The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium (original) (raw)
References
Ahmad, S., Weisburg, W.G. and Jensen, R.A. (1990) Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria. J. Bacterial 172: 1051–1061. CAS Google Scholar
Alefounder, P.R. and Perham, R.N. (1989) Identification, molecular cloning and sequence analysis of a gene cluster encoding the Class II fructose 1,6-biphosphate aldolase, 3-phospho-glycerate kinase and a second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli. Moke. Microbiol. 3: 723–732. CAS Google Scholar
Bachmann, B.J. (1990) Linkage map of Escherichia coli K-12. Microbiol. Rev. 54: 130–197. PubMedCAS Google Scholar
Benson, N.R. and Goldman, B.S. (1992) Rapid mapping in Salmonella typhimurium with Mud-P prophages. J. Bacieriol. 174: 1673–1681. CAS Google Scholar
Brenner, D.J. (1992) Introduction to the family Enterobacteriaceae. In: H. Balows, H.G. Triiper, M. Dworkin, W. Harder and K.-H. Schliefer (eds): The Prokaryotes, second edition, Volume III. Springer-Verlag, New York, pp. 2673–2695. Google Scholar
Burland, V., Plunkett III, G., Daniels, D. and Blattner F.R. (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16: 551–561. ArticlePubMedCAS Google Scholar
Carlson, T.A. and Chelm, B.K. (1986) Apparent eukaryotic origin of glutamine synthetase II from Bradyrhizobium japonicum. Nature 322: 568–570. ArticleCAS Google Scholar
Casse, F., Pascal, M.-C. and Chippaux, M. (1973) Comparison between the chromosomal maps of Escherichia coli and Salmonella typhimurium — length of the inverted segment in the trp region. Mol Gen. Genet. 124: 253–257. ArticlePubMedCAS Google Scholar
Curtiss III, R. and Kelly, S.M. (1987) Salmonella typhimurium deletion mutants lacking adenlylate cyclase and cyclic AMP receptor protein are avirulent and immunogenic. Infect. Immun. 55: 3035–3043. PubMedCAS Google Scholar
Daniels, D.L., Plunkett, III, G., Burland, V. and Blattner, F.R. (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257: 771–778. ArticlePubMedCAS Google Scholar
Davis, R.W., Botstein, D. and Roth, J.R. (1980) Advanced Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY Google Scholar
Devereux, J., Haeberli, P. and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387–395. ArticlePubMedCAS Google Scholar
Doolittle, R.F., Feng, D.F., Anderson, K.L. and Alberro, M.R. (1990) A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote. J. Mol. Evol. 31: 383–388. ArticlePubMedCAS Google Scholar
Dorman, C.J., Chatfield, S., Higgins, C.F., Hayward, C. and Dougan, G. (1989) Characterization of porin and ompR mutants of a virulent strain of Salmonella typhimurium : ompR mutants are attentuated in vivo. Infect. Immun. 57: 2136–2140. PubMedCAS Google Scholar
Dowson, C.G., Hutchison, A., Brannigan, J.A., George, