Evolution of metabolisms: A new method for the comparison of metabolic pathways using genomics information

Journal of Computational Biology

Volumn 6, Issue 3-4, 1999, Pages 343-360

  Forst, Christian V ^a   Schulten, Klaus ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Citric acid cycle; Electron transfer; Metabolic networks; Microbial genomes; Phylogeny

Indexed keywords

CITRIC ACID CYCLE; CONFERENCE PAPER; ELECTRON TRANSPORT; ENZYME LOCALIZATION; ENZYME SUBSTRATE COMPLEX; GENE SEQUENCE; METABOLIC REGULATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; CITRIC ACID CYCLE; DATABASES, FACTUAL; ELECTRON TRANSPORT; EVOLUTION; FERREDOXINS; GENOME; METABOLISM; PHYLOGENY; SPECIES SPECIFICITY;

EID: 0032744302     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652799318319     Document Type: Conference Paper

References (60)

1. Beth, M., Strauss, G., Huber, R., Stetter, K., and Fuchs, G. 1993. Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch. Microbiol. 160, 306-311.
2. Blattner, F., Plunkett, G., Bloch, C., Perna, N., et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277, 1435-1474.
3. Bult, C., White, O., Olsen, G., Zhou, L., et al. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
4. Cole, S., Brosch, R., Parkhill, J., Garnier, T., et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537-544.
5. Dayhoff, M., Schwartz, R., and Orcutt, B. 1978. A model of evolutionary change in proteins, 345-352. In Dayhoff, M., ed., Atlas of Protein Sequence and Structure, Vol. 5. National Biomedical Research Foundation, Washington, D.C.
6. Deckert, G., Warren, P., Gaasterland, T., Young, W., et al. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature (London) 392, 353-358.
7. T. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
8. Felsenstein, J. 1997. Phylip software. http://evolution.genetics.washington.edu/phylip.html.
9. Fitch, W. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19, 99-113.
10. Fleischmann, R., Adams, M., White, O., Clayton, R., et al., 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
11. Forst, C.V., and Schulten, K. 1999. Phylogenetic analysis of metabolic pathways. J. Mol. Evol. Submitted.
12. Fraser, C., Casjens, S., Huang, W., Sutton, G., et al. 1997. Genomic sequence of a lyme disease spirochaete, Borrelia burgdorferi. Nature (London) 390, 580-586.
13. Fraser, C., Gocayne, J., White, O., Adams, M., et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
14. Fraser, C., Norris, S., Weinstock, G., White, O., et al. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281, 375-388.
15. Genome Therapeutics Corporation. Clostridium acetobutylicum genome, strain ATCC824. http://www.genomecorp. com/genesequences/clostridium/clospage.html.
16. Gest, H. 1981. Evolution of the citric acid cycle and respiratory energy conversion in prokaryotes. FEMS Microbiol. Lett. 12, 209-215.
17. Goffeau, A., et al. 1997. The yeast genome directory. Nature (London) 387, 5-105.
18. Haldane, J. 1928. The origin of life. Rationalist Ann. 148, 3-10.
19. Hartman, H. 1975. Speculations on the origin and evolution. J. Mol. Evol. 4, 359-370.
20. Henikoff, S., and Henikoff, J. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89, 10915-10919.
21. Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B., and Herrmann, R. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24, 4420-4449.
22. Huson, D.H. 1998. Splitstree: Analyzing and visualizing evolutionary data. Bioinformatics 14, 68-73.
23. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., et al. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3, 109-136.
24. Karp, P., and Riley, M. 1993. Representations of metabolic knowledge, 207-215. In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology. AAAI Press, New York.
25. Karp, P., Riley, M., and Pellegrini-Toole, A. 1996. EcoCyc: Electronic encyclopedia of E. coli genes and metabolism. Nucleic Acids Res. 24, 32-40, 1996. URL: http://ecocyc.PangeaSystems.com/ecocyc/ecocyc.html.
