glycine loop within the winged helix-turn-helix domain of CtsR is responsible for thermosensing. Dual control of CtsR activity during different stresses was demonstrated for the first time in this work. In addition to heat-dependent de-repression, CtsR is inactivated by thiol-specific stress conditions. This latter de-repression depends on a molecular redox-switch that is independent of CtsR auto-regulation. In Bacillus subtilis and its closest relatives the McsA/McsB stress-sensing complex is responsible for CtsR de-repression during redox stress conditions. McsA is able to sense the redox state of the cell via its highly conserved cysteine residues. When these cysteines are reduced, McsA is able to bind and inhibit McsB. But when these cysteine residues are oxidized, McsB is released from McsA. Thereby, McsB is activated and removes CtsR from the DNA. However, the McsA/McsB complex is not present in all low GC, Gram-positive bacteria. In the species lacking this complex, ClpE is able to act as a redox-sensor probably via its highly conserved N-terminal zinc finger domain. When these cysteine residues are oxidized, ClpE is activated which results in CtsR de-repression. In addition to the transcriptional regulation of CtsR low GC, Gram-positive protein quality control systems are regulated post-transcriptionally. The expression of the McsA/McsB adaptor pair is regulated by CtsR. However, McsB activity is also tightly regulated by three different regulatory proteins (McsA/ClpC/YwlE). McsB is needed to target specific substrates to ClpC, either for refolding or degradation by the ClpCP protease. It was demonstrated that only the auto- phosphorylated form of McsB is able to bind to its substrates. This McsB function is inhibited in non-stressed cells by a direct interaction with ClpC. Consequently, McsB is activated by a release from ClpC during protein stress. In addition, McsB activation depends on the presence of its activator McsA. Accordingly, McsB cannot be activated as an adaptor protein during thiol-specific stress because McsA is no longer able to bind to McsB under these conditions. However, also active McsB is subject to post-translational control. Activated McsB is either de-phosphorylated by McaP or degraded by ClpCP ensuring an appropriate shut-down of the McsB adaptor. Both McaP and ClpC inhibit McsB activity with different intensities. ClpC possesses a stronger impact on McsB activity than McaP but both proteins are needed for an adequate silencing of McsB activity. In addition, it was shown for the first time that B. subtilis McsB is a global adaptor that influences the stability of multiple proteins. The B. subtilis ClpC protein is unlike most members of the Hsp100 family because it not only requires several adaptor proteins for substrate recognition but also for its general ATP- dependent activity. Biochemical analysis revealed how ClpC is activated by distinct adaptor proteins. McsB modulates ClpC activity by regulatory phosphorylation of arginine residues. Moreover, McaP (formerly YwlE) was identified as an arginine phosphatase that modulates the McsB mediated ClpC activity. MecA, another known adaptor protein for ClpC, activates ClpC independently of these arginine phosphorylations, which demonstrates the existence of multiple pathways for ClpC activation.
Staphylococcus aureus is a pathogenic bacterium infecting the human host. It’s multifaced adaptation to various environmental conditions is mediated by a tight regulation of the virulence factors influencing the host’s immune system. In this thesis two regulators of gene expression were analysed: (i) the global influence of the two-component system SaePQRS and (ii) the regulation of superantigen gene expression by the alternative sigma factor σB. At the outset of this thesis, single target genes induced by SaeRS were known (hla, hlb, cap5, fnbA, coa). In order to get a general idea of the Sae-regulon, the influence of SaePQRS on gene-expression was analysed in two strain backgrounds by proteomics and transcriptomics aproaches. Recapitulatory, expression of at least 18 secreted and two covalently cell-wall bound proteins was decreased following inactivation of the Sae-system. Sae-dependently expressed were, amongst others, well decribed virulence factors like the y-hemolysins HlgA, HlgB, HlgC, LukM and LukF, the innate immune system modulating proteins Efb, CHIPS and SCIN-B as well as the enterotoxin SEB. SaeR acts as an activator of its target genes. Some proteins were detected in increased amounts in the extracellular proteome of the Sae-deficient strain. However, these changes did not occur at the transcriptional level. The expression of virulence factors is determined by other global regulators. No influence of SaePQRS on the transcription of five substancial regulators, namely the Agr-system and its effector molecule RNAIII, the alternative sigma factor σB, the two-component system ArlRS and the DNA-binding protein SarA, could be shown. In the second part of this thesis the issue was broached to the regulation of gene-expression of a subgroup of virulence factors, the superantigens (SAgs) of S. aureus by SaePQRS and σB. In contrast to their well described molecule structure and function, the regulation of their gene expression was largely unknown. Six different S. aureus strains (two laboratory strains and four clinical isolates) encoding one to seven SAg-genes each, were used for analysis of a total of twelve SAgs regarding their transcription and mitogenic activity. The transcriptional units were characterized using Northern-Blotting. The expression of SAgs could be correlated to the respective growth phase. While egc-SAgs were expressed mainly at low optical densities, seb was induced during late growth phase. In contrast, the transcription of sea, seh, sek, tst and sep remained constant and growth-phase independent. The transcriptional dataset was verified using T-cell proliferation assays. The expression of seh, tst and the egc-operon was dependent on σB. A potential σB-dependent promotor could be identified preceeding seo, the first gene of the egc-operon. In contrast, the expression of seb was increased in sigB-deficient background. This might be due to indirect effects. Expression of seb required SaePQRS. Transcriptional datasets were verified by Immuno-Blotting and T-cell-proliferation assays. In conclusion, the same mutation in sigB but in different strain backgrounds could result in opposite phenotypes with respect to their mitogenic activity. Besides well characterized virulence factors, some secreted proteins with so far unknown function belong to the Sae-regulon. Given that the influence of SaePQRS was restricted to virulence factors and induced especially modulators of the innate immune system, it can be assumed, that these proteins potentially play a role in virulence of S. aureus. In the third part of this thesis, one of these potential new virulence factors, namely SACOL0908, was analysed in detail. In cooperation with the group of Prof. Stehle, Tübingen, the crystal structure was solved. The protein folding of SACOL0908 is new with only minor similarities to described protein structures. Recombinantly expressed SACOL0908 binds to granulocytes. These cells belong to the innate immune system, incorporate bacteria by phagocytosis and kill them. The receptor for SACOL0908 on the surface of granulocytes could not be identified using immunoprecipitation, antibody-blocking assays and functional assays in cooperation with the group of Prof. Peschel, Tübingen. The gene encoding SACOL0908 was deleted in two S. aureus strain backgrounds (COL and Newman). These mutants are currently in use to characterize their phenotype in mouse-infection studies.
