Evaluating the suitability of essential genes as targets for antibiotic screening assays using proteomics

References

[1] Alekshun, M.N., and Levy, S.B. (2007). Molecular mechanisms of antibacterial multidrug resistance. Cell 128, 1037–1050 17382878.
[2] Bandow, J.E., Br?tz, H., Leichert, L.I.O., Labischinski, H., and Hecker, M. (2003). Proteomic approach to understanding antibiotic action. Antimicrob Agents Chemother 47, 948–955 12604526.
[3] Br?tz-Oesterhelt, H., Bandow, J.E., and Labischinski, H. (2005). Bacterial proteomics and its role in antibacterial drug discovery. Mass Spectrom Rev 24, 549–565 15389844.
[4] Brun, V., Dupuis, A., Adrait, A., Marcellin, M., Thomas, D., Court, M., Vandenesch, F., and Garin, J. (2007). Isotope-labelled Protein Standards. Mol Cell Proteomics 6, 2139–2149 17848587.
[5] Domon, B., and Aebersold, R. (2010). Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol 28, 710–721 20622845.
[6] Fischbach, M.A., and Walsh, C.T. (2009). Antibiotics for emerging pathogens. Science 325, 1089–1093 19713519.
[7] Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 7542800.
[8] Gao, F., and Zhang, R.R. (2011). Enzymes are enriched in bacterial essential genes. PLoS One 6, e2168321738765.
[9] Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W., and Gygi, S.P. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100, 6940–6945 12771378.
[10] Goh, S., Boberek, J.M., Nakashima, N., Stach, J., and Good, L. (2009). Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli. PLoS One 4, e606119557168.
[11] Hutchison, C.A. III, Peterson, S.N., Gill, S.R., Cline, R.T., White, O., Fraser, C.M., Smith, H.O., and Venter, J.C. (1999). Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286, 2165–2169 10591650.
[12] Jordan, I.K., Rogozin, I.B., Wolf, Y.I., and Koonin, E.V. (2002). Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12, 962–968 12045149.
[13] Kline, K.G., and Sussman, M.R. (2010). Protein quantitation using isotope-assisted mass spectrometry. Annu Rev Biophys 39, 291–308 20462376.
[14] Laurent, J.M., Vogel, C., Kwon, T., Craig, S.A., Boutz, 000Daniel, R., Huse, H.K., Nozue, K., Walia, H., Whiteley, M., Ronald, P.C., Marcotte, E.M. (2010). Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics 10, 4209–4212 .
[15] Lu, P., Vogel, C., Wang, R., Yao, X., and Marcotte, E.M. (2007). Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25, 117–124 17187058.
[16] Maier, T., Güell, M., and Serrano, L. (2009). Correlation of mRNA and protein in complex biological samples. FEBS Lett 583, 3966–3973 19850042.
[17] Mayya, V., Rezual, K., Wu, L., Fong, M.B., and Han, D.K. (2006). Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol Cell Proteomics 5, 1146–1157 16546994.
[18] McDevitt, D., and Rosenberg, M. (2001). Exploiting genomics to discover new antibiotics. Trends Microbiol 9, 611–617 11728875.
[19] Mushegian, A.R., and Koonin, E.V. (1996). A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93, 10268–10273 8816789.
[20] Singh, S.B., Phillips, J.W., and Wang, J. (2007). Highly sensitive target-based whole-cell antibacterial discovery strategy by antisense RNA silencing. Curr Opin Drug Discov Devel 10, 160–166 17436551.
[21] Van Hoek, A.H.A.M., Mevius, D., Guerra, B., Mullany, P., Roberts, A.P., and Aarts, H.J.M. (2011). Acquired Antibiotic Resistance Genes: An Overview. Front Microbiol 2, 1–27 21716958.
[22] Wei, J.R., Krishnamoorthy, V., Murphy, K., Kim, J.H., Schnappinger, D., Alber, T., Sassetti, C.M., Rhee, K.Y., and Rubin, E.J. (2011). Depletion of antibiotic targets has widely varying effects on growth. Proc Natl Acad Sci U S A 108, 4176–4181 21368134.