Molecular and evolutionary relationships among enteric bacteria

References

1. Ahmad S., Weisburg W. G., Jensen R. A. 1990; Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria. Journal of Bacteriology 172:1051–1061
   [Google Scholar]
2. Alefounder P. R., Perham R. N. 1989; Identification, molecular cloning and sequence analysis of a gene cluster encoding the Class II fructose 1,6-biphosphate aldolase, 3-phosphoglycerate kinase and a second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli. Molecular Microbiology 3:723–732
   [Google Scholar]
3. Bachmann B. J. 1990; Linkage map of Escherichia coli K-12, edition 8. Microbiological Reviews 54:130–197
   [Google Scholar]
4. Beck E., Bremer E. 1980; Nucleotide sequence of the gene ompA coding the outer membrane protein II* of Escherichia coli K-12. Nucleic Acids Research 8:3011–3024
   [Google Scholar]
5. Bergström S., Lindberg P., Olsson O., Normark S. 1983; Comparison of the overlapping frd and ampC operons of Escherichia coli with the corresponding DNA sequences in other gram-negative bacteria. Journal of Bacteriology 155:1297–1305
   [Google Scholar]
6. Branlant G., Branlant C. 1985; Nucleotide sequence of the Escherichia coli gap gene: different evolutionary behavior of the NAD⁺-binding domain and of the catalytic domain of the d-glyceraldehyde-3-phosphate dehydrogenase. European Journal of Biochemistry 150:61–66
   [Google Scholar]
7. Branlant C., Oster T., Branlant G. 1989; Nucleotide sequence determination of the DNA region coding for Bacillus stearothermo-philus glyceraldehyde-3-phosphate dehydrogenase and of the flanking DNA regions required for its expression in Escherichia coli. Gene 75:145–155
   [Google Scholar]
8. Braun G., Cole S. T. 1984; DNA sequence analysis of the Serratia marcescens ompA gene: implication for the organisation of an enterobacterial outer membrane protein. Molecular and General Genetics 195:321–328
   [Google Scholar]
9. Brenner D. J. 1978; Characterization and clinical identification of Enterobacteriaceae by DNA hybridization. Progress in Clinical Pathology 1:71–117
   [Google Scholar]
10. Brenner D. J. 1981; Introduction to the family Enterobacteriaceae. The Prokaryotes: a Handbook on Habitats, Isolation and Identification of Bacteria 21105–1127 Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. Berlin: Springer-Verlag;
    [Google Scholar]
11. Brenner D. J. 1984; Enterobacteriaceae. Bergey’s Manual of Systematic Bacteriology 1408–420 Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
12. Brenner D. J., Falkow S. 1971; Molecular relationships among members of the Enterobacteriaceae. Advances in Genetics 16:81–118
    [Google Scholar]
13. Brenner D. J., Farmer J. J. III, Fanning G. R., Steigerwalt A. G., Klykken P., Wathen H. G., Hickman F. W., Ewing W. H. 1978; Deoxyribonucleic acid relatedness of Proteus and Providencia species. International Journal of Systematic Bacteriology 28:269–282
    [Google Scholar]
14. Brenner D. J., Steigerwalt A. G., Gorman G. W., Weaver R. E., Feeley J. C., Cordes L. G., Wilkinson H. W., Patton C., Thomason B. M., Lewallen Sasseville K. R. 1980; Legionella bozemanii sp. nov. and Legionella dumoffii sp. nov.: classification of two additional species of Legionella associated with human pneumonia. Current Microbiology 4:111–116
    [Google Scholar]
15. Brenner D. J., Davis B. R., Steigerwalt A. G., Riddle C. F., McWhorter A. C., Allen S. D., Farmer J. J. III, Saitoh Y., Fanning G. R. 1982a; Atypical biogroups of Escherichia coli found in clinical specimens and description of Escherichia hermannii sp. nov. Journal of Clinical Microbiology 15:703–713
    [Google Scholar]
16. Brenner D. J., McWhorter A. C., Leete Knutson J. K., Steigerwalt A. G. 1982b; Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. Journal of Clinical Microbiology 15:1133–1140
    [Google Scholar]
17. Burgess N. R. H., McDermott S. N., Whiting J. 1973; Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis. Journal of Hygiene 11:1–7
    [Google Scholar]
18. Cocks G. T., Wilson A. C. 1972; Enzyme evolution in the Enterobacteriaceae. Journal of Bacteriology 110:793–802
    [Google Scholar]
