Outlook Second Generation Proteomics and New Fields in S aureus Physiology and Infection Biology

The panorama view of proteomics visualizes cellular events never seen before. Not just a few interesting proteins, but almost all proteins of the cell can be followed by proteomics. The challenge now is not to get lost in the mass of data and not to remain on the surface of the problem, but to leave the first, descriptive level which is absolutely required for a comprehensive and mechanistic understanding of the phenomena to be studied. The panorama view of proteomics, however, allows selection of the most interesting phenomena that deserve more detailed study. To understand life processes, more detailed first-level proteomics (protein expression profiling) must be combined with second-level proteomics in combination with biochemistry and molecular genetics. This second-level proteomics allows crucial questions to be addressed, such as analyzing:

• The fate of each individual protein (protein targeting/protein secretion)

• The protein interaction network (interactome)

• Post-translational modifications such as protein phosphorylation at the proteomic scale

• Protein aging or protein damage at the proteomic scale

Finally, it also

• Allows researchers to follow the stability or proteolysis rate of each individual protein separated by 2-D PAGE

These proteomic studies of the second generation require gel-based and non-gel-based proteomics relying on multidimensional chromatography followed by highly sophisticated MS/MS techniques. This proteomics of the second generation will in the future open new and fascinating fields of S. aureus physiology not yet addressed in a systematic way, an essential part and great challenge for S. aur-eus cell physiology in the postgenome era. The combination of first- and second-level proteomics with comparative genomics, structural genomics, transcrip-tomics, metabolomics, and bioinformatics will open the way towards a comprehensive understanding of life, ending up in a systems biology approach to S. aur-eus in the near future.

66 I 3 Physiological Proteomics of Bacillus subtilis and Staphylococcus aureus ... Acknowledgments

We are very grateful to all coworkers and students for their excellent data on the proteomics of Bacillus and Staphylococcus species. The support of Jörg Bernhardt and Stephan Fuchs in preparing the figures is acknowledged. We also thank Uwe Völker, Jörg Hacker, Wilma Ziebuhr, Knut Ohlsen, Christof von Eiff, and Fritz Götz for longstanding and fruitful collaboration, and Decodon GmbH (Greifswald) for providing Delta-2D software. This work was supported by grants from the Bundesministerium für Bildung und Forschung (031U107A/-207A; 031U213B), the Deutsche Forschungsgemeinschaft (GK212/3-00; HE1887/7-1; HE1887/7-2; HE1887/6-5; HE1887/6-6), the European Union (Bacell factory QLK3-CT-1999-00413; Bacell network GLG2-CT-1999-01455) and the Fonds der Chemischen Industrie to M. H.

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