Skip to main content

Comparative Genome Analysis of the Mollicutes

  • Chapter

Abstract

The Mollicutes are Eubacteria that have probably been derived from Lactobacilli, Bacilli, and Streptococci by regressive evolution and genome reduction to produce the smallest and simplest free-living and self-replicating cells. The life style is in general Chapausitic. Structurally, the Mollicutes are characterized by the complete lack of a cell wall, and the presence of an internal cytoskeleton27,46.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  2. Aravind, L. and E. V. Koonin. 1998. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23:469–472.

    Article  PubMed  CAS  Google Scholar 

  3. Bjork, G. R., K. Jacobsson, K. Nilsson, M. J. Johansson, A. S. Bystrom, and O. P. Persson. 2001. A primordial tRNA modification required for the evolution of life? EMBO J. 20:231–239.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  4. Blattner, F. R., C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474.

    Article  PubMed  CAS  Google Scholar 

  5. Bolotin, A., S. Mauger, K. Malarme, S. D. Ehrlich, and A. Sorokin. 1999. Low-redundancy sequencing of the entire Lactococcus lactis IL 1403 genome. Antonie Van Leeuwenhoek 76:27–76.

    Article  PubMed  CAS  Google Scholar 

  6. Bork, P., C. Ouzounis, G. Casari, R. Schneider, C. Sander, M. Dolan, W. Gilbert, and P. M. Gillevet. 1995. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol. Microbiol. 16:955–967.

    Article  PubMed  CAS  Google Scholar 

  7. Chambaud, I., R. Heilig, S. Ferris, V. Barbe, D. Samson, F. Galisson, I. Moszer, K. Dybvig, H. Wroblewski, A. Viari, E. P. Rocha, and A. Blanchard. 2001. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 29:2145–2153.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  8. Dandekar, T., M. Huynen, J. T. Regula, B. Ueberle, C. U. Zimmermann, M. A. Andrade, T. Doerks, L. Sanchez-Pulido, B. Snel, M. Suyama, Y. P. Yuan, R. Herrmann, and P. Bork. 2000. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res. 28:3278–3288.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  9. Dhandayuthapani, S., W. G. Rasmussen, and J. B. Baseman. 1999. Disruption of gene mg218 of Mycoplasma genitalium through homologous recombination leads to an adherence-deficient phenotype. Proc. Natl. Acad. Sci. USA 96:5227–5232.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  10. Ferretti, J. J., W. M. McShan, D. Ajdic, D. J. Savic, G. Savic, K. Lyon, C. Primeaux, S. Sezate, A. N. Suvorov, S. Kenton, H. S. Lai, S. P. Lin, Y. Qian, H. G. Jia, F. Z. Najar, Q. Ren, H. Zhu, L. Song, J. White, X. Yuan, S. W. Clifton, B. A. Roe, and R. McLaughlin. 2001. Complete genome sequence of an Ml strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 98:4658–4663.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  11. Fischer, D. and D. Eisenberg. 1997. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc. Natl. Acad. Sci. USA 94:11929–11934.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  12. Fraser, C. M., J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, and J. M. Kand. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397–403.

    Article  PubMed  CAS  Google Scholar 

  13. Garcia-Vallve, S., A. Romeu, and J. Palau. 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10:1719–1725.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  14. Gelfand, M. S. and E. V. Koonin. 1997. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res. 25:2430–2439.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  15. Glass, J. I., E. J. Lefkowitz, J. S. Glass, C. R. Heiner, E. Y. Chen, and G. H. Cassell. 2000. The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407:757–762.

    Article  PubMed  CAS  Google Scholar 

  16. Gumulak-Smith, J., A. Teachman, A. H. Tu, J. W. Simecka, J. R. Lindsey, and K. Dybvig. 2001. Variations in the surface proteins and restriction enzyme systems of Mycoplasma pulmonis in the respiratory tract of infected rats. Mol. Microbiol. 40:1037–1044.

    Article  PubMed  CAS  Google Scholar 

  17. Hamet, M., C. Bonissol, and P. Cartier. 1979. Activities of enzymes of purine and pyrimidine metabolism in nine Mycoplasma species. Adv. Exp. Med. Biol. 122B:231–235.

    Google Scholar 

  18. Herrmann, R. and B. Reiner. 1998. Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species. Curr. Opin. Microbiol. 1:572–579.

    Article  PubMed  CAS  Google Scholar 

  19. Himmelreich, R., H. Hilbert, H. Plagens, E. Pirkl, B. C. Li, and R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:4420–4449.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  20. Himmelreich, R., H. Plagens, H. Hilbert, B. Reiner, and R. Herrmann. 1997. ComChapautive analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25:701–712.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  21. Hutchison III, C. A., S. N. Peterson, S. R. Gill, R. T. Cline, O. White, C. M. Fraser, H. O. Smith, and J. C. Venter. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165–2169.

    Article  PubMed  CAS  Google Scholar 

  22. Huynen, M., B. Snel, and P. Bork. 2000. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10:1204–1210.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  23. Huynen, M., T. Doerks, F. Eisenhaber, C. Orengo, S. Sunyaev, Y. Yuan, and P. Bork. 1998. Homology-based fold predictions for Mycoplasma genitalium proteins. J. Mol. Biol. 280:323–326.