Proteolysis represents the final step in the life of a protein. It is one of the most important cellular processes assisted by chaperone systems and ensures an appropriate protein homeostasis. Protein degradation is essential for the removal of cytotoxic protein aggregates and mis-translated/mal-folded proteins, „unemployed“ and regulatory proteins to enable rapid cell adaptation to altering environmental conditions (Gottesman, 2003; Wiegert & Schumann, 2001; Parker, 1981; Stansfield et al., 1998; Drummond & Wilke, 2008; Goldberg, 1972; Gerth et al., 2008). The bacterial Clp (caseinolytic proteins) protease complexes are analogous to the eukaryotic 26S proteasome and consist of Hsp100/Clp proteins of the AAA+ superfamily and an associated barrel-like proteolytic chamber (e.g. ClpP). The Clp proteases seem to be responsible for the major protein turnover in low GC, Gram+ bacteria. The main goal of this thesis was to develop new methods and tools to investigate global proteolysis more precisely and to get a detailed understanding of protein degradation during starvation conditions and it´s regulation in low GC, Gram-positive bacteria. To analyse protein degradation under starvation conditions the well established glucose starvation model was used. In Bacillus subtilis it could be shown that approximately 200 proteins are selectively degraded in a glucose depletion induced stationary phase. Furthermore radioactive pulse-chase labelling experiments coupled with 2D-PAGE analysis revealed that mainly the ClpCP protease complex is involved in the degradation of proteins in the stationary growth phase. To investigate proteolysis in the human pathogen Staphylococcus aureus in the same way, a newly developed chemically defined medium was established suitable for radioactive pulse-chase labelling experiments under stable glucose starvation conditions. The degradation kinetics of individual 2D spots was significantly better resolved using 14C-BSA as an internal marker protein for the sample normalisation. A rather huge overlap was found within the functional protein classes that were degraded in B. subtilis and S. aureus the stationary phase. Among others, especially proteins involved in amino acid, nucleotide and cell wall biosynthesis were rapidly degraded, whereby not always the same and sometimes another enzymes from a biosynthetic chain were targeted for proteolysis. Despite the resolution power of the 2D-PAGE method, there are some drawbacks such as a limited "protein window" with regard to the molecular weight and isoelectric point, loss of low abundance proteins and a rather low reproducibility for time course experiments. Therefore a mass spectrometry based approach for the simultaneous detection of protein synthesis, accumulation and degradation was developed. This pulse-chase SILAC approach provides a very good reliability with a broad spectrum of proteins that can be analysed. Through the combination with ultracentrifugation even non-soluble and aggregated proteins could be analysed. Several hundred proteins were degraded in S. aureus during glucose starvation. Among them was the functional cluster of ribosomal proteins which is degraded in the early stationary phase. Furthermore proteins belonging to complexes were degraded with the same kinetic (e.g. NrdE, NrdF). In addition selective protein degradation took place according to functional categories (e.g., ribosomal proteins, biosynthetic, glycolytic enzymes) and not to regulatory groups (e.g. CcpA, SigB regulon).The investigation of a clpP deletion mutant in S. aureus revealed a greater susceptibility to aggregation, where the cells try to counteract with the expression of chaperones like GroEL/ES, ClpB and DnaK. The renaturation process is very ATP consuming and only takes place in energy rich phases of growth (e.g. from exponential to transient growth phase). Protein aggregation was found enhanced in the stationary phase. Furthermore, a higher GTP level compared to the wild-type probably resulted in a stronger CodY mediated repression with a rather low level of amino acids in clpP mutant cell. In addition substances like glycerol, which thermodynamically stabilise proteins in refolding processes (Maeda et al., 1996; Feng & Yan, 2008), were found in higher levels compared to the wild-type. A strong response to reactive oxygen species was detected in the clpP mutant strain, which is probably due to ROS production during the early stages of protein aggregation. Altogether, different methods were used for investigation protein degradation at a proteome-wide scale. Hundreds of degradation candidates were identified by gel-based and gel-free approaches in S. aureus wild-type cells. “Unemployed” proteins (e.g. ribosomal proteins, biosynthetic enzymes) were degraded and proteins particularly required and synthesized in glucose-starved cells such as TCA cycle enzymes were stable in the stationary phase. Investigation of the clpP mutant strain supports a proposed model for the pleiotropic phenotype and provides a deeper insight in the fine-tuned protein quality control and the important role of ClpP during starving conditions.
