Skip to main content
SpringerLink
Log in

Overlapping genes in bacterial and phage genomes

  • Published:
Molecular Biology Aims and scope Submit manuscript

Abstract

Overlapping of genes was first reported for small viruses and was initially considered a phenomenon related to the natural selection favoring the trend of genome size reduction. Later, overlapping genes were found in the genomes of bacteria, mitochondria, and chloroplasts; numerous evidence of their transcriptional and posttranscriptional interaction was provided. We suggest that overlapping of the genes is important for complex regulation of gene expression and/or for better interaction at the transcriptional or translational level. This review describes various types of overlapping genes and operons and the molecular mechanisms of overlapping gene interaction.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Barrel, B.G., Air, G.M., and Hutchison, C.A.,Nature, 1976, vol. 264, pp. 34–40.

    Article  Google Scholar 

  2. Goldson, G.N., Barrell, B.G., Staden, R., and Fiddes, J.C.,Nature, 1978, vol. 276, pp. 236–247.

    Article  Google Scholar 

  3. Oppenheim, D.S. and Yanofsky, C.,Genetics, 1980, vol. 95, pp. 785–795.

    PubMed  CAS  Google Scholar 

  4. Barnes, W.M. and Tuley, E.,J. Mol. Biol., 1983, vol. 165, pp. 443–459.

    Article  PubMed  CAS  Google Scholar 

  5. McKenney, K., Shimatake, H., Court, D., Schmeissner, U., Brady, C., and Rosenberg, M.,Gene Amplif. Anal., 1981, vol. 2, pp. 383–415.

    PubMed  CAS  Google Scholar 

  6. Cole, S.T.,Eur. J. Biochem., 1982, vol. 122, pp. 479–484.

    Article  PubMed  CAS  Google Scholar 

  7. Linney, E. and Hayashi, M.,Nature New Biol., 1973, vol. 245, pp. 6–8.

    PubMed  CAS  Google Scholar 

  8. Dunn, J.J. and Studier, F.W.,J. Mol. Biol., 1981, vol. 148, pp. 303–330.

    Article  PubMed  CAS  Google Scholar 

  9. Shaw, J.E. and Murialdo, H.,Nature, 1980, vol. 283, pp. 30–35.

    Article  PubMed  CAS  Google Scholar 

  10. Gesteland, R.F. and Atkins, J.F.,Annu. Rev. Biochem., 1996, vol. 65, pp. 741–768.

    Article  Google Scholar 

  11. O'Connor, M.,J. Mol. Biol., 1998, vol. 279, pp. 727–736.

    Article  PubMed  Google Scholar 

  12. Retteberg, C.C., Prere, M.F., Gesteland, R.F., Atkins, J.F., and Fayet, O.,J. Mol. Biol., 1999, vol. 286, pp. 1365–1378.

    Article  Google Scholar 

  13. Das, A. and Yanofsky, C.,Nucleic Acids Res., 1989, vol. 17, pp. 9333–9340.

    Article  PubMed  CAS  Google Scholar 

  14. Liljestrom, P., Laamanen, I., and Palva, E.T.,J. Mol. Biol., 1988, vol. 201, pp. 663–673.

    Article  PubMed  CAS  Google Scholar 

  15. Mashko, S.V., Lapidus, A.L., Trukhan, M.E., Lebedeva, M.I., Podkovyrov, S.M., Kashlev, M.V., Mochul'skii, A.V., Eremashvili, M.R., Isotova, L.S., Strongin, A.Ya., Skvortsova, M.A., Sterkin, V.E., Lebedev, A.N., Rebentish, B.A., Kozlov, Yu.I., Monastyrskaya, G.S., Tsarev, S.A., Sverdlov, E.D., and Debabov, V.G.,Mol. Biol., 1987, vol. 21, pp. 1297–1309.

