1887

Abstract

Obligatory intracellular parasites have undergone significant genome reduction by gene loss over time in the context of their obligate associations with the host. The flux, streamlining and elimination of genes in these genomes constitute a selective and ongoing process. Comparative analyses of five completely sequenced obligatory intracellular parasite genomes reveal that these genomes display marked similarities in patterns of protein length and frequency distribution, with substantial sharing of a ‘backbone genome’. From category distribution based on the database of cluster of orthologous groups of proteins (COG), it is clear that habitat is a major factor contributing to genome reduction. It is also observed that, in all five obligatory intracellular parasites, the reduction in number of genes/proteins is greater for proteins with lengths of 200–600 amino acids. These comparative analyses highlight that gene loss is function-dependent, but is independent of protein length. These comparisons enhance our knowledge of the forces that drive the extreme specialization of the bacteria and their association with the host.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63090-0
2004-11-01
2024-11-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/6/ijs541937.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63090-0&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 J. O., Andersson S. G. 2001; Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. Mol Biol Evol 18:829–839 [CrossRef]
    [Google Scholar]
  3. Andersson S. G., Kurland C. G. 1998; Reductive evolution of resident genomes. Trends Microbiol 6:263–268 [CrossRef]
    [Google Scholar]
  4. 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]
  5. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Wheeler D. L. 2003; GenBank: update. Nucleic Acids Res 32:D23–D26
    [Google Scholar]
  6. Bergthorsson U., Ochman H. 1998; Distribution of chromosome length variation in natural isolates of Escherichia coli . Mol Biol Evol 15:6–16 [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. Frank A. C., Amiri H., Andersson S. G. 2002; Genome deterioration: loss of repeated sequences and accumulation of junk DNA. Genetica 115:1–12 [CrossRef]
    [Google Scholar]
  9. 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]
  10. Lawrence J. G., Hendrix R. W., Casjens S. 2001; Where are the pseudogenes in bacterial genomes?. Trends Microbiol 9:535–540 [CrossRef]
    [Google Scholar]
  11. Natale D. A., Galperin M. Y., Tatusov R. L., Koonin E. V. 2000; Using the COG database to improve gene recognition in complete genomes. Genetica 108:9–17 [CrossRef]
    [Google Scholar]
  12. Ochman H., Moran N. 2001; Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096–1099 [CrossRef]
    [Google Scholar]
  13. 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]
  14. Perna N. T., Plunkett G., 3rd, Burland V. 25 other authors 2001; Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. Nature 409:529–533 [CrossRef]
    [Google Scholar]
  15. Sakharkar K. R., Chow V. T. K. 2004; PPD – Proteome Profile Database. In Silico Biol 4:0019
    [Google Scholar]
  16. 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]
  17. Tamas I., Klasson L. M., Sandstrom J. P., Andersson S. G. 2001; Mutualists and parasites: how to paint yourself into a (metabolic) corner. FEBS Lett 498:135–139 [CrossRef]
    [Google Scholar]
  18. Tamas I., Klasson L. M., Canback B., Naslund A. K., Eriksson A. S., Wernegreen J. J., Sandstorm J. P., Moran N. A., Andersson S. G. 2002; 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:2376–2379 [CrossRef]
    [Google Scholar]
  19. Zomorodipour A., Andersson S. G. 1999; Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis . FEBS Lett 452:11–15 [CrossRef]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.63090-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63090-0
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