Fig. 3.5 Multicolor imaging of expression patterns under different growth conditions in B. subtilis. Delta-2D software (Decodon) was used to visualize complex protein expression patterns on the 2-D gel image in the standard pH range 4-7. The color code is presented in the top left corner. Proteins only induced by single stresses are colored red (H, heat), light-blue (O, oxidative stress), and orange

(E, ethanol), respectively Proteins induced by oxidative stress as well as heat stress are colored yellow, proteins induced by ethanol stress and heat stress are colored dark-blue, proteins induced by oxidative and ethanol stress can be recognized as purple spots, and, finally, proteins induced by all three stimuli are displayed in green. (This figure also appears with the color plates.)

able, but strongly induced by glucose starvation, are colored red, forming the glucose starvation stimulon. Collecting all these proteome data combined with basic physiological knowledge, one can gain a comprehensive picture what is happening in the cell, understanding cell physiology as a entity.

The proteomic signatures of stress or starvation stimuli [14] can be used as diagnostic tools for prediction of the physiological state of cells grown in a bioreactor or in a biofilm, etc. This is valid not only for growing cells (proteome signatures indicate the availability of nutrients for instance), but also for nongrowing cells. On the basis of the proteomic signatures, one can predict whether nongrowing cells have suffered from heat or oxidative stress or from glucose or phosphate starvation (Fig. 3.7, see page 54). During the stationary phase of B. Ucheniformis cells there is a strong proteomic signature of oxidative stress (KatA, AhpC etc.), followed by a signature of protein stress, indicated by the induction of ClpC [15]. Pro-teomic signatures can also be used to predict the action mechanism of unknown drugs. Nitrofurantoin, for instance, an antibiotic that has been in use for a long time, induces almost the same signature as diamide does, strongly suggesting

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