Chance and necessity in the evolution of minimal metabolic networks (original) (raw)

References

  1. Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004)
    Article ADS CAS PubMed Google Scholar
  2. Koonin, E. V. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Rev. Microbiol. 1, 127–136 (2003)
    Article CAS Google Scholar
  3. Reed, J. L., Vo, T. D., Schilling, C. H. & Palsson, B. O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4, R54 (2003)
    Article PubMed PubMed Central Google Scholar
  4. Price, N. D., Reed, J. L. & Palsson, B. O. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Rev. Microbiol. 2, 886–897 (2004)
    Article CAS Google Scholar
  5. Edwards, J. S. & Palsson, B. O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA 97, 5528–5533 (2000)
    Article ADS CAS PubMed PubMed Central Google Scholar
  6. Gil, R., Latorre, A. & Moya, A. Bacterial endosymbionts of insects: insights from comparative genomics. Environ. Microbiol. 6, 1109–1122 (2004)
    Article CAS PubMed Google Scholar
  7. Klasson, L. & Andersson, S. G. Evolution of minimal-gene-sets in host-dependent bacteria. Trends Microbiol. 12, 37–43 (2004)
    Article CAS PubMed Google Scholar
  8. Burgard, A. P., Vaidyaraman, S. & Maranas, C. D. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol. Prog. 17, 791–797 (2001)
    Article CAS PubMed Google Scholar
  9. Moran, N. A. & Mira, A. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2, research0054 (2001)
    Article CAS PubMed PubMed Central Google Scholar
  10. Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y. & Ishikawa, H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407, 81–86 (2000)
    Article ADS CAS PubMed Google Scholar
  11. van Ham, R. C. et al. Reductive genome evolution in Buchnera aphidicola. Proc. Natl Acad. Sci. USA 100, 581–586 (2003)
    Article ADS CAS PubMed PubMed Central Google Scholar
  12. Tamas, I. et al. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296, 2376–2379 (2002)
    Article ADS CAS PubMed Google Scholar
  13. Akman, L. et al. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nature Genet. 32, 402–407 (2002)
    Article CAS PubMed Google Scholar
  14. Nakabachi, A. & Ishikawa, H. Provision of riboflavin to the host aphid, Acyrthosiphon pisum, by endosymbiotic bacteria, Buchnera. J. Insect Physiol. 45, 1–6 (1999)
    Article CAS PubMed Google Scholar
  15. Baumann, P. et al. Genetics, physiology, and evolutionary relationships of the genus _Buchnera_—intracellular symbionts of aphids. Ann. Rev. Microbiol. 49, 55–94 (1995)
    Article CAS Google Scholar
  16. Hanley, J. A. & McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29–36 (1982)
    Article CAS PubMed Google Scholar
  17. Kumari, S., Tishel, R., Eisenbach, M. & Wolfe, A. J. Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli. J. Bacteriol. 177, 2878–2886 (1995)
    Article CAS PubMed PubMed Central Google Scholar
  18. Zientz, E., Dandekar, T. & Gross, R. Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol. Mol. Biol. Rev. 68, 745–770 (2004)
    Article CAS PubMed PubMed Central Google Scholar
  19. Nogge, G. Significance of symbionts for the maintenance of an optimal nutritional state for successful reproduction in haematophagous arthropods. Parasitology 82, 101–104 (1981)
    Google Scholar
  20. Cormen, T. H., Leiserson, C. E., Rivest, R. L. & Stein, C. Introduction to Algorithms (MIT Press, Cambridge, MA, 2001)
    MATH Google Scholar
  21. Burgard, A. P., Nikolaev, E. V., Schilling, C. H. & Maranas, C. D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14, 301–312 (2004)
    Article CAS PubMed PubMed Central Google Scholar
  22. Travisano, M., Mongold, J. A., Bennett, A. F. & Lenski, R. E. Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267, 87–90 (1995)
    Article ADS CAS PubMed Google Scholar
  23. Mushegian, A. R. & Koonin, E. V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA 93, 10268–10273 (1996)
    Article ADS CAS PubMed PubMed Central Google Scholar
  24. Gil, R., Silva, F. J., Pereto, J. & Moya, A. Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68, 518–537 (2004)
    Article CAS PubMed PubMed Central Google Scholar
  25. Westers, H. et al. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol. Biol. Evol. 20, 2076–2090 (2003)
    Article CAS PubMed Google Scholar
  26. Kolisnychenko, V. et al. Engineering a reduced Escherichia coli genome. Genome Res. 12, 640–647 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  27. Hutchison, C. A. et al. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286, 2165–2169 (1999)
    Article CAS PubMed Google Scholar
  28. Nilsson, A. I. et al. Bacterial genome size reduction by experimental evolution. Proc. Natl Acad. Sci. USA 102, 12112–12116 (2005)
    Article ADS CAS PubMed PubMed Central Google Scholar
  29. Oliver, S. G. From DNA sequence to biological function. Nature 379, 597–600 (1996)
    Article ADS CAS PubMed Google Scholar
  30. Mira, A. & Moran, N. A. Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria. Microb. Ecol. 44, 137–143 (2002)
    Article CAS PubMed Google Scholar

Download references