Experimental Evolution of Ribitol Dehydrogenase

  • B. S. Hartley
Part of the Monographs in Evolutionary Biology book series (MEBI)


This project began in 1968, when the impact of amino acid sequencing and protein crystallography had revealed a flood of data with great impact on evolutionary theory. These facts allowed the following important conclusions:
  1. 1.

    The conformation of the same protein from different species is carefully conserved throughout evolution.

  2. 2.

    Internal amino acid residues that clearly contribute to that conformation are generally, but not invariably, conserved.

  3. 3.

    Surface amino acids are more variable, except for those that clearly contribute to the catalytic activity. This encouraged the concept of “neutral mutations.”

  4. 4.

    Evolutionary trees can be constructed from a matrix of species differences, either overall or by translating back to DNA sequences via the known genetic code or by assuming “invariant” and “variable” regions. These evolutionary trees can be made to bear a satisfying resemblance to the known fossil record.

  5. 5.

    The rate of sequence variation appears to correlate with time rather than with the assumed number of generations between species. This led to the “neutral drift” theory of Kimura (1969).

  6. 6.

    Protein families with similar functions, such as myoglobin and hemoglobin, or the pancreatic serine proteases, also have almost superimposable conformations. Divergence from a common ancestor via gene duplication was clearly implied.

  7. 7.

    Sequence variations between these similar proteins in the same individual follow the same pattern as species differences for a single protein. Hence, evolutionary trees implying distance from a common ancestor could be constructed.

  8. 8.

    Specificity differences between chymotrypsin, trypsin, and elastase appeared to require only one or two amino acid changes, respectively, with no significant conformational change in the specificity sites (Hartley and Shotton, 1971).

  9. 9.

    Convergent evolution to a common enzyme mechanism from two completely different protein ancestors was obvious from the structures of chymotrypsin and subtilisin (Kraut et al., 1971).



Dilution Rate Tryptic Peptide Experimental Evolution Xylitol Dehydrogenase Xylitol Concentration 
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  1. Altosaar, I., and Hartley, B. S., 1976, Comparison of ribitol dehydrogenase from E. coli C and K. aerogenes, in: Proceedings 10th International Congress of Biochemistry, p. 200, Abstract 04-6-319.Google Scholar
  2. Awad, W. M., Soto, A. R., Siegel, S., Skiba, W. E., Bernstrom, G. G., and Ochoa, M. S., 1972, The proteolytic enzymes of the K-1 strain of Streptomyces griseus, J. Biol. Chem. 247:4144–4145.PubMedGoogle Scholar
  3. Burleigh, B. D., Rigby, P. W. J., and Hartley, B. S., 1974, A comparison of wild-type and mutant ribitol dehydrogenases from K. aerogenes, Biochem. J. 143:341–352.PubMedGoogle Scholar
  4. Charnetzky, W. T., and Mortlock, R. P., 1974a, Ribitol catabolic pathway in Klebsiella aerogenes, J. Bacteriol. 119:162–169.PubMedGoogle Scholar
  5. Charnetzky, W. T., and Mortlock, R. P., 1974b, d-Arabitol catabolic pathway in Klebsiella aerogenes, J. Bacteriol. 119:170–175.PubMedGoogle Scholar
  6. Charnetzky, W. T., and Mortlock, R. P., 1974c, Close genetic linkage of the determinants of the ribitol and d-arabitol catabolic pathways in K. aerogenes, J. Bacteriol. 119:176–182.PubMedGoogle Scholar
  7. Dothie, J. M., Giglio, J. R., Moore, C. H., Taylor, S. S., and Hartley, B. S., 1984, Ribitol dehydrogenase from K. aerogenes: Sequences and properties of wild-type and mutant strains, Biochem J. (submitted).Google Scholar
  8. Folk, W. R., and Berg, P., 1971, Duplication of the structural gene for glycyl-transfer RNA synthetase in Escherichia coli, J. Mol. Biol. 58:595–610.PubMedCrossRefGoogle Scholar
  9. Hartley, B. S., 1966, Enzymes are proteins, Adv. Sci. 1966(May):47-54.Google Scholar
  10. Hartley, B. S., 1974, Enzyme families, in: Evolution in the Microbial World (M. J. Carlile and J. J. Skehel, eds.), Elsevier, Amsterdam, pp. 151–182.Google Scholar
  11. Hartley, B. S., and Shotton, D. M., 1971, Pancreatic elastase, in: The Enzymes, Vol. 3, 3rd ed. (P. D. Boyer, ed.), Academic Press, New York, pp. 323–373.Google Scholar
  12. Hartley, B. S., Burleigh, B. D., Midwinter, G. G., Moore, C. H., Morris, H. R., Rigby, P. W. J., Smith, M. J., and Taylor, S. S., 1972, Where do new enzymes come from?, in: Enzymes: Structure and Function (J. Drenth, R. A. Oosterbaan, and C. Veeger, eds.), North-Holland, Amsterdam, pp. 151–176.Google Scholar
  13. Hartley, B. S., Altosaar, I., Dothie, J. M., and Neuberger, M. S., 1976, Experimental evolution of a xylitol dehydrogenase, in: Proceedings of the Third John Innes Symposium (R. Markham and R. W. Home, eds.), North-Holland, Amsterdam, pp. 191–200.Google Scholar
  14. Herbert, D., Ellsworth, R., and Telling, R. C., 1956, The continuous culture of bacteria: A theoretical and experimental study, J. Gen. Microbiol. 14:601–622.PubMedGoogle Scholar
  15. Herbert, D., Phipps, P. J., and Tempest, D. W., 1965, The chemostat design and instrumentation, Lab. Practice 14:1150–1161.Google Scholar
  16. Hill, C. W., Foulds, J., Soll, L., and Berg, P., 1969, Instability of a missense suppressor resulting from a duplication of genetic material, J. Mol. Biol. 39:563–581.PubMedCrossRefGoogle Scholar
  17. Horiuchi, T., Horiuchi, S., and Novick, A., 1963, The genetic basis of hypersynthesis of β-galactosidase, Genetics 48:157–169.PubMedGoogle Scholar
  18. Kimura, M., 1969, The rate of molecular evolution considered from the standpoint of molecular genetics, Proc. Natl. Acad. Sci. USA 63:1181–1183.PubMedCrossRefGoogle Scholar
  19. Kraut, J., Robertus, J. D., Birktoft, J. J., Alden, R. A., Wilcox, P. E., and Powers, J. C., 1971, The aromatic binding site in subtilisin BPN’ and its resemblance to chymotrypsin, Cold Spring Harbor Symp. Quant. Biol. 36:117–124.CrossRefGoogle Scholar
  20. Lerner, S. A., Wu, T. T., and Lin, E. C. C., 1964, Evolution of catabolic pathway in bacteria, Science 146:1313–1315.PubMedCrossRefGoogle Scholar
  21. McLachlan, R. D., and Shotton, D. M., 1971, Structural similarities between α-lytic protease of Myxobacter 495 and elastase, Nature New Biol. 229:202–205.PubMedCrossRefGoogle Scholar
  22. Morris, H. R., Williams, D. H., Midwinter, G. G., and Hartley, B. S., 1974, A mass-spectrometric sequence study of the enzyme ribitol dehydrogenase from Klebsiella aerogenes, Biochem. J. 141:701–713.PubMedGoogle Scholar
  23. Mortlock, R. P., Fossitt, D. D., and Wood, W. A., 1965, A basis for utilization of unnatural pentoses and pentitols by Aerobacter aerogenes, Proc. Natl. Acad. Sci. USA 54:572–579.PubMedCrossRefGoogle Scholar
  24. Muller-Hill, B., Fanning, T., Geisler, N., Gho, D., Kania, J., Kathmaan, P., Meissner, H., Schlotmann, M., Schmitz, A., Triesch, I., and Beyruther, K., 1975, The active sites of lac repressor, in: Protein—Ligand Interactions (H. Sund and G. Blauer, eds.), Walter de Gruyter, Berlin, pp. 211–224.Google Scholar
  25. Pechurkin, N. S., 1969, Continuous cultivation of microorganisms as a means of their autoselection by growth rate in set conditions, in: Continuous Culture of Microorganisms (I. Malek, K. Beran, Z. Fencl, V. Munk, J. Ricica, and H. Smrckova, eds.), Academic Press, London, pp. 315–322.Google Scholar
  26. Powell, E. O., 1965, Theory of the chemostat, Lab. Practice 14:1145–1149.Google Scholar
  27. Reiner, A. M., 1975, Genes for ribitol and d-arabitol metabolism in E. coli: Their loci in C strains and absence in K-12 and B strains, J. Bacteriol. 123:530–536.PubMedGoogle Scholar
  28. Rigby, P. W. J., 1971, An Experimental Approach to Enzyme Evolution, Ph.D. Thesis, University of Cambridge.Google Scholar
  29. Rigby, P. W. J., Burleigh, B. D., and Hartley, B. S., 1974, Gene duplication in experimental enzyme evolution, Nature 251:200–204.PubMedCrossRefGoogle Scholar
  30. Rigby, P. W. J., Gething, M. J., and Hartley, B. S., 1976, Construction of intergeneric hybrids using bacteriophage P1CM: Transfer of the K. aerogenes ribitol dehydrogenase gene to E. coli, J. Bacteriol. 125:728–738.PubMedGoogle Scholar
  31. Rosner, J. L., 1972, Formation, induction and curing of bacteriophage P1 lysogens, Virology 48:679–689.PubMedCrossRefGoogle Scholar
  32. Russell, R. L., Abelson, J. N., Landy, A., Gefter, M. L., Brenner, S., and Smith, J. D., 1970, Duplicate genes for tyrosine tRNA in E. coli, J. Mol. Biol. 47:1–13.PubMedCrossRefGoogle Scholar
  33. Scangos, G. A., and Reiner, A. M., 1978, Ribitol and d-arabitol catabolism in Escherichia coli, J. Bacteriol. 134:492–500.PubMedGoogle Scholar
  34. Streicher, S. L., Bender, R. A., and Magasanik, B., 1971, Transduction of the nitrogen-fixation genes in Klebsiella pneumoniae, J. Bacteriol. 121:320–331.Google Scholar
  35. Taylor, S. S., Rigby, P. W. J., and Hartley, B. S., 1974, Ribitol dehydrogenase from K. aerogenes: Purification and subunit structure, Biochem. J. 141:693–700.PubMedGoogle Scholar
  36. Tempest, D. W., 1970, The continuous cultivation of micro-organisms: 1. Theory of the chemostat, in: Methods in Microbiology, Vol. 2 (J. R. Norris and D. W. Ribbons, eds.), Academic Press, London, pp. 259–276.Google Scholar
  37. Wright, C. S., Alden, R. A., and Kraut, J., 1969, Structure of subtilisin BPN’ at 2.5 Å resolution, Nature 221:235–242.PubMedCrossRefGoogle Scholar
  38. Wu, T. T., Lin, E. C. C., and Tanaka, S., 1968, Mutants of Aerobacter aerogenes capable of using xylitol as a novel carbon source, J. Bacteriol. 96:447–456.PubMedGoogle Scholar
  39. Zabin, I., and Fowler, A. V., 1980, β-Galactosidase, the lactosepermease protein, and thiogalactoside transacetylase, in: The Operon (J. H. Miller and W. S. Reznikoff, eds.), Cold Spring Harbor Laboratory, New York, pp. 89–122.Google Scholar

Copyright information

© Plenum Press, New York 1984

Authors and Affiliations

  • B. S. Hartley
    • 1
  1. 1.Department of BiochemistryImperial College of Science and TechnologyLondonEngland

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