26. Kawarabayasi, Y., et al. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5, 55-76.
27. Klenk, H., Clayton, R., Tomb, J., White, O., et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature (London) 390, 365-370.
28. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A., et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (London) 390, 249-256.
29. Lipmann, F. 1965. Fox, S.W., ed. The Origin of Prebiological Systems and of Their Molecular Matrices, 259-280. Academic Press, New York.
30. Meléndez-Hevia, E., Waddell, T.G., and Cascante, M. 1996. The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution. J. Mol. Evol. 43, 293-303.
31. Miller, S.L. 1953. A production of amino acids under possible primitive earth conditions. Science 117, 528-529.
32. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34.
33. Oparin, A.I. 1967. The origin of life. In Bernal, J., ed. The Origin of Life. World, Cleveland.
34. Also published in Proiskhozhdenie Zhizny. IZD Moskovishii Rabochii, Mowcow, 1924.
35. Orgel, L.E. 1968. Evolution of the genetic apparatus. J. Mol. Biol. 38, 381-383.
36. Overbeek, R., Larsen, N., Smith, W., Maltsev, N., and Selkov, E. 1997. Representation of function: The next step. Gene 191, GC1-GC9.
37. Overbeek, R., Pusch, G., Dsouza, M., Larsen, N., Selkov, E., Jr., Selkov, E., and Maltsev, N. 1998. What is there - interactive metabolic reconstruction on the web. http://wit.mcs.anl.gov/WIT2/wit.html, WIT2.
38. Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science 276, 734-740.
39. Popper, K.R. 1957. The Poverty of Historicism. Routledge & Kegan Paul, London.
40. Popper, K.R. 1963. Conjectures & Refutations. Routledge & Kegan Paul, London.
41. Romano, A., and Conway, T. 1996. Evolution of carbohydrate metabolic pathways. Res. Microbiol. 147, 448-555.
42. Smith, D., Doucette-Stamm, L. Deloughery, C, H.L.C., et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155.
43. Tatusov, R., Koonin, E., and Lipman, D. 1997. A genomic perspective on protein families. Science 278, 631-637.
44. The Institute of Genome Research. Deinococcus radiodurans genome. ftp://ftp.tigr.org/pub/data/d_radiodurans/.
45. The Institute of Genome Research. Enterococcus faecalis genome. ftp://ftp.tigr.org/pub/data/e_faecalis/.
46. The Institute of Genome Research. Neisseria meningitidis. ftp://ftp.tigr.org/pub/data/n_meningitidis/.
47. The Institute of Genome Research. Streptococcus pneumoniae genome. ftp://ftp.tigr.org/pub/data/s_pneumoniae/.
48. The Institute of Genome Research and Forsyth Dental Center. Porphyromonas gingivalis genome http://www.forsyth. org/pggp/.
49. The Sanger Centre. Campylobacter jejuni genome. ftp://ftp.sanger.ac.uk/pub/pathogens/cj/.
50. The Sanger Centre. Mycobacterium leprae genome. ftp://ftp.tigr.org/pub/data/m_tuberculosis/.
51. The Sanger Centre. Yersinia pestis genome. http://www.sanger.ac.uk/Projects/Y_pestis/.
52. Thompson, J., Higgins, D., and Gibson, T. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
53. Tomb, J.-F., White, O., Kerlavage, A., Clayton, R., et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature (London) 388, 539-547.
54. University of Chicago and Institute of Molecular Genetics, CSFR. Rhodobacter capsulatus. http://capsulapedia. uchicago.edu/.
55. University of Oklahoma. Neisseria gonorrhoeae genome. ftp://ftp.genome.ou.edu/pub/gono.
56. University of Oklahoma. Streptococcus pyogenes genome. http://dnal.chem.uoknor.edu/strep.html.
57. Univeristy of Washington and PathoGenesis. Pseudomonas aeruginosa genome. http://www.pseudomonas.com/.
58. Wächtershäuser, G. 1990. Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. U.S.A. 87, 200-204.
59. Weitzman, P. 1985. Evolution in the citric acid cycle, 253-275. In Schleifer, K.H., and Stackebrandt, E., eds., Evolution of Prokaryotes, Volume 29 of FEMS Symposium. Academic Press, Orlando, FL.
60. Woese, C. 1998. The universal ancestor. Proc. Natl. Acad. Sci. U.S.A. 95, 6854-6859.