    Article  PubMed  CAS  Google Scholar 

  24. Karlin, S. and A. M. Campbell. 1994. Which bacterium is the ancestor of the animal mitochondrial genome? Proc. Natl. Acad. Sci. USA 91:12842–12846.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  25. Kokotovic, B., G. Bolske, P. Ahrens, and K. Johansson. 2000. Genomic variations of Mycoplasma capricolum subsp. capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis. FEMS Microbiol. Lett. 184:63–68.

    Article  PubMed  CAS  Google Scholar 

  26. Koonin, E. V. and P. Bork. 1996. Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes. Trends Biochem. Sci. 21:128–129.

    Article  PubMed  CAS  Google Scholar 

  27. Krause, D. C. 1996. Mycoplasma pneumoniae cytadherence: unravelling the tie that binds. Mol. Microbiol. 20:247–253.

    Article  PubMed  CAS  Google Scholar 

  28. Manolukas, J. T., M. F. Barile, D. K. Chandler, and J. D. Pollack. 1988. Presence of anaplerotic reactions and transamination, and the absence of the tricarboxylic acid cycle in mollicutes. J. Gen. Microbiol. 134 (Pt 3):791–800.

    PubMed  CAS  Google Scholar 

  29. Miyata, M. and S. Seto. 1999. Cell reproduction cycle of mycoplasma. Biochimie 81:873–878.

    Article  PubMed  CAS  Google Scholar 

  30. Musco, G., G. Stier, C. Joseph, M. A. Castiglione Morelli, M. Nilges, T. J. Gibson, and A. Pastore. 1996. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Cell 85:237–245.

    Article  PubMed  CAS  Google Scholar 

  31. Mushegian, A. R. and E. V. Koonin. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93:10268–10273.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  32. Neimark, H. C. and C. S. Lange. 1990. Pulse-field electrophoresis indicates full-length Mycoplasma chromosomes range widely in size. Nucleic Acids Res. 18:5443–5448.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  33. Pollack, J. D. 1997. Mycoplasma genes: a case for reflective annotation. Trends Microbiol. 5:413–419.

    Article  PubMed  CAS  Google Scholar 

  34. Pollack, J. D. 2001. Ureaplasma urealyticum: an opportunity for combinatorial genomics. Trends Microbiol. 9:169–175.

    Article  PubMed  CAS  Google Scholar 

  35. Pollack, J. D., M. V. Williams, and R. N. McElhaney. 1997. The comChapautive metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells. Crit. Rev. Microbiol. 23:269–354.

    Article  PubMed  CAS  Google Scholar 

  36. Pyle, L. E., L. N. Corcoran, B. G. Cocks, A. D. Bergemann, J. C. Whitley, and L. R. Finch. 1988. Pulsed-field electrophoresis indicates larger-than-expected sizes for mycoplasma genomes. Nucleic Acids Res. 16:6015–6025.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  37. Robertson, J. A., L. E. Pyle, G. W. Stemke, and L. R. Finch. 1990. Human Ureaplasmas show diverse genome sizes by pulsed-field electrophoresis. Nucleic Acids Res. 18:1451–1455.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  38. Rychlewski, L., B. Zhang, and A. Godzik. 1998. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des. 3:229–238.

    Article  PubMed  CAS  Google Scholar 

  39. Snel, B., G. Lehmann, P. Bork, and M. A. Huynen. 2000. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28:3442–3444.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  40. Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108–110.

    Article  PubMed  CAS  Google Scholar 

  41. Sokal, R. R. and C. D. Michener. 1958. A statistical method of evaluating systematic relationships. Univ. Kansas Sci. bull. 28:1409–1438.

    Google Scholar 

  42. Suyama, M. and P. Bork. 2001. Evolution of prpkaryotic gene order: genome rearrangements in closely related species. Trends Genet. 17:10–13.

    Article  PubMed  CAS  Google Scholar 

  43. Teichmann, S. A. and G. Mitchison. 1999. Is there a phylogenetic signal in prokaryote proteins? J. Mol. Evol. 49:98–107.

    Article  PubMed  CAS  Google Scholar 

  44. Teichmann, S. A., A. G. Murzin, and C. Chothia. 2001. Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Struct. Biol. 11:354–363.

    Article  PubMed  CAS  Google Scholar 

  45. Teichmann, S. A., C. Chothia, and M. Gerstein. 1999. Advances in structural genomics. Curr. Opin. Struct. Biol. 9:390–399.

    Article  PubMed  CAS  Google Scholar 

  46. Trachtenberg, S. 1998. Mollicutes-wall-less bacteria with internal cytoskeletons. J. Struct. Biol. 124:244–256.

    Article  PubMed  CAS  Google Scholar 

  47. Wolf, Y. I., N. V. Grishin, and E. V. Koonin. 2000. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. 299:897–905.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer Science+Business Media New York

About this chapter

Cite this chapter

Dandekar, T. et al. (2002). Comparative Genome Analysis of the Mollicutes. In: Razin, S., Herrmann, R. (eds) Molecular Biology and Pathogenicity of Mycoplasmas. Springer, Boston, MA. https://doi.org/10.1007/0-306-47606-1_11

Download citation

  • DOI: https://doi.org/10.1007/0-306-47606-1_11

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4757-8232-5

  • Online ISBN: 978-0-306-47606-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics