Gene Essentiality Analysis Based on DEG, a Database of Essential Genes

  • Chun-Ting Zhang
  • Ren Zhang
Part of the Methods in Molecular Biology™ book series (MIMB, volume 416)

Abstract

Essential genes are the genes that are indispensable for the survival of an organism. The genome-scale identification of essential genes has been performed in various organisms, and we consequently constructed DEG, a Database that contains currently available essential genes. Here we analyzed functional distributions of essential genes in DEG, and found that some essential-gene functions are even conserved between the prokaryote (bacteria) and the eukaryote (yeast), e.g., genes involved in information storage and processing are overrepresented, whereas those involved in metabolism are underrepresented in essential genes compared with non-essential ones. In bacteria, species specificity in functional distribution of essential genes is mainly due to those involved in cellular processes. Furthermore, within the category of information storage and processing, function of translation, ribosomal structure, and biogenesis are predominant in essential genes. Finally, some potential pitfalls for analyzing gene essentiality based on DEG are discussed.

Key Words

COG database DEG essential gene 

References

  1. 1.
    Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.CrossRefPubMedGoogle Scholar
  2. 2.
    Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.CrossRefPubMedGoogle Scholar
  3. 3.
    Cho, M. K., Magnus, D., Caplan, A. L., and McGee, D. (1999) Policy forum: genetics. Ethical considerations in synthesizing a minimal genome. Science 286, 2087, 2089–2090.CrossRefPubMedGoogle Scholar
  4. 4.
    Hutchison, C. A., 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.CrossRefPubMedGoogle Scholar
  5. 5.
    Mushegian, A. (1999) The minimal genome concept. Curr. Opin. Genet. Dev. 9, 709–714.CrossRefPubMedGoogle Scholar
  6. 6.
    Koonin, E. V. (2000) How many genes can make a cell: the minimal-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1, 99–116.CrossRefPubMedGoogle Scholar
  7. 7.
    Fisher, L. M., Lawrence, J. M., Josty, I. C., Hopewell, R., Margerrison, E. E., and Cullen, M. E. (1989) Ciprofloxacin and the fluoroquinolones. New concepts on the mechanism of action and resistance. Am. J. Med. 87, 2S–8S.CrossRefPubMedGoogle Scholar
  8. 8.
    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.CrossRefPubMedGoogle Scholar
  9. 9.
    Bruccoleri, R. E., Dougherty, T. J., and Davison, D. B. (1998) Concordance analysis of microbial genomes. Nucleic Acids Res. 26, 4482–4486.CrossRefPubMedGoogle Scholar
  10. 10.
    Thanassi, J. A., Hartman-Neumann, S. L., Dougherty, T. J., Dougherty, B. A., and Pucci, M. J. (2002) Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res. 30, 3152–3162.CrossRefPubMedGoogle Scholar
  11. 11.
    Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati, G., Andersen, K. K., Arnaud, M., et al. (2003) Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. U.S.A. 100, 4678–4683.CrossRefPubMedGoogle Scholar
  12. 12.
    Gerdes, S. Y., Scholle, M. D., Campbell, J. W., Balazsi, G., Ravasz, 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.CrossRefPubMedGoogle Scholar
  13. 13.
    Akerley, B. J., Rubin, E. J., Novick, V. L., Amaya, K., Judson, N., and Mekalanos, J. J. (2002) A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc. Natl. Acad. Sci. U.S.A. 99, 966–971.CrossRefPubMedGoogle Scholar
  14. 14.
    Ji, Y., Zhang, B., Van, S. F., Horn, W. P., Woodnutt, G., Burnham, M. K., and Rosenberg, M. (2001) Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293, 2266–2269.CrossRefPubMedGoogle Scholar
  15. 15.
    Forsyth, R. A., Haselbeck, R. J., Ohlsen, K. L., Yamamoto, R. T., Xu, H., Trawick, J. D., et al. (2002) A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol. Microbiol. 43, 1387–1400.CrossRefPubMedGoogle Scholar
  16. 16.
    Judson, N., and Mekalanos, J. J. (2000) TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes. Nat. Biotechnol. 18, 740–745.CrossRefPubMedGoogle Scholar
  17. 17.
    Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391.CrossRefPubMedGoogle Scholar
  18. 18.
    Zhang, R., Ou, H. Y., and Zhang, C. T. (2004) DEG: a database of essential genes. Nucleic Acids Res. 32 (Database issue), D271–D272.CrossRefPubMedGoogle Scholar
  19. 19.
    Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., et al. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30, 31–34.CrossRefPubMedGoogle Scholar
  20. 20.
    Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22–28.CrossRefPubMedGoogle Scholar
  21. 21.
    Doolittle, R. F., Feng, D. F., Tsang, S., Cho, G., and Little, E. (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470–477.CrossRefPubMedGoogle Scholar
  22. 22.
    Peterson, S. N., and Fraser, C. M. (2001) The complexity of simplicity. Genome Biol. 2, comment 2002.1–2002.8.Google Scholar

Copyright information

© Humana Press Inc., a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Chun-Ting Zhang
    • 1
  • Ren Zhang
    • 2
  1. 1.Department of PhysicsTianjin UniversityTianjinChina
  2. 2.Department of Epidemiology and BiostatisticsTianjin Cancer Institute and HospitalTianjinChina

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