Rainbow trout (Oncorhynchus mykiss) represents the third most produced species of diadromous fish, with the total production of 0,732 million tonnes in 2009. More than one third of this production comes from Europe, where it is dominated by Norway, Italy and France. Germany is the fifth biggest producer in Europe, producing 21 thousand tonnes of rainbow trout in the value of 6,1 million Euro. However, the conditions in the intensive aquaculture often increase the disease susceptibility to many pathogens. One of the highest economic threats for a salmonids aquaculture is the causative agent of furunculosis, Aeromonas salmonicida subsp. salmonicida. Several strategies have been developed to protect the fish, but the traditional methods are either laborious or represent a potential risk for the environment. The selective breeding established more than 35 years ago in the brackish waters of Baltic Sea represent a attractive alternative, delivering a novel strain of rainbow trout better adapted to the brackish environment and exhibiting reduced mortality in the infection with A.salmonicida. Nevertheless, no information was available about the fundaments of this phenomenon. Thus, the aim of presented study was the identification of immune adaptations, which occurred during the 30 years of selection and favoured increased survival of “born” trout to the bacterial diseas es. In the presented work, the peritoneal cavity of rainbow trout has been used as a model for the investigation of disease resistance in fish. In the first chapter, the peritoneal cavity has been described as a unique niche of teleost immune system and the kinetic of peritoneal leukocytes induced by the stimulation has been analysed. Furthermore, a unique set of monoclonal antibodies has been used to evaluate the contribution of distinct cell populations on the inflammation and its resolution. In the second part of the study, the transcriptional changes of peritoneal leukocytes have been evaluated using the GRASP microarray. The following analysis provided unique insights into the local immune response in rainbow trout. The unprecedented combination of both data sets offers an unparalleled description of the local immune response in teleost fish and can be summarized into following facts. In general, the obtained results revealed, that the unstimulated peritoneal cavity is populated predominantly by lymphocytes with IgM+ Bcells being the major cells type. The rapid changes in the composition induced by the stimulation were underlined by the upregulation of major proinflammatory molecules such as IL1β, IL8 and TNFα within 12hpi. Although the initial phase of the reaction was dominated by myeloid cells, the cavity underwent within 72 hours two complete changes in the composition corresponding with the massive changes in the transcriptome. Eventually, the resolution of inflammation was marked by an increasing number of lymphocytes and correlated with the downregulation of pro-inflammatory genes to the initial level and upregulation of anti-inflammatory cytokines IL10 and TGFβ. Besides the general observations common to all treatments and both strains, our experiments revealed also remarkable differences between the antigenic stimulation and reaction towards pathogen. From these differences following conclusions can be drawn; the infection induces comparable reaction pattern as the stimulation, although the intensity of the reaction and number of cells is higher. These observations correlated with the higher expression of inflammatory molecules after the infection. Viable bacteria also prolong the myeloid phase of the reaction and delay the resolution of inflammation. Finally, model of peritoneal inflammation caused by A. salmonicida has been applied also to the second strain of rainbow trout, known for its higher resistance to infection. The comparison of obtained data suggested that resistant trout reacted to the antigenic stimulation and infection with a lower number of cells despite minor differences in the expression level of major pro-inflammatory molecules during early stages of the infection. Eventually, the resolution of inflammation and onset of adaptive immune response occurred in resistant trout almost 24 hours earlier and was correlating with an increased expression of anti-inflammatory cytokines IL10 and TGFβ. Notably, the increased survival of resistant strain correlates with the increased expression of antibacterial proteins such as NRAMP and hepcidin. Taken together, obtained data provided unprecedented insights into the local immune response in teleost fish and identified features conserved during the selection breeding in the brackish water of Baltic Sea. Additionally, combination of cellular and molecular data elucidates the peritoneal inflammation in fish and suggested high conservation of the immune response in the evolution.
