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3 Fig. 3.6 Dynamics of protein synthesis profiles of growing and glucose-starved cells of B. subtilis. A Individual dual-channel 2-D patterns of protein synthesis and accumulation recorded during the different phases of the growth curve are assembled into a "life movie." B Growth curve (optical density at 500 nm) and 35S-l-methionine incorporation (million cpm per 60ig protein). C Patterns of selected examples representing different branches of cellular physiology. Sample points correspond to the following growth phases depicted are shown in the growth curve: 1, 2, exponential growth; 3-7, glucose starvation; 8, 9, recovery of growth after readdition of glucose. The bar graphs on the left display normalized relative synthesis rates of the individual proteins at the different time points. (This figure also appears on page 52.)

oxidative stress

heat stress oxidative stress

3 Fig. 3.7 Proteomic signatures of B. subtilis of different physiological stress/starved conditions. Comparisons ofthe protein profile of both exponentially growing and stressed B. subtilis cells reveal signature-like changes that are specific to certain stress stimuli (e.g., induction ofthe catalase KatA by oxidative stress). The individual sections ofthe 2-D gels display typical parts of the proteomic signatures of oxidative or heat stress, the stringent response or limitation of glucose or phosphate. (This figure also appears on page

3 Fig. 3.9 Assignment of proteins identified in S. aureus COL to biochemical pathways and other essential cellular components. Proteins that have not been identified in the 2-D gel images thus far are colored green. A Purine and pyrimidine metabolism, B glycolysis, pentose phosphate shunt, and citric acid cycle, C oxidative stress resistance, D ATPase components, E proteolysis, F components of the translational machinery, G amino acid metabolism, H fatty acid synthesis and metabolism of cell wall components, and I biotin metabolism. (This figure also appears on pages 58/59.)

â–  metabolism: ia glycolysis

B tricarboxylic acid cycle a fermentation

Aerotitc growth

30 min anaefot« growth

Fig. 3.10 Protein pattern of cells of S. aureus COL grown under aerobic (green) and anaerobic (red) conditions in synthetic medium. Cells were pulse-labeled (5 min) with 35S-l-methionine under aerobic conditions and 30 min after imposition of anaerobic growth conditions. Radioactively labeled proteins were visualized by the phosphoimaging technique. Proteins whose synthesis was increased after shifting to anaerobic growth conditions are shown in red (e.g., enzymes involved in glycolysis and fermentation) and those whose synthesis was decreased are shown in green (e.g., enzymes involved in the TCA cycle). (This figure also appears on page 60.)

pH 10 pH3

sAnn ?o

SA20j SA20971

time (mir)

Fig. 3.12 The extracellular proteome of S. aur- Ruby. Extracellular proteins present in eus RN6390 at low (green image) and high cell increased amounts at high cell densities are densities (red image). 250 ig proteins of the labeled red and those proteins only present supernatant of cells grown in TSB medium at at low cell densities are labeled green. (This an optical density OD540 = 1 and 5 were sepa- figure also appears on page 63.) rated by 2-D gels and stained with Sypro

Fig. 3.13 A Growth of S. aureus RN6390 in TSB-Medium. The sampling is indicated by an arrow and a letter in the respective growth curve. B, C Virulence factors of S. aureus RN6390 whose amount depends on the growth phase. The amount of the respective proteins at OD540 = 1 (green) of cells grown in TSB medium was compared with the amount of these proteins at higher optical densities

Fig. 3.13 A Growth of S. aureus RN6390 in TSB-Medium. The sampling is indicated by an arrow and a letter in the respective growth curve. B, C Virulence factors of S. aureus RN6390 whose amount depends on the growth phase. The amount of the respective proteins at OD540 = 1 (green) of cells grown in TSB medium was compared with the amount of these proteins at higher optical densities

(red). B Virulence factors only present at low cell densities. C Virulence factors only present at high cell densities. In addition, the amount ofthe respective proteins in the wild type strain was compared to the amount of these proteins in various regulatory mutants (agr, sarA, sigB) known to be impaired in virulence. Proteins were stained with Sypro Ruby. (This figure also appears on page 64.)

Fig. 5.2 Comparison of the genetic organization of GEI IINissle1917 and the pheV-associated PAI of E. coli strain CFT073 (A) demonstrating the loss of the a-hemolysin-encoding determinant (hly) and of large parts ofthe P fimbria! operon (pap) in strain Nissle 1917. The DNA sequences comparison of the two islands is visualized using Artemis and ACT [104]. Identical regions of the two islands are highlighted in red. Functionally related DNA regions are indicated by different colors as shown. (B) Enlarged section of GEI IINissle1917 comprising the partially deleted P fimbrial determinant. (This figure also appears on page 98.)

pheV

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