Essential Genes in E. coli

This page was last updated March 2004. It provides links to data on essential genes in E. coli, and shows a short list of E. coli essential genes identified from the Neidhardt E. coli books (Neidhardt and Curtiss, 1996). I define essential genes as those genes which are required in WT strain MG1655 for the formation of colonies on solid rich medium within 24 hours of incubation at 37 degrees C. One method of establishing the essentiality of a gene is the the failure to obtain a null mutation in it. This approach is subject to both false postives and false negatives (see Gerdes et al. 2003 and Kang et al. 2004). In order to unequivocally identify an essential gene, a conditional lethal mutant must be made (see Herring and Blattner, 2004).

The best source of data on the identity of essential genes in E. coli is table # S2 made by Svetlana Gerdes and others from Integrated Genomics, associated with their recent paper (Gerdes et al. 2003). It is available here. It compares the essentiality determinations from 3 sources: the PEC database, the Blattner lab systematic Tn5 mutagenesis project, and their own work.

Another excellent source is the PEC (Profiling of Escherichia coli chromosome) database, which is lists essential genes identified from literature searches. It may also contain some experimental data, but this is not totally clear.

Another potential source is from the antisense mutants made by the folks at Elitra Pharmaceuticals. They have not published their work, but much of the data is available from U.S. patent application numbers 20020045592 and 20020022718, available here. Their work with Staphylococcus has been published (Forsyth et al. 2002).

Partial list of essential genes identified from the Neidhardt E. coli and Salmonella books (Neidhardt et al. 1996). Note that in March 2004 I removed some of the genes previously listed (dinD, ftsE, ftsX, glmS, glmU, htrA, htrB, htrC, infC, lnt, nusB, rfaD, ribB, rpoE, surA) because they did not meet my definition of essential genes (they were only required under certain conditions, like high temperature or low salt). This data should be used with caution - extensive investigation of the primary references was NOT performed.

Other Essential Gene Sites:

DEG: Database of Essential Genes

Yeast Genome Deletion Project

References

Forsyth, R.A., Haselbeck, R.J., Ohlsen, K.L., Yamamoto, R.T., Xu, H., Trawick, J.D., Wall, D., Wang, L., Brown-Driver, V., Froelich, J.M., C, K.G., King, P., McCarthy, M., Malone, C., Misiner, B., Robbins, D., Tan, Z., Zhu Zy, Z.Y., Carr, G., Mosca, D.A., Zamudio, C., Foulkes, J.G. and Zyskind, J.W.: A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43 (2002) 1387-400. [PubMed]

Gerdes, S.Y., Scholle, M.D., Campbell, J.W., Balazsi, G., Ravasz, E., Daugherty, M.D., Somera, A.L., Kyrpides, N.C., Anderson, I., Gelfand, M.S., Bhattacharya, A., Kapatral, V., D'Souza, M., Baev, M.V., Grechkin, Y., Mseeh, F., Fonstein, M.Y., Overbeek, R., Barabasi, A.L., Oltvai, Z.N. and Osterman, A.L.: Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185 (2003) 5673-84. [PubMed] [PMC]

Herring, C.D. and Blattner, F.R.: Conditional lethal amber mutations in essential Escherichia coli genes. J Bacteriol 186 (2004) 2673-81. [PubMed] [PMC]

Kang, Y., Durfee, T., Glasner, J.D., Qiu, Y., Frisch, D., Winterberg, K.M. and Blattner, F.R.: Systematic mutagenesis of the Escherichia coli genome. J Bacteriol 186 (2004) 4921-30. [PubMed] [PMC]

Neidhardt, F.C. (ed. in chief), Curtiss, R.,3rd, Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaechter, M., and Umbarger, H. E. (eds): Escherichia coli and Salmonella : cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C., 1996.