Thiol or sulfhydryl groups are highly reactive functional groups in cellular systems. Molecules carrying thiol groups are mostly derivatives of the amino acid cysteine and are grouped as low molecular weight (LMW)-thiols: coenzyme A (CoA), glutathione (GSH) or bacillithiol (BSH). LMW-thiols can help in the maintenance of the reduced cellular environment as so called redox-buffers. Additionally, they act as co-factors in enzyme reactions or help in the detoxification of reactive oxygen or nitrogen species, electrophilic compounds or thiophilic metalloids (arsenite, tellurite). In proteins from different organisms cysteine is underrepresented compared to other amino acids, but still overtakes diverse roles. It is an important determinant in the tertiary and quaternary structure of proteins. The nucleophilic character of the thiol or thiolate group, respectively, makes cysteine the catalytically active amino acids of different enzymes. As a precursor cysteine participates in the formation of Fe-S clusters and coordinates different co-factors like heme, iron or zinc. The main goal of this study was the investigation of the different cellular thiol pools, now defined as the thiolome. The thiolome is the entity of the cellular thiol pools, i.e. LMW-thiols and protein thiols, and the dynamics between these pools. In Bacillus subtilis and Staphylococcus aureus mixed disulfides between protein thiols and free LMW-thiols, so called S-thiolations, were identified in different proteins in response to the thiol specific reagent diamide. Some of these S-thiolations were located at catalytically active cysteine residues. Subsequent analysis of metabolites supports this: the S-thiolation of the cobalamine-independent methionine-synthase MetE led to a decrease of the cellular methionine content. Additionally, the conversion of threonine to different branched-chain amino acids (BCAAs) was disrupted by the S-thiolation of the branched-chain amino acid aminotransferase YwaA, thereby probably inducing the synthesis of ppGpp, the alarmon of the stringent response. In addition to the identification of S-thiolations a technique was established which allowed the discrimination between intra- and intermolecular disulfides. The non-reducing/ reducing diagonal gel electrophoresis was applied to B. subtilis and S. aureus and confirmed known existing disulfide bonds, e.g. in alkyl hydroperoxide reductase AhpC or the thiol peroxidase Tpx. In response to diamide an increase of specific disulfide bonds in different proteins was observed. The analysis of the LMW-thiol content by an HPLC-approach allowed the observation of the dynamics of the thiolome. In response to diamide the reduced LMW-thiol content decreased by 75%, reduced protein thiols by 60%. Collaborations with other working groups allowed the identification of BSH in this approach. Additionally, an unknown thiol was found that is likely a derivative of BSH. Screening of the LMW-thiol content of different S. aureus-strains under various growth conditions revealed that strains 8325-4 and SH1000 lack BSH. The lack of BSH was attributed to an 8 bp-duplication in the bshC-gene that encodes the last enzyme of the BSH-synthesis. BSH-production was restored by transducing plasmid-borne functional BshC from strain Newman into strains 8325-4 and SH1000. The reconstitution of the BSH-synthesis aided in the resistance to the antibiotic fosfomycin but did not increase the resistance to different oxidants (diamide, sodium hypochlorite, hydrogen peroxide). The production of BSH had also positive effects on the survival of S. aureus inside human bronchial epithelial cells and murine macrophages in phagocytosis assays. Additionally, a GSH-uptake was observed into S. aureus which has before been known as a GSH-free bacterium. Taken together, this thesis provides the first insights into both, the LMW-thiol- and protein thiol pool of low GC, Gram-positive bacteria under different conditions. A plethora of different methodologies was used to describe the thiolome. The bacterial thiolome is a sophisticated system which is tightly regulated, but also flexible enough to not rely on determined molecules like BSH. The influences of the thiolome are not restricted to its own system and regulation, but also affect different branches of cellular physiology like the metabolism of BCAAs.
This thesis will discuss the different fields of application of the two soft ionization techniques ESI and MALDI in microbial proteomics and their importance for a better understanding of bacteria physiology. The general development in the past 25 years coming from 2D-gel analysis and protein identification by peptide mass fingerprint analysis via MALDI-TOF to genome wide quantitative LC-ESI-MS experiments with fast and sensitive ESI instruments is exemplary shown for the Gram-positive bacterium Bacillus subtilis in article I. Even though 2D-PAGE in conjunction with MALDI-MS is still an important tool in proteomic research, the more recently established global quantitative LC-ESI-MS workflows gain more and more relevance as they overcome 2D-PAGE based protein restrictions and enable the acquisition of higher accurate protein quantities. In article II such a workflow was used to analyze the physiological adaptation of Staphylococcus aureus to vancomycin treatment on a global-scale. Also post-translational modifications of proteins, that are important for regulation of their activity and allow rapid adaption to changed environmental conditions, could be analyzed by LC-ESI-MS workflows using special enrichment strategies (article III and IV). Despite the mentioned discrimination and less accurate quantification of proteins, 2D-PAGE analyses are still advantageous when analyzing large-scale time series experiments. To gain highly time resolved data but also very accurate relative quantities on a global-scale, 2D-PAGE-MALDI-MS and LC-ESI-MS techniques have been combined to investigate dynamic proteome adaptations of B. subtilis during nutrition shift as part of a global systems biology approach (article V). Also absolute quantities of proteins are of high interest for systems biology, but are still challenging to obtain on large-scale as well as with sufficient accuracy. In article VI a method that again combined 2D-PAGE-MALDI-MS and LC-ESI-MS was introduced to gain absolute protein quantities on global-scale. Utilizing the complementarity of 2D-PAGE and LC-ESI-MS this new workflow enabled fast and cost efficient data acquisition on absolute scale. In article VII we described for the first time a global quantitative LC-MALDI-MS workflow. Cross validation with an LTQ Orbitrap proofed that LC-MALDI-MS is able to process complex samples and obtain highly reliable quantities. The comparative analysis of data gained with both instrument types revealed biases for certain biochemical properties of MALDI as well as ESI instruments, resulting in a general complementarity of both ionization techniques. Article I Becher, D., Büttner, K., Moche, M., Hessling, B., Hecker, M., 2011. From the genome sequence to the protein inventory of Bacillus subtilis. Proteomics 11, 2971–2980. Article II Hessling,B., Bonn,F., Herbst,F.-A., Rappen,G.-M., Bernhardt,J., Hecker,M. and Becher,D. Global proteome analysis of vancomycin stress in Staphylococcus aureus. Submitted to Mol. Cell Proteomics. Article III Elsholz, A.K.W., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mäder, U., Bernhardt, J., Becher, D., Hecker, M., Gerth, U., 2012. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 109, 7451–7456. Article IV Chi, B.K., Gronau, K., Mäder, U., Hessling, B., Becher, D., Antelmann, H., 2011. S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics. Mol. Cell Proteomics 10, M111.009506. Article V Buescher,J.M., Liebermeister,W., Jules,M., Uhr,M., Muntel,J., Botella,E., Hessling,B., Kleijn,R.J., Le Chat,L., Lecointe,F., et al. (2012) Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science, 335, 1099–1103. Article VI Maass, S., Sievers, S., Zühlke, D., Kuzinski, J., Sappa, P.K., Muntel, J., Hessling, B., Bernhardt, J., Sietmann, R., Völker, U., Hecker, M., Becher, D., 2011. Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics. Anal. Chem. 83, 2677–2684. Article VII Hessling,B., Büttner,K., Hecker,M. and Becher,D. Global relative quantification with LC-MALDI – cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences. Submitted to Mol. Cell Proteomics.
The general stress response comprises approximately 200 genes and is driven by the alternative sigma factor SigB. Besides the process of sporulation with approximately 500 involved gene products under initial control of Spo0A are the two most significant and extensive cellular responses that can be observed in B. subtilis. The general stress response provides vegetative growing as well as non-growing and non-sporulating cells with a comprehensive cross-protective and preventive multiple stress resistance to various hostile environmental conditions. In contrast, the endospore is the most resistant but also dormant cell type produced by B. subtilis. The scope of this study was the identification of regulatory cascades driven by the general stress response sigma factor SigB to further elucidate the structure and function of the general stress regulon itself and to uncover potential intersections between the SigB response and other major developmental programs in the regulatory network of B. subtilis. It could be shown that the general stress regulon member yqgZ encodes a functional paralogue of Spx, the global regulator of the diamide stress regulon in B. subtilis. Global transcriptome and proteome studies led to the characterization of an YqgZ sub-regulon consisting of 53 positively and 18 negatively regulated genes. Due to its stringent SigB-dependent expression as well as its concerted action with SigB in regulation of its target genes YqgZ was renamed to MgsR which stands for “modulator of the general stress response”. Activity control of MgsR is stringently controlled at multiple levels. In addition to induction by SigB these mechanisms include (i) a positive autoregulatory loop of MgsR on the transcription level of its own structural gene, (ii) a post-translational redox-sensitive activation step by the formation of an intramolecular disulfide-bond within a conserved -CXXC-motif and (iii) rapid proteolytic degradation of MgsR by the ClpCP and ClpXP proteases, resul ting in extremely short in vivo half-lifes below 6 minutes. It was demonstrated that the activation of SigB is a prerequisite but not sufficient for a full expression of all general stress genes and that the SigB-dependent expression of MgsR provides the opportunity for additional redox-sensitive signal-reception, -processing and -integration beyond the primary decision of SigB activation. Our results describe a regulatory cascade integrating secondary oxidative stress signals into a SigB mediated regulatory cascade that is aimed at a precise fine tuning of target gene expression whose products are necessary for proper management of oxidative stress. Although primary oxidative stress stimuli do not typically induce SigB, our observation of redox-sensitive control by MgsR and several other reports that pointed at the implication of the general stress proteins in oxidative stress management led to the proposal that secondary oxidative stress may be a common component of multip le severe physical stress stimuli. This assumption could be supported by the results of a comprehensive phenotype screening of 94 mutants in single general stress genes upon treatment with hydrogen peroxide and the superoxide generating agent paraquat. A substantial amount of 62 mutants (66%) displayed significantly decreased survival rates in response to oxidative stress. The information gained by this phenotypic screening analysis provides a valuable basis for more directed assays to elucidate the biochemical functions of many so far uncharacterized general stress proteins and demonstrates that the SigB response and the regulatory fine tuning by MgsR plays a pivotal role in protection from secondary oxidative stress. Furthermore, it has been intensively discussed throughout the literature of the last years that the general stress response and the process of sporulation may represent mutually exclusive survival strategies of a non-growing B. subtilis cell, but the molecular basis for this assumption was missing until recently. By the identification of a functional SigB-type promoter (PsigB) adjacent to the spo0E, this gene was newly assigned to the general stress regulon. The spo0E gene encodes a phosphatase that specifically inactivates the master regulator of sporulation Spo0A~P by dephosphorylation. The SigB dependent induction of spo0E causes a block of sporulation specific transcription and produces a sporulation deficient phenotype. This effect was overcome by a deletion of the spo0E-SigB promoter, thus clearly addresses SigB activity. This regulatory mechanism is the first example for an integration of SigB inducing stimuli into the decision making process of sporulation initiation that provides a link to interconnect these two dominant and very likely mutually exclusive responses in the regulatory network of B. subtilis. The data presented here provide deeper insights into the structure and function of the general stress regulon in stress management.