    CAS  Google Scholar 

  16. Bell, A.W., Buckel, S.D., Groarke, J.M., Hope, J.N., Kingsley, D.H., and Hermodson, M.A.,J. Biol. Chem., 1986, vol. 261, pp. 7652–7658.

    PubMed  CAS  Google Scholar 

  17. Selivanov, N.A., Prilipov, A.G., Efimov, V.P., Marusich, E.I., and Mesyanzhinov, V.V.,Biomed. Sci., 1990, vol. 1, pp. 55–62.

    PubMed  CAS  Google Scholar 

  18. Navarro, C., Wu, L.F., and Mandrand-Berthelot, M.A.,Mol. Microbiol., 1993, vol. 9, pp. 1181–1191.

    Article  PubMed  CAS  Google Scholar 

  19. Vysotskaya, V.S., Shcherbakov, D.V., and Garber, M.B.,Gene, 1997, vol. 193, pp. 23–30.

    Article  PubMed  CAS  Google Scholar 

  20. Dandekar, T., Snel, B., Huynen, M., and Bork, P.,Trends Biochem. Sci., 1998, vol. 23, pp. 324–328.

    Article  PubMed  CAS  Google Scholar 

  21. Turner, R.J., Lu, Y., and Switzer, R.L.,J. Bacteriol., 1994, vol. 176, pp. 3708–3722.

    PubMed  CAS  Google Scholar 

  22. Sipley, J., Stassi, D., Dunn, J., and Goldman, E.,Gene Expr., 1991, vol. 1, pp. 127–136.

    PubMed  CAS  Google Scholar 

  23. Condron, B.G., Atkins, J.F., and Gesteland, R.F.,J. Bacteriol., 1991, vol. 173, pp. 6998–7003.

    PubMed  CAS  Google Scholar 

  24. Levin, M.E., Hendrix, R.W., and Casjens, S.R.,J. Mol. Biol., 1993, vol. 234, pp. 124–139.

    Article  PubMed  CAS  Google Scholar 

  25. Katsura, I. and Kuhl, P.W.,J. Mol. Biol., 1975, vol. 91, pp. 257–273.

    Article  PubMed  CAS  Google Scholar 

  26. Model, P., Webster, R.E., and Zinder, N.D.,Cell, 1979, vol. 18, pp. 235–246.

    Article  PubMed  CAS  Google Scholar 

  27. Fiers, W., Contreras, R., Duerinck, F., Haegeman, G., Iserentant, D., Merregaert, J., Min Jou, W., Molemans, F., Raeymaekers, A., van den Berghe, A., Volckaert, G., and Ysebaert, M.,Nature, 1976, vol. 260, pp. 500–507.

    Article  PubMed  CAS  Google Scholar 

  28. Atkins, J.F., Steitz, J.A., Anderson, C.W., and Model, P.,Cell, 1979, vol. 18, pp. 247–256.

    Article  PubMed  CAS  Google Scholar 

  29. Beremand, M.N. and Blumenthal, T.,Cell, 1979, vol. 18, pp. 257–266.

    Article  PubMed  CAS  Google Scholar 

  30. Kastelein, R.A., Remaut, E., Fiers, W., and van Duin, J.,Nature, 1982, vol. 295, pp. 35–41.

    Article  PubMed  CAS  Google Scholar 

  31. De Mars Cody, J. and Conway, T.W.,J. Virol., 1981, vol. 37, pp. 813–820.

    PubMed  Google Scholar 

  32. Davies, R.W.,Nucleic Acids Res., 1980, vol. 8, pp. 1765–1782.

    Article  PubMed  CAS  Google Scholar 

  33. Ptaschne, M.,Perekluchenie genov (Gene Switching), Russian translation, Moscow: Mir, 1988.

    Google Scholar 

  34. Normark, S., Bergstrom, S., Edlund, T., Grundstrom, T., Jaurin, B., Lindberg, F.P. and Olsson, O.,Annu. Rev. Genet., 1983, vol. 17, pp. 499–525.

    Article  PubMed  CAS  Google Scholar 

  35. Zajanckauskaite, A., Malys, N., and Nivinskas, R.,Gene, 1997, vol. 194, pp. 157–162.

    Article  PubMed  CAS  Google Scholar 

  36. Garrett, J., Fusselman, R., Hise, J., Chiou, L., Smith-Grillo, D., Schulz, J., and Young, R.,Mol. Gen. Genet., 1981, vol. 182, pp. 326–331.

    Article  PubMed  CAS  Google Scholar 

  37. Hanych, B., Kedzierskas, S., Walderich, B., Uznanski, B., and Taylor, A.,Gene, 1993, vol. 129, pp. 1–8.

    Article  PubMed  CAS  Google Scholar 

  38. Kedzierska, S., Wawrzynow, A., and Taylor, A.,Gene, 1996, vol. 168, pp. 1–8.

    Article  Google Scholar 

  39. Blasi, U., Nam, K., Lubitz, W., and Young, R.,J. Bacteriol., 1990, vol. 172, pp. 5617–5623.

    PubMed  CAS  Google Scholar 

  40. Linney, E. and Hayashi, M.,Nature New Biol., 1973, vol. 245, pp. 6–8.

    PubMed  CAS  Google Scholar 

  41. Johnson, R.C., Yin, J.C., and Reznikoff, W.S.,Cell, 1982, vol. 30, pp. 873–882.

    Article  PubMed  CAS  Google Scholar 

  42. De la Cruz, N.B., Weinreich, M.D., Wiegand, T.W., Krebs, M.P., and Reznikoff, W.S.,J. Bacteriol., 1993, vol. 175, pp. 6932–6938.

    PubMed  Google Scholar 

  43. Rosenberg, A.H., Patel, S.S., Johnson, K.A., and Studier, F.W.,J. Biol. Chem., 1992, vol. 267, pp. 15005–15012.

    PubMed  CAS  Google Scholar 

  44. Nishiyama, M., Kukimoto, M., Beppu, T., and Horinouchi, S.,Microbiology, 1995, vol. 141, pp. 1211–1219.

    Article  PubMed  CAS  Google Scholar 

  45. Yen, T.S. and Webster, R.E.,J. Biol. Chem., 1981, vol. 256, pp. 11259–11265.

    PubMed  CAS  Google Scholar 

  46. Fulford, W., and Model, P.,J. Mol. Biol., 1984, vol. 178, pp. 137–153.

    Article  PubMed  CAS  Google Scholar 

  47. Fulford, W. and Model, P.,J. Mol. Biol., 1988, vol. 203, pp. 49–62.

    Article  PubMed  CAS  Google Scholar 

  48. Kokoska, R.J. and Steege, D.A.,J. Bacteriol., 1998, vol. 180, pp. 3245–3249.

    PubMed  CAS  Google Scholar 

  49. Jalajakumari, M.B., Thomas, C.J., Halter, R., and Maning, P.A.,Mol. Microbiol., 1989, vol. 3, pp. 1685–1695.

    Article  PubMed  CAS  Google Scholar 

  50. Tsuchihashi, Z. and Kornberg, A.,Proc. Natl. Acad. Sci. USA, 1990, vol. 87, pp. 2516–2520.

    Article  PubMed  CAS  Google Scholar 

  51. Kim, S. and Marians, K.J.,Nucleic Acids. Res., 1995, vol. 23, pp. 1374–1379.

    Article  PubMed  CAS  Google Scholar 

  52. Larsen, B., Wills, N.M., Gesteland, R.F., and Atkins, J.F.,J. Bacteriol., 1994, vol. 176, pp. 6842–6851.

    PubMed  CAS  Google Scholar 

  53. Yurieva, O., Skangalis, M., Kuriyan, J., and O'Donnell, M.,J. Biol. Chem., 1997, vol. 272, pp. 27131–27139.

    Article  PubMed  CAS  Google Scholar 

  54. Johnsrud, L.,Mol. Gen. Genet., 1979, vol. 169, pp. 213–218.

    Article  PubMed  CAS  Google Scholar 

  55. Ghosal, D., Sommer, H., and Saedler, H.,Nucleic Acids Res., 1979, vol. 6, pp. 1111–1122.

    Article  PubMed  CAS  Google Scholar 

  56. Klaer, R., Kuhn, S., Tillmann, E., Fritz, H.J., and Starlinger, P.,Mol. Gen. Genet., 1981, vol. 181, pp. 169–175.

    Article  PubMed  CAS  Google Scholar 

  57. Kroger, M. and Hobom, G.,Nature, 1982, vol. 297, pp. 159–162.

    Article  PubMed  CAS  Google Scholar 

  58. Kumamoto, C.A. and Nault, A.K.,Gene, 1989, vol. 75, pp. 167–175.

    Article  PubMed  CAS  Google Scholar 

  59. Merino, E., Balbas, P., Puente, J.L., and Bolivar, F.,Nucleic Acids Res., 1994, vol. 22, pp. 1903–1908.

    Article  PubMed  CAS  Google Scholar 

  60. Alff-Steinberger, C.,Nucleic Acids Res., 1984, vol. 12, pp. 2235–2241.

    Article  PubMed  CAS  Google Scholar 

  61. Rak, B., Lusky, M., and Hable, M.,Nature, 1982, vol. 297, pp. 124–128.

    Article  PubMed  CAS  Google Scholar 

  62. Horowitz, H. and Platt, T.,Nucleic Acids Res., 1982, vol. 10, pp. 5447–5465.

    Article  PubMed  CAS  Google Scholar 

  63. Wellington, C.L., Taggart, A.K., and Beatty, J.T.,J. Bacteriol., 1991, vol. 173, pp. 2954–2961.

    PubMed  CAS  Google Scholar 

  64. Silke, J.,Gene, 1997, vol. 194, pp. 143–145.

    Article  PubMed  CAS  Google Scholar 

  65. Cebrat, S., Mackiewicz, P., and Dudek, M.R.,Biosystems, 1998, vol. 45, pp. 165–176.

    Article  PubMed  CAS  Google Scholar 

  66. Jaurin, B., Grundstrom, T., Edlund, T., and Normark, S.,Nature, 1981, vol. 290, pp. 221–225.

    Article  PubMed  CAS  Google Scholar 

  67. Normark, S. and Burman, L.G.,J. Bacteriol., 1977, vol. 132, pp. 1–7.

    PubMed  CAS  Google Scholar 

  68. Jaurin, B. and Normark, S.,J. Bacteriol., 1979, vol. 138, pp. 896–902.

    PubMed  CAS  Google Scholar 

  69. Jones, H.M. and Gunsalus, R.P.,J. Bacteriol., 1987, vol. 169, pp. 3340–3349.

    PubMed  CAS  Google Scholar 

  70. Engel, P., Trageser, M., and Unden, G.,Arch. Microbiol., 1991, vol. 156, pp. 463–470.

    PubMed  CAS  Google Scholar 

  71. Grundstrom, T. and Normark, S.,Mol. Gen. Genet., 1985, vol. 198, pp. 411–415.

    Article  PubMed  CAS  Google Scholar 

  72. Bergstrom, S., Lindberg, F.P., Olsson, O., and Normark, S.,J. Bacteriol., 1983, vol. 155, pp. 1297–12305.

    PubMed  CAS  Google Scholar 

  73. Lindquist, S., Lindberg, F., and Normark, S.,J. Bacteriol., 1989, vol. 171, pp. 3746–3753.

    PubMed  CAS  Google Scholar 

  74. Lindberg, F., Westman, L., and Normark, S.,Proc. Natl. Acad. Sci. USA, 1985, vol. 82, pp. 4620–4624.

    Article  PubMed  CAS  Google Scholar 

  75. Honore, N., Nicolas, M.H., and Cole, S.T.,EMBO J., 1986, vol. 5, pp. 3709–3714.

    PubMed  CAS  Google Scholar 

  76. Cole, S.T.,Eur. J. Biochem., 1987, vol. 167, pp. 481–488.

    Article  PubMed  CAS  Google Scholar 

  77. Tuomanen, E., Lindquist, S., Sande, S., Galleni, M., Light, K., Gage, D., and Normark, S.,Science, 1991, vol. 251, pp. 201–204.

    Article  PubMed  CAS  Google Scholar 

  78. Bishop, R.E. and Weiner, J.H.,FEMS Microbiol. Lett., 1993, vol. 114, pp. 349–354.

    Article  PubMed  CAS  Google Scholar 

  79. Sherbakov, D.V.,Cand. Sci. (Biol.) Dissertation, Moscow: Moscow State Univ., 1999.

    Google Scholar 

  80. Lindahl, L., Sor, F., Archer, R.H., Nomura, M., and Zengel, J.M.,Biochim. Biophys. Acta, 1990, vol. 1050, pp. 337–342.

    PubMed  CAS  Google Scholar 

  81. Nomura, M., Yates, J.L., Dean, D., and Post, L.E.,Proc. Natl. Acad. Sci. USA, 1980, vol. 77, pp. 7084–7088.

    Article  PubMed  CAS  Google Scholar 

  82. Pfeiffer, T., Jorcke, D., Feltens, R., and Hartmann, R.K.,Gene, 1995, vol. 167, pp. 141–145.

    Article  PubMed  CAS  Google Scholar 

  83. Wellington, C.L. and Beatty, J.T.,J. Bacteriol., 1991, vol. 173, pp. 1432–1433.

    PubMed  CAS  Google Scholar 

  84. Wellington, C.L., Taggart, A.K., and Beatty, J.T.,J. Bacteriol., 1991, vol. 173, pp. 2954–2961.

    PubMed  CAS  Google Scholar 

  85. Umbarger, H.E.,Annu. Rev. Biochem., 1978, vol. 47, pp. 532–606.

    Article  PubMed  CAS  Google Scholar 

  86. Wek, R.C. and Hatfield, G.W.,J. Biol. Chem., 1986, vol. 261, pp. 2441–2450.

    PubMed  CAS  Google Scholar 

  87. Rhee, K.Y., Senear, D.F., and Hatfield, G.W.,J. Biol. Chem., 1998, vol. 273, pp. 11257–11266.

    Article  PubMed  CAS  Google Scholar 

  88. Chen, J.W., Bennett, D.C., and Umbarger, H.E.,J. Bacteriol., 1991, vol. 173, pp. 2328–2340.

    PubMed  CAS  Google Scholar 

  89. Pagel, J.M. and Hatfield, G.W.,J. Biol. Chem., 1991, vol. 266, pp. 1985–1996.

    PubMed  CAS  Google Scholar 

  90. Rhee, K.Y., Parekh, B.S., and Hatfield, G.W.,J. Biol. Chem., 1996, vol. 271, pp. 26499–26507.

    Google Scholar 

  91. Sameshima, J.H., Wek, R.C., and Hatfield, G.W.,J. Biol. Chem., 1989, vol. 264, pp. 1224–1231.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Protein Research, Russian Academy of Sciences, 142292, Pushchino, Russian

    D. V. Scherbakov & M. B. Garber

Authors
  1. D. V. Scherbakov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. B. Garber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to D. V. Scherbakov.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Scherbakov, D.V., Garber, M.B. Overlapping genes in bacterial and phage genomes. Mol Biol 34, 485–495 (2000). https://doi.org/10.1007/BF02759558

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02759558

Key words

Search

Navigation