Table 1.
Stress experiments included in the proteome signature library.
Figure 1.
The relational database model.
Aureolib uses a MySQL database to store expression data and relevant information on protein annotation, statistical analyses, and experimental setups.
Figure 2.
Functions and graphical user interface of Aureolib.
(A) Aureolib consists of three different levels for data management, data processing and visualization of data. (B) Combined with an intuitive user interface accessible by generic web browsers Aureolib provides helpful tools for expression data analyses and data visualization.
Figure 3.
Intra-experimental comparison of protein synthesis patterns in response to different stimuli.
Quantification data for all detected protein spots were normalized (total) and standardized (z-score). Significant changes of spot intensities were determined for each experiment (ANOVA, α = 0.1, distribution based on 1000 permutations) and the corresponding expression values were used for hierarchical sample clustering (HCL, Euclidean distance, complete linkage). Accordingly, the stimuli can be divided into two classes: (A) Stimuli causing continuous changes of the protein synthesis pattern and (B) stimuli transiently affecting the protein synthesis pattern.
Figure 4.
General aspects of S. aureus stress response.
Inter-experimental analyses of stress induced protein synthesis patterns revealed general and specific effects on global protein synthesis. (A) The majority of the synthesis profiles showed a significant (ANOVA, α = 0.1, p-values based on 1000 permutations, absolute threshold of 2.5) induction or repression rate in response to one or two stimuli. (B) To identify more general effects a pairwise comparison of all experiments was performed using protein synthesis profiles significantly changed at least one time point following exposure to the different stimuli (t-test, α = 0.1; p-values based on all possible permutations, adjusted Bonferroni correction). The number of induced (orange) and repressed (blue) protein synthesis profiles shared by the respective stimuli is shown. The total number of synthesis profiles significantly induced or repressed by the respective stimulus are given on the right side. (C) Overlap of marker proteins induced in response to diamide, puromycin, and heat as well as to nitric oxide, fermentation, and nitrate respiration are shown.
Figure 5.
Inter-experimental expression profiles of selected proteins.
Synthesis ratios (stress vs. control) are shown as log2 values. Fold changes above 2.5 and below 0.4 are colored in orange and blue, respectively. Significant changes are marked by an asterisk (*). Synthesis profiles of proteins belonging to the Rex (A) and Ctsr/HrcA (B) regulon as well as proteins involved in leucine biosynthesis (C) are shown in more detail.
Figure 6.
Differential expression of protein isoforms in response to diamide (A) and nitrosative stress (B).
Sectors of 2D gels covering the regions where CysK, GuaB, Upp, SACOL0618 and SACOL1895 are located. Proteins represented by multiple spots indicate post translational modifications. In the present approach the synthesis of protein isoforms differing in pI and/or molecular weight was separately analyzed.
Table 2.
Regulons in S. aureus.
Figure 7.
Expression clusters of σB-dependent proteins.
(A) Hierarchical clustering (Euclidian distance/complete linkage) of synthesis profiles of proteins for which transcription of the respective genes has been shown to be influenced by σB [48], [49], [50]. (B) Expression profiles of solely σB-dependent proteins. Abbreviations for stress conditions are: O (H2O2), D (diamide), P (paraquat), N (nitrogen monoxide), F (fermentation), A (nitrate respiration), H (heat stress), U (puromycin), and M (mupirocin). 1) Support for a σB-dependent transcriptional start point: experimental (black square), predicted (gray square), not identified yet (white square) [37], [43], [70]. 2) Impact of σB: solely σB-dependent/major effect on expression (black square), co-regulated by additional factors (gray squares), or not determined (white square) [50], [70]. Csb (controlled by sigma B) nomenclature based on Gertz et al. [50].
Figure 8.
Response of S. aureus to H2O2.
(A) S. aureus COL was cultivated in synthetic medium at 37°C and treated with 10 mM H2O2 at OD500 0.5 (0 min). (B) Protein synthesis profiles were normalized using total normalization and standardized (z-score). Significantly changed synthesis profiles were determined by ANOVA (α = 0.1, distribution based on all permutations, absolute threshold of 2.5). Based on their expression kinetics in response to H2O2, proteins can be allocated to three groups: proteins which are induced during the acute phase immediately after imposition of stress (red lines), proteins induced during resumption of growth (blue lines) and proteins highly expressed in the tolerance phase (green lines).