19. Doolittle R. F., Feng D. F., Anderson K. L., Alberrro M. R. 1990; A naturally occurring gene transfer from a eukaryote to a prokaryote. Journal of Molecular Evolution 31:383–388
    [Google Scholar]
20. Edwards P. R., Ewing W. H. 1962 Identification of Enterobacteriaceae Minneapolis: Burgess;
    [Google Scholar]
21. Farmer J. J. III, Fanning G. R., Davis B. R., O’Hara C. M., Riddle C., Hickman-Brenner F. W., Asbury M. A., Lowery V. A. III, Brenner D. J. 1985; Escherichia fergusonii and Enterobacter taylorae, two new species of Enterobacteriaceae isolated from clinical specimens. Journal of Clinical Microbiology 21:77–81
    [Google Scholar]
22. Felsenstein J. 1985; Confidence limits on phylogenies with a molecular clock. Systematic Zoology 34:152–161
    [Google Scholar]
23. Freudl R., Cole S. T. 1983; Cloning and molecular characterization of the ompA gene from Salmonella typhimurium. European Journal of Biochemistry 134:497–502
    [Google Scholar]
24. Galliard C., Strauss F. 1990; Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Research 18:378
    [Google Scholar]
25. Grimont P. A. D., Grimont F., Richard C., Davis B. R., Steigerwalt A. G., Brenner D. J. 1978; Deoxyribonucleic acid relatedness between Serratia plymuthica and other Serratia species, with a description of Serratia odorifera sp. nov. (type strain: ICPB 3995). International Journal of Systematic Bacteriology 28:453–463
    [Google Scholar]
26. Jensen R. A. 1985; Biochemical pathways can be traced backward through evolutionary time. Molecular Biology and Evolution 2:92–108
    [Google Scholar]
27. Kocher T. D., Thomas W. K., Meyer A., Edwards S. V., Pääbo S. V., Villablanca F. X., Wilson A. C. 1989; Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America 866196–6200
    [Google Scholar]
28. Martin W., Cerff R. 1986; Prokaryotic features of a nucleus-encoded enzyme. European Journal of Biochemistry 159:323–331
    [Google Scholar]
29. Meyer T. E., Cusanovich M. A., Kamen M. D. 1986; Evidence against the use of bacterial amino acid sequence data for construction of all inclusive phylogenetic trees. Proceedings of the National Academy of Sciences of the United States of America 83217–220
    [Google Scholar]
30. Normore W. M., Brown J. R. 1970; Guanine plus cytosine (G+C) composition of bacteria. Handbook of Biochemistry: Selected Data for Molecular Biology, 2nd.H24–H74 Sober H. A. Cleveland: The Chemical Rubber Co;
    [Google Scholar]
31. Ochman H., Wilson A. C. 1987; Evolutionary history of enteric bacteria. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology1649–1654 Niedhardt F. D. Washington, DC: American Society for Microbiology;
    [Google Scholar]
32. Ochman H., Wilson A. C. 1988; Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. Journal of Molecular Evolution 26:74–86
    [Google Scholar]
33. Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N. A. 1985; Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354
    [Google Scholar]
34. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. 1988; Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
    [Google Scholar]
35. Sawyer S., Dykhuizen D., DuBose R. F., Green L., Mutangadura-Mhlanga T., Wolczyk D. F., Hartl D. L. 1987; Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics 115:51–63
    [Google Scholar]
36. Sharp P. M. 1990; Processes of genome evolution reflected by base frequency differences among Serratia marcescens genes. Molecular Microbiology 4:119–122
    [Google Scholar]
37. Sharp P. M., Li W. H. 1987a; Rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Molecular Biology and Evolution 4:222–230
    [Google Scholar]
38. Sharp P. M., Li W. H. 1987b; The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15:1281–1295
    [Google Scholar]
39. Stone E. M., Rothblum K. N., Alevy M. C., Kuo T. M., Schwartz R. J. 1985; Complete sequence of the chicken glyceraldehyde-3-phosphate dehydrogenase gene. Proceedings of the National Academy of Sciences of the United States of America 821628–1632
    [Google Scholar]
40. Taylor M. F. J., Kreitman M. E. 1989; PCR amplification of conserved genes from novel genomes with peptide specific primers. Journal of Cellular Biochemistry S13E:309
    [Google Scholar]
41. Woese C. R. 1987; Bacterial evolution. Microbiological Reviews 51:221–271
    [Google Scholar]