Pa0943

Protein Map Comparisons Table 2 (Continued)

Function Protein (gene)

Estimated pI MW (kDa) Locus3 Level4

Conserved hypothetical protein Conserved hypothetical protein Conserved hypothetical protein Conserved hypothetical protein Hypothetical protein

Hypothetical protein Hypothetical protein Hypothetical protein

Conserved hypothetical protein Conserved hypothetical protein

7.61 16

7.25 19

8.78 29

8.23 29

PA1746 -18

PA2575 -18.48

PA3313 +18.48

PA3731 +48 PA4352 -18.48

PA4453 +18

PA4463 -18-48

PA4495 -48

PA4739 -48 PA5178 -18.48

Notes/aProtein identification number according to Pseudomonas genome project database (http:/ /www.pseudomonas.com).

b+, overexpressed; -, underexpressed; superscript, duration of incubation.

alliance of the proteomic approach with classical tools of molecular biology (e.g., mutagenesis aapproaches) will probably allow in the near future to propose new targets against harmful biofilms (e.g., by identifying key proteins such as genetic determinants of biofilm resistance to antimicrobials).

4. Notes

1. All materials must be sterilized at 120°C during 15 min before use.

2. The device has been described in the paper by Vilain et al. (6).

3. Caution, explosive after contact with air, work in a chemical hood.

4. Experiments should be performed in a bacteriological hood.

5. A calibration curve must be built by using increasing concentrations of bovine serum albumin (Sigma).

6. Better results are obtained by substituting Bromophenol Blue with Coomassie Brilliant Blue (6).

7. Fill from the top with a pipet.

8. Use a micropipet and eliminate air bubbles.

9. Avoid air bubbles.

10. The gel must be made the previous day.

11. The solutions must be precooled at 4°C.

References

1. Costerton, J. W., Lewandowski, Z., Caldwell, D. E., Korber, D. R. and Lappin-Scott, H. M. (1995) Microbial biofilms. Annu. Rev. Microbiol. 49, 711-745.

2. Davies, D. (2003) Understanding biofilm resistance to antibacterial agents. Nature Rev. 2, 114-122.

3. Fleischmann, R. D., Adams, M. D., White, O., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-521.

4. Wilkins, M. R., Sanchez, J. C., Gooley, A. A., Appel, R. D., Humphery-Smith, I., Hochstrasser, D. F., and Williams, K. L. (1995) Progress in proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev. 13, 19-50.

5. Sauer, K. (2003) The genomics and proteomics of biofilm formation. Genome Biol. 4, 219.

6. Vilain, S., Cosette, P., Zimmerlin, I., Dupont, J.-P., Junter, G.-A., and Jouenne, T. (2004) The biofilm proteome: homogeneity or versatility? J. Proteome Res. 3, 132-136.

7. Caldwell, D. E. (1995) Cultivation and study of biofilm communities. In: Microbial Biofilms, Lappin-Sott, H. M. and J.W. Costerton, eds., Cambridge University Press, Cambridge, UK, pp. 64-79.

8. Brown, M. R. W. and Barker, J. (1999) Unexplored reservoirs of pathogenic bacteria: protozoa and biofilms. Trends Microbiol. 7, 46-50.

9. Schembri, M. A. and Klemm, P. (2001) Coordinate gene regulation by fimbriae-induced signal transduction. EMBO J. 20, 3074-3081.

10. Otto, K. and Silahvy, T. J. (2002) Surface sensing and adhesion of Escherichia coli under control of the Cpx signalling pathway. Proc. Nat. Acad. Sci. USA 99, 2287-2292.

11. Aires, J. R., Köhler, T., Nikaido, H., and Plesiat, P. (1999) Involvement of an active efflux system in the natural resistance of Pseudomonas aeruginosa to aminoglycosides. Antimicrob. Agents Chemother. 43, 2624-2628.

12. Köhler, T., Michea-Hamzehpour, M., Epp, S. F., and Pechere, J. C. (1999) Carbapenem activities against Pseudomonas aeruginosa: respective contributions of OprD and efflux systems. Antimicrob. Agents Chemother. 43, 424-427.

13. Sauer, K. and Camper, A. K. (2001) Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J. Bacteriol. 183, 6579-6589.

14. Svensäter, G., Welin, J., Wilkins, J. C., Beighton, D., and Hamilton, I. R. (2001) Protein expression by planktonic and biofilm cells of Streptococcus mutans. FEMSMicrobiol. Lett. 205, 139-146.

15. Sauer, K., Camper, A. K., Erlich, G. A., Costerton, J. W., and Davies, D. G. (2002) Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J. Bacteriol. 184, 1140-1154.

16. Schembri, M. A., Kjsrgaard, K., and Klemm, P. (2003) Global gene expression in Escherichia coli biofilms. Mol. Microbiol. 48, 253-267.

17. Vilain, S., Cosette, P., Hubert, M., Lange, C., Junter, G.-A., and Jouenne, T. (2004) Comparative proteomic analysis of planktonic and immobilized Pseudomonas aeruginosa cells: a multivariate statistical approach. Anal. Biochem. 329,120-130.

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