Reactive oxygen species (ROS) can damage all cellular macromolecules and also produce secondary reactive intermediates, like reactive electrophilic species (RES) that include quinones or aldehydes. Low molecular weight (LMW) thiols are small thiol-containing compounds that play essential roles in the defense against ROS and RES in all organisms. The best studied LMW thiol is the tripeptide glutathione (GSH). Firmicutes bacteria including Bacillus und Staphylococcus species have been recently discovered to utilize the redox buffer bacillithiol (BSH). LMW thiols function as redox buffers to maintain the reduced state of the cytoplasm. Under conditions of oxidative stress, LMW thiols also react with protein thiols to form mixed LMW thiol – protein disulfides, termed S-thiolations, as major protection mechanism. Investigating the role of BSH in oxidative stress response and ROS-induced S-thiolations in Firmicutes bacteria was one subject of this PhD thesis. Specifically, the regulatory mechanisms and post-translational thiol-modifications in response to NaOCl stress were studied in the model bacterium for low-GC Gram-positive bacteria Bacillus subtilis. The transcriptome profile after NaOCl stress was indicative of disulfide stress and overlapped strongly with the response to diamide. NaOCl stress caused induction of the thiol- and oxidative stress-specific Spx, CtsR, PerR and OhrR regulons. Thiol redox proteomics identified only few NaOCl-sensitive proteins with reversible thiol-oxidations. Using mass spectrometry, eleven proteins were identified that were oxidized to mixed BSH protein disulfides (S-bacillithiolated) in B. subtilis cells after NaOCl-exposure. Methionine synthase MetE is the most abundant S-bacillithiolated protein in B. subtilis and other Bacillus species after NaOCl exposure. S-bacillithiolation of OhrR repressor leads to upregulation of the OhrA peroxiredoxin that confers together with BSH specific protection against NaOCl. S-bacillithiolation of MetE, YxjG, PpaC, and SerA causes hypochlorite-induced methionine starvation as supported by the induction of the S-box regulon. To further assess the conservation of targets for S-bacillithiolations in other Firmicutes bacteria, we studied the S-bacillithiolomes of Bacillus megaterium, Bacillus pumilus, Bacillus amyloliquefaciens, and Staphylococcus carnosus under NaOCl stress conditions. In total, 54 S-bacillithiolated proteins were identified, including 29 unique proteins and 8 conserved proteins involved in amino acid and cofactor biosynthesis, nucleotide metabolism, translation, protein quality control, redox and antioxidant functions. Together our data support a major role of BSH redox buffer in redox control and thiol protection of conserved and essential proteins against irreversible oxidation by S-bacillithiolations in Firmicutes bacteria. In response to ROS and RES, bacteria also activate the expression of antioxidant and detoxification enzymes, such as catalases, peroxidases, thiol-dependent peroxiredoxins and other specific oxidoreductases to detoxify ROS and RES. These defense mechanisms are often controlled by redox-sensitive transcription factors. B. subtilis encodes redox-sensing MarR-type regulators belonging to the OhrR and DUF24-families that are conserved among bacteria. Hence, we were further interested in this PhD thesis to study at the molecular and structural level the redox-sensing mechanisms of novel redox-sensing MarR/DUF24-type regulators in B. subtilis. We have characterized the regulatory mechanisms of HypR, YodB and CatR that sense and respond to hypochlorite, diamide and quinones stress. HypR is the first DUF24-family regulator whose crystal structure was resolved. HypR senses specifically disulfide stress and controls positively expression of the flavin oxidoreductase HypO after NaOCl and diamide stress. HypR resembles a 2-Cys-type regulator with a reactive nucleophilic N-terminal Cys14 and a second C-terminal Cys49. Besides HypR, B. subtilis encodes further MarR/DUF24-family members including the paralogous YodB and CatR repressors that sense quinones and diamide. YodB controls the azoreductase AzoR1, the nitroreductase YodC, and the Spx regulator. YodB resembles a 2-Cys-type MarR/DUF24-family regulator with three Cys residues (Cys6, Cys101, and Cys108) that form intermolecular disulfides in vivo under oxidative stress. YodB and its paralog CatR were further identified as repressors of the catDE operon encoding a catechol-2,3-dioxygenase that also contributes to quinone resistance. Although CatR is a 1-Cys-type regulator, our data showed that CatR also forms intermolecular disulfide in response to diamide and quinones in vitro. Thus, HypR, YodB and CatR are controlled by 2-Cys-type thiol-disulfide redox switches to sense disulfide and RES stress conditions, and to control specific RES detoxification enzymes.
