1887

Abstract

Overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. In this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. The results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. The genomes of two closely related obligatory intracellular parasites – and – were investigated further. Detailed analyses of these two genomes revealed that mutations at the ends of coding regions and elimination of intergenic DNA are the main forces that determine overlapping of genes.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63446-0
2005-05-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/3/ijs551205.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63446-0&mimeType=html&fmt=ahah

References

  1. Andersson J. O., Andersson S. G. 1999; Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev 9:664–671 [CrossRef]
    [Google Scholar]
  2. Andersson S. G., Zomorodipour A., Andersson J. O. 7 other authors 1998; The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133–140 [CrossRef]
    [Google Scholar]
  3. Burge C. B., Karlin S. 1998; Finding the genes in genomic DNA. Curr Opin Struct Biol 8:346–354 [CrossRef]
    [Google Scholar]
  4. Cebrat S., Dudek M. R., Mackiewicz P., Kowalczuk M., Fita M. 1997; Asymmetry of coding versus noncoding strand in coding sequences of different genomes. Microb Comp Genomics 2:259–268 [CrossRef]
    [Google Scholar]
  5. Chen S. M., Takiff H. E., Barber A. M., Dubois G. C., Bardwell J. C., Court D. L. 1990; Expression and characterization of RNase III and Era proteins. Products of the rnc operon of Escherichia coli . J Biol Chem 265:2888–2895
    [Google Scholar]
  6. Clark M. A., Baumann L., Thao M. L., Moran N. A., Baumann P. 2001; Degenerative minimalism in the genome of a psyllid endosymbiont. J Bacteriol 183:1853–1861 [CrossRef]
    [Google Scholar]
  7. Cole S. T., Eiglmeier K., Parkhill J. 41 other authors 2001; Massive gene decay in the leprosy bacillus. Nature 409:1007–1011 [CrossRef]
    [Google Scholar]
  8. Eyre-Walker A. 1995; The distance between Escherichia coli genes is related to gene expression levels. J Bacteriol 177:5368–5369
    [Google Scholar]
  9. Fraser C. M., Gocayne J. D., White O. 25 other authors 1995; The minimal gene complement of Mycoplasma genitalium . Science 270:397–403 [CrossRef]
    [Google Scholar]
  10. Fukuda Y., Washio T., Tomita M. 1999; Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae . Nucleic Acids Res 27:1847–1853 [CrossRef]
    [Google Scholar]
  11. Fukuda Y., Nakayama Y., Tomita M. 2003; On dynamics of overlapping genes in bacterial genomes. Gene 323:181–187 [CrossRef]
    [Google Scholar]
  12. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B. C., Herrmann R. 1996; Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae . Nucleic Acids Res 24:4420–4449 [CrossRef]
    [Google Scholar]
  13. Inokuchi Y., Hirashima A., Sekine Y., Janosi L., Kaji A. 2000; Role of ribosome recycling factor (RRF) in translational coupling. EMBO J 19:3788–3798 [CrossRef]
    [Google Scholar]
  14. Kalman S., Mitchell W., Marathe R. 7 other authors 1999; Comparative genomes of Chlamydia pneumoniae and C. trachomatis . Nat Genet 21:385–389 [CrossRef]
    [Google Scholar]
  15. Keese P. K., Gibbs A. 1992; Origins of genes: “big bang” or continuous creation?. Proc Natl Acad Sci U S A 89:9489–9493 [CrossRef]
    [Google Scholar]
  16. Krakauer D. C. 2000; Stability and evolution of overlapping genes. Evolution Int J Org Evolution 54:731–739 [CrossRef]
    [Google Scholar]
  17. Lipman D. J. 1997; Making (anti)sense of non-coding sequence conservation. Nucleic Acids Res 25:3580–3583 [CrossRef]
    [Google Scholar]
  18. Miyata T., Yasunaga T. 1978; Evolution of overlapping genes. Nature 272:532–535 [CrossRef]
    [Google Scholar]
  19. Normark S., Bergstrom S., Edlund T., Grundstrom T., Jaurin B., Lindberg F. P., Olsson O. 1983; Overlapping genes. Annu Rev Genet 17:499–525 [CrossRef]
    [Google Scholar]
  20. Ogata H., Audic S., Renesto-Audiffren P. 8 other authors 2001; Mechanisms of evolution in Rickettsia conorii and R. prowazekii . Science 293:2093–2098 [CrossRef]
    [Google Scholar]
  21. Pavesi A., De Iaco B., Granero M. I., Porati A. 1997; On the informational content of overlapping genes in prokaryotic and eukaryotic viruses. J Mol Evol 44:625–631 [CrossRef]
    [Google Scholar]
  22. Rocha E. P., Danchin A. 2001; Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol 18:1789–1799 [CrossRef]
    [Google Scholar]
  23. Rogozin I. B., Spiridonov A. N., Sorokin A. V., Wolf Y. I., Jordan I. K., Tatusov R. L., Koonin E. V. 2002; Purifying and directional selection in overlapping prokaryotic genes. Trends Genet 18:228–232 [CrossRef]
    [Google Scholar]
  24. Sander C., Schulz G. E. 1979; Degeneracy of the information contained in amino acid sequences: evidence from overlaid genes. J Mol Evol 13:245–252 [CrossRef]
    [Google Scholar]
  25. Shigenobu S., Watanabe H., Hattori M., Sakaki Y., Ishikawa H. 2000; Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407:81–86 [CrossRef]
    [Google Scholar]
  26. Shimizu T., Ohtani K., Hirakawa H. 7 other authors 2002; Complete genome sequence of Clostridium perfringens , an anaerobic flesh-eater. Proc Natl Acad Sci U S A 99:996–1001 [CrossRef]
    [Google Scholar]
  27. Smith T. F., Waterman M. S. 1981; Overlapping genes and information theory. J Theor Biol 91:379–380 [CrossRef]
    [Google Scholar]
  28. Stephens R. S., Kalman S., Lammel C. J. 9 other authors 1998; Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis . Science 282:754–759 [CrossRef]
    [Google Scholar]
  29. Yelin R., Dahary D., Sorek R. 13 other authors 2003; Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21:379–386 [CrossRef]
    [Google Scholar]
  30. Zheng Y., Szustakowski J. D., Fortnow L., Roberts R. J., Kasif S. 2002; Computational identification of operons in microbial genomes. Genome Res 12:1221–1230 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63446-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63446-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error