Abstract
We present a conceptual review of transposition-based strategies for determining gene essentiality on a one-by-one basis in bacteria. Many of the techniques are described in greater detail in individual chapters of this volume. The second section of this chapter deals with transposition-deletion—based strategies for determining the essentiality of blocks of genes. This latter approach has the potential to experimentally define the minimal required genome for a given organism.
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References
Chandler, M., and Mahillon, J. (2002) Insertion sequences revisited. In: Craig, N., Craigie, R., Gellert, M., and Lambowitz, A. M. eds. Mobile DNA II. Washington, DC: ASM Press, pp. 305–366.
Berg, C. M., Berg, D. E., and Groisman, E. (1989) Transposable elements and the genetic engineering of bacteria. In: Berg, D. E., and Howe, M. M., eds. Mobile DNA. Washington, DC: ASM Press, pp. 879–925.
Hensel, M., Shea, J. E., Gleeson, C., Jones, M. D., Dalton, E., and Holden, D. W. (1995) Simultaneous identification of bacterial virulence genes by negative selection. Science 269, 400–403.
Hutchison, C. A. III, Peterson, S. N., Gill, S. R., Cline, R. T., White, O., Fraser, C. M., et al. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286, 2165–2169.
Badarinarayana, V., Estep, P. W. III, Shendure, J., Edwards, J., Tavazoie, S., Lam, F., and Church, G. M. (2001) Selection analyses of insertional mutants using subgenic-resolution arrays. Nat. Biotech. 19, 1060–1065.
Sassetti, C. M., Boyd, D. H., and Rubin, E. J. (2001) Comprehensive identification of conditionally essential genes in mycobacteria. Proc. Nat. Acad. Sci. U.S.A. 98, 12712–12717.
Murry, J. P., Sassetti, C. M., Lane, J. M., Xie, Z., and Rubin, E. J. (2007) Transposon site hybridization (TraSH) in Mycobacterium tuberculosis. This volume, Chapter 4.
Liberati, N. T., Urbach, J. M., Miyata, S., Lee, D. G., Drenkard, E., Wu, G., et al. (2006) An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc. Nat. Acad. Sci. U.S.A. 103, 2833–2838.
Liberati, N. T., Urbach, J. M., Holmes, T. K., Wu, G., and Ausubel, F. M. (2006) Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality. This volume, Chapter 10.
Jacobs, M. A., Alwood, A., Thaipisuttikul, I., Spencer, D., Haugen, E., Ernst, S., et al. (2003) Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc. Nat. Acad. Sci U.S.A. 100, 14339–14344.
Jacobs, M. A. (2006) How to: make a defined near-saturation mutant library. Case 1: Pseudomonas aeruginosa PAO1. This volume, Chapter 9.
Goryshin, I. Y., Naumann, T. A., Apodaca, J., and Reznikoff, W. S. (2003) Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis. Genome Res. 13, 644–653.
Akerley, B. J., Rubin, E. J., Camilli, A., Lampe, D. J., Robertson, H. M., and Mekalanos, J. J. (1998) Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Nat. Acad. Sci. U.S.A. 95, 8927–8932.
Wong, S. M. S., and Akerley, B. J. (2006) Identification and analysis of essential genes in Haemophilus influenzae. This volume, Chapter 3.
Ross-Macdonald, P., Coelho, P. S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., et al. (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413–418.
Kumar, A. (2006) Multipurpose transposon insertion libraries for large-scale analysis of gene function in yeast. This volume, Chapter 8.
Kang, Y., Durfee, T., Glasner, J. D., Qiu, Y., Firsch, D., Winterberg, K., and Blattner, F. R. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186, 4921–4930.
Goryshin, I. Y., Jendrisak, J., Hoffman, L., Meis, R., and Reznikoff, W. S. (2000) Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes. Nat. Biotech. 18, 97–100.
Yu, B. J., Sung, B. H., Koob, M. D., Lee, C. H., Lee, J. H., Lee, W. S., et al. (2002) Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat. Biotech. 20, 1018–1023.
Gerdes, S. Y., Scholle, M. D., Campbell, J. W., Balázsi, G., Rayasz, E., Daugherty, M.D., et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185, 5673–5684.
Scholle, M. D., and Gerdes, S. Y. (2006) Whole-genome detection of conditionally essential and dispensable genes in E. coli via genetic footprinting. This volume, Chapter 6.
Winterberg, K. M., Luecke, J., Bruegl, A. S., and Reznikoff, W. S. (2005) Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries using whole genome oligonucleotide microarrays. Appl. Environ. Microbiol. 71, 451–459.
Yu, B. J., and Kim, S. C. (2006) Minimization of the Escherichia coli genome using the Tn5-targeted Cre/loxP excision system. This volume, Chapter 17.
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Reznikoff, W.S., Winterberg, K.M. (2008). Transposon-Based Strategies for the Identification of Essential Bacterial Genes. In: Osterman, A.L., Gerdes, S.Y. (eds) Microbial Gene Essentiality: Protocols and Bioinformatics. Methods in Molecular Biology™, vol 416. Humana Press. https://doi.org/10.1007/978-1-59745-321-9_2
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DOI: https://doi.org/10.1007/978-1-59745-321-9_2
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