Bats are ancient mammals that evolved more than 50 million years ago. There are 1,240 different species (> 20% of mammalian species) described so far, which represent one of the most abundant, diverse and widely distributed mammalian groups. Bats are the only mammals which actively fly and therefore can migrate to different areas of the world. It has been increasingly recognized that bats are reservoirs for more than 100 virus species, and several are associated with animal and human epidemics. As natural hosts of rabies virus (RABV) and related lyssaviruses, bats have become a focus of research not only in South America and Africa, but also in Europe and North America. Bats are also considered to be unique in their potential to host emerging and re-emerging zoonotic viruses. To evaluate and reduce the potential risk of rabies transmission to humans or carnivore hosts (like fox, raccoon and dog etc.), active and passive surveillance studies of bat have been performed. Using these approaches diverse lyssaviruses have been detected in bats. However, these studies did not explain the rarely discovered epidemics and the underlying resistance or immune mechanisms in bats as natural hosts for lyssaviruses. Probably, bats are more resistant to lyssavirus infections than other animals. This hypothesis is introducing the research questions of the present thesis: (1) How do the innate immune responses protect bats from fatal outcome of lyssavirus infections? Interferon (IFN) responses which can be induced by the recognition of viruses by pattern recognition receptors act as the first line of defense against lyssavirus infections. Therefore, type I and type III IFNs from European bats were cloned and functionally characterized in this thesis (Chapter 2 and 4). (2) How do the lyssaviruses adapt to escape the host defenses by counteracting the IFN-mediated immune responses? And how do the bats control the viral replication via the IFN responses? To explore the complicated interactions and understand how European bats (Eptesicus serotinus, Myotis myotis and Nyctalus noctula) interact with European bat lyssaviruses (EBLV-1 and 2), a natural host related model for investigations of the bat´s immune system and the virus-host interactions has to be established. Since all of 52 identified European bats species are endangered and strictly protected, stable cell lines from different tissues of M. myotis for in vitro studies were developed and used for molecular and functional studies (Chapter 3 and 4). The data obtained from this thesis revealed that: (a) European bat IFNs do have similar but also distinct molecular characteristics compared with other mammalian IFNs (Chapter 2 and 4); (b) Both investigated bat type I IFNs, IFN-Kappa; and IFN-Omega; present potent anti-lyssaviral activities and display a pathogen associated pattern in the tested cell line (Chapter 2); (c) The established immortalized M. myotis cell lines are differently susceptible to lyssaviruses and contain a functional IFN-mediated signaling cascade (Chapter 3); (d) Bat type III IFN-Lambda;s display cell-type specific functions due to the distinct expression of the IFN-Lambda; receptor (Chapter 4); (e) In bat cell lines a possible evasive strategy of lyssavirus is based on the counteraction of IFN production and/or IFN-mediated defensive pathways (Chapter 3); (f) The higher resistance of brain derived cell line MmBr compared to other cell lines to lyssavirus infection indicates the natural ability of bat´s central nervous system to control the growth of neurotropic virus, which might be an essential reason for the nonclinical outcome (Chapter 3). Overall, the present thesis provides first insights into IFN-mediated innate immune responses against RABV and EBLVs infection in their natural reservoir hosts and an useful toolbox for comparative analysis of virus-host interactions.
In this study the potential of molecular RT-PCR based methods for diagnostic or epidemiological investigations concerning negative-sense RNA viruses should be demonstrated exemplary for orthobunyaviruses (segmented genome) and lyssaviruses (non segmented genome). The recent discovery of a novel orthobunyavirus from the Simbu serogroup, Schmallenberg virus (SBV), via next generation sequencing and metagenome analysis led to the development of novel molecular detection methods. Due to the potential emergence of further orthobunyaviruses from the Simbu serogroup, a generic pan-Simbu real-time RT-PCR system was developed. This system was able to detect all tested Simbu serogroup viruses. As additional feature a species classification via sequencing is possible. Moreover, the novel pan-Simbu real-time RT-PCR system seems to offer a broad detection spectrum for orthobunyaviruses in general. Hence, this protocol allows a broad screening of samples predominantly for Simbu serogroup virus genomes but also might allow the identification of some related orthobunyaviruses in mammalian or insect samples. A comparison of the pan-Simbu real-time RT-PCR system with diagnostic real-time RT-PCRs revealed an overall higher sensitivity of the diagnostic assays for SBV detection. The diagnostic SBV-S3 assay convinced with the highest sensitivity and reliability for SBV detection. Additionally, the SBV-M1 assay turned out as highly specific for SBV and therefore is a valuable tool for a precise diagnosis in geographical regions where multiple orthobunyaviruses are endemic. Furthermore, the SBV genome diversity in Germany was investigated using a molecular epidemiological approach. Genome variability was extremely high in the N-terminal region of the putative envelope glycoprotein Gc which might have an impact on immunogenicity or host-cell infection. Phylogenetic analyses indicated that sequence variation is independent of host species and geographical distribution. In contrast to SBV as a novel pathogen, rabies encephalitis (caused by the prototype lyssavirus Rabies virus) is known for more than 4000 years. Thus numerous molecular techniques have been developed for lyssavirus detection, considering the diversity of this genus they all have certain limitations as regards their diagnostic range. Results of a lyssavirus ring trial among European laboratories indicate that RT-PCR could be a highly reliable diagnostic tool if at least two independent tests with broad diagnostic range are applied. Another approach suggested that a change from two-step to one-step PCR strategy or a variation of the RT-chemistry may have a remarkable influence on assay performance. However, no ultimate approach or strategy has been found yet, that would facilitate rabies routine diagnosis or epidemiological surveys on molecular grounds. Thus, there is a need for a potent, reliable and practical system for lyssavirus diagnosis and characterization, suitable as a second diagnostic line next to classical techniques like the fluorescent antibody test. For this purpose a diagnostic two level cascade protocol was developed with emphasis on the most relevant European lyssaviruses. On a first level two independent generic pan-lyssavirus screening assays, targeting different genomic regions, were applied. On a second level two probe-based species-specific multiplex PCR systems for the rapid classification of European lyssaviruses were used. All applied assays displayed an overall highly sensitive and specific detection with an excellent reproducibility and repeatability. Moreover, the diagnostic cascade protocol combines all known advantages of the real-time PCR technology including speed and reduced risk of cross-contamination with improved safety of molecular testing based on a double-check strategy for the screening as well as the confirmatory assays. In the frame of the second Bokeloh bat lyssavirus case in a German bat, the capability of real-time PCR for the quantification of viral loads was demonstrated. Another convenient example for the potential of molecular RT-PCR based methods is the epidemiological investigation of the rabies epizootic in Namibian kudu antelopes. Phylogenetic analyses of a 602 bp fragment of the nucleoprotein gene indicated a separate grouping of the Rabies virus (RABV) isolates from kudu apart from RABV isolates from jackals. Full genome sequencing revealed unique mutations in the glycoprotein gene of RABV isolates from kudu, suggesting an independent rabies cycle in Namibian kudu antelopes. All given examples were used to illustrate the application spectrum of molecular RT-PCR based methods for diagnostic or epidemiological purposes. The advantages of molecular techniques were emphasized and in particular real-time RT-PCR systems proved their fitness for purpose and appear to represent standard techniques for the next decade.
Microbial infections can be either caused by a single species or complex multi-species consortia. One of the most prominent opportunistic human pathogens leading to mono- or mixed-species infections is the Gram-negative bacterium Pseudomonas aeruginosa. Understanding the molecular basis of its adaptation to infection-related stresses is an essential prerequisite for the prevention and treatment of P. aeruginosa infections. We therefore employed state-of-the-art proteomics approaches to elucidate the molecular adaptation mechanisms of P. aeruginosa to infection-related conditions. Moreover, structure, function and interaction of complex microbial consortia containing P. aeruginosa and causing catheter-associated urinary tract infections were investigated by metaproteomics analyses. Our investigations revealed that the adaptation of P. aeruginosa during infection is either based on gene expression changes caused by environmental signal integration or by gene mutations leading to a selective advantage in a particular host environment. In study I, investigating the proteome response of P. aeruginosa biofilms to the clinical relevant antibiotic ciprofloxacin, global changes in the protein profile were observed. Ciprofloxacin induced the expression of proteins involved in the Lex-induced SOS-response, drug efflux pumps and gene products of the ciprofloxacin-responsive prophage cluster and repressed the expression of porins and DNA-binding proteins. In study II the transcriptome and proteome of two clonal P. aeruginosa lineages during long-term colonization of cystic fibrosis (CF) patient’s lungs were analyzed. Point mutations in global regulator genes, i.e. retS, gacS, and gacA, were identified by genomic sequencing. Inactivation of RetS, found two years after the initial colonization, induced the expression of genes involved in chronic infections and coding for the type 6-secretion system (T6SS). Additional mutations in the GacS/GacA two-component regulatory system (TCS) were found to repress the expression of T6SS proteins and to induce the expression of proteins belonging to the type 3-secretion system (T3SS). In study III we elucidated the niche-specific adaptation of P. aeruginosa isolates from different infection sites by investigating their protein expression patterns and glucose metabolic fluxes. We could show that isolates from the urinary tract express a higher amount of proteins involved in the acquisition of micronutrients (i.e. iron) and carbohydrates compared to isolates from the CF lung. In study IV 16S rDNA sequencing and metaproteomics were employed to demonstrate that the investigated CAUTI-related biofilms consisted of two to five different species with one or two species dominating the mixed community. Following this line of research, we investigated in study V structure and function of a biofilm of a long-term catheterized patient, which was predominantly composed of P. aeruginosa and Morganella morganii, but also contained a minor proportion of the obligate anaerobe Bacteroides sp.. The comparison of in vivo and in vitro protein expression profiles of P. aeruginosa and M. morganii indicated that iron and carbohydrates are the major growth-limiting factors in the bladder. These results indicate different nutritional strategies of the two pathogens in the bladder environment. A comparison of urinary protein profiles of healthy persons and catheterized patients suggested that the human innate immune system is induced by CAUTIs. Moreover, numerous proteins involved in nutritional immunity, e.g. iron-, calcium- and magnesium-binding proteins, were found to be more abundant in the urine of catheterized patients. A follow-up (meta)proteomics study (study VI) aiming at the elucidation of interspecies interactions during multi-species infections indicated that the urease-positive uropathogen Proteus mirabilis induces the precipitation of metal ions by urine alkalization and thereby limits the availability of these important micronutrients for other co-infecting bacteria. This limitation seems to be sensed by the P. aeruginosa PhoP-PhoQ two-component system (TCS) leading to an increased resistance to antimicrobial peptides and biofilm-forming capacity of the pathogen. Also during co-cultivation of P. aeruginosa with Staphylococcus aureus a slight increase in the expression of the PhoP-PhoQ TCS and the alkaline protease could be observed (study VII). In study VIII a combined metagenomics and metaproteomics approach was employed to investigate structure and function of the lichen Lobaria pulmonaria, a complex consortium consisting of a fungus, an algal partner, cyanobacteria, and a highly diverse bacterial microbiome. The results presented in this work contribute to a better understanding of the manifold and complex bacterial adaptation mechanisms to infection-related and environmental stress and thereby foster the development of novel treatment and prevention strategies.