1887

Abstract

Summary: The pattern and extent of DNA sequence variability at the locus (encoding ribosomal protein L24) has been investigated in nine strains of . Overall, there is a very low level of nucleotide diversity, even at silent sites, which is probably due to selection among synonymous codons. By analogy with , there may also be some effect of the relative proximity of to the chromosomal origin of replication. The small number of nucleotide substitutions are non-randomly distributed: all of the synonymous changes are in valine codons. From the sequence differences the strains can be divided into two groups, which are not coincident with their previous classification; this observation is consistent with recombination among strains.

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1992-01-01
2024-12-12
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References

  1. AHN K.S., WAKE R. G. 1991; Variations and coding features of the sequence spanning the replication terminus of Bacillus subtilis168 and W23 chromosomes. Gene 98:107–112
    [Google Scholar]
  2. BIRNBOIM H.C, DOLY J. 1979; A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research 7:1513–1523
    [Google Scholar]
  3. CANTWELL B.A, SHARP P.M, GORMLEY E., MCCONNELL D.J. 1988; Molecular cloning of Bacillus beta-glucanases. Biochemistry and Genetics of Cellulose Degradation181–201 In pp Edited By Aubert J.P., Beguin P., Millet J. London: Academic Press;
    [Google Scholar]
  4. CARRIGAN C.M., HAARSMA J.A., SMITH M.T., WAKE R.G. 1987; Sequence features of the replication terminus of the Bacillus subtilis chromosome. Nucleic Acids Research 158501–8509
    [Google Scholar]
  5. COLLINS J.F., COULSON A.F.W. 1990; Significance of protein sequence similarities. Methods in Enzymology 183:474–487
    [Google Scholar]
  6. HANSMAN D., LINARES J., TOMASZ A., MAYNARD SMITH J., SPRATT B.G. 1989; Horizontal transfer of penicillin-binding protein genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae . Proceedings of the National Academy of Sciences of the United States of America 86:8842–8846
    [Google Scholar]
  7. DUBNAU D. 1989; The competence regulon of Bacillus subtilis . Regulation of Prokaryotic Development147–166 In pp Edited By Smith I., Slepecky R.A., Setlow P. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  8. DUBOSE R.F., DYKHUIZEN D.E., HARTL D.L. 1988; Genetic exchange among natural isolates of bacteria: recombination within phoA gene of Escherichia coli . Proceedings of the National Academy of Sciences of the United States of America 857036–7040
    [Google Scholar]
  9. DUNCAN K.E., ISTOCK C.A., GRAHAM J.B., FERGUSON N. 1989; Genetic exchange between Bacillus subtilis Bacillus licheniformisvariable hybrid sterility and the nature of bacterial species. Evolution 43:1585–1609
    [Google Scholar]
  10. FITCH W.M. 1977; On the problem of discovering the most parsimonious tree. American Naturalist 111:223–257
    [Google Scholar]
  11. HENKIN T.M., MOON S.H., MATTEAKIS L.C., NOMURA M. 1989; Cloning and analysis of the spc ribosomal operon of Bacillus subtilis: comparison with the spc operon of Escherichia coli . Nucleic Acids Research 177469–7486
    [Google Scholar]
  12. KIMURA M. The Neutral Theory y f Molecular Evolution Cambridge: Cambridge University Press;
    [Google Scholar]
  13. LEWIS P.J., WAKE R.G. 1989; DNA and protein sequence conservation at the replication terminus in Bacillus168 and W23. Journal of Bacteriology 171:1402–1408
    [Google Scholar]
  14. LI W.H., GOUY M. 1990; Statistical tests of molecular phylogenies. Methods in Enzymology 183:645–659
    [Google Scholar]
  15. Li W.H., Wu C.I., Luo C.C. 1985; A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 2:150–174
    [Google Scholar]
  16. MANIATIS T., FRITSCH E.F., SAMBROOK J. 1982 Molecular Cloning:a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  17. MAYNARD SMITH J., DOWSON C.G., SPRATT B.G. 1991; Localized sex in bacteria. Nature London: 349:29–31
    [Google Scholar]
  18. MILKMAN R., BRIDGES M.M. 1990; Molecular evolution of the Escherichia colichromosome.II Clonal segments. Genetics 126:505–517
    [Google Scholar]
  19. MILKMAN R., STOLTZFUS A. 1988; Molecular evolution of the Escherichia colichromosome.II Clonal segments. Genetics 120:359–366
    [Google Scholar]
  20. NAKAMURA L. K. 1989; Taxonomic relationships of black-pigmented Bacillus subtilisstrains and a proposal for Bacillus atrophaeussp. nov. International Journal of Systematic Bacteriology 39:295–300
    [Google Scholar]
  21. OCHMAN H., SELANDER R. K. 1984; Evidence for clonal population structure inEscherichia coli . Proceedings of the National Academy of Sciences of the United States of America 81198–201
    [Google Scholar]
  22. PIFFARETTI J.-C., KRESSBUCH H., AESCHBACHER M., BILLE J., BANNERMAN E., MUSSER J. M., SELANDER R.K., ROCOURT J. 1989; Genetic characterization of clones of the bacterium Listeria monocytogenes causing epidemic disease. Proceedings of the National Academy of sciences of the United States of America 863818–3822
    [Google Scholar]
  23. PIGGOT P. J., AMJAD M., WU J.-J., SANDOVAL H., CASTRO J. Genetic and physical maps of Bacillus subtilis 168. Molecular Biological Methods for Bacillus557–569 In pp Edited By Harwood C.R., Cutting S.M. Chichester: John Wiley;
    [Google Scholar]
  24. PRIEST F. G., GOODFELLOW M., TODD C. 1988; A numerical classification of the genus Bacillus . Journal of General Microbiology 134:1847–1882
    [Google Scholar]
  25. RODRIGUEZ R.L, TAIT R.C. 1983 Recombinant DNA Techniques: An Introduction Reading, MA: Addison-Wesley;
    [Google Scholar]
  26. SELANDER R.K., LEVIN B. R. 1980; Genetic diversity and structure inEscherichia colipopulations. Science 210:545–547
    [Google Scholar]
  27. SELANDER R. K., MCKINNEY R. M., WHITTAM T. S., BIBB W. F., BRENNER D. J., NOLTE F. S., PATTISON P. E. 1985; Genetic structure of populations of Legionella pneumophila . Journal of Bacteriology 163:1021–1037
    [Google Scholar]
  28. SELANDER R. K., CAUGANT D. A., WHITTAM T. S. 1987 Genetic structure and variation in natural populations of Escherichia coli . Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology1625–1648 In pp Edited By Neidhardt F. C., Ingraham J. L., Low K. B., Magasanik B., Schaechter M., Umbarger H. E. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  29. SHARP P. M., LI W.-H. 1987a; The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15:1281–1295
    [Google Scholar]
  30. SHARP P. M., LI W.-H. 1987b; The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Molecular Biology and Evolution 4:222–230
    [Google Scholar]
  31. SHARP P. M., SHIELDS D. C., WOLFE K. H., LI W.-H. 1989; Chromosomal location and evolutionary rate variation in Enterobacterial genes. Science 246:808–810
    [Google Scholar]
  32. SHARP P. M., HIGGINS D. G., SHIELDS D. C., Devine K. M. 1990a Protein-coding genes: DNA sequence database and codon usage. Molecular Biological Methods for Bacillus557–569 In pp Edited By Harwood C. R., Cutting S. M. Chichester: John Wiley;
    [Google Scholar]
  33. SHARP P. M., HIGGINS D. G., SHIELDS D. C., DEVINE K. M., HOCH J. A. 1990b Bacillus subtilisgene sequences. Genetics and Biotechnology of Bacilli 389–98 In pp Edited By Zukowski M. M., Ganesan A. T., Hoch J. A. San Diego: Academic Press;
    [Google Scholar]
  34. SHIELDS D.C., SHARP P. M. 1987; Synonymous codon usage in Bacillus subtilisreflects both translational selection and mutational biases. Nucleic Acids Research 15:8023–8040
    [Google Scholar]
  35. WOESE C. R. 1987; Bacterial evolution. Microbiological Reviews 51:221–271
    [Google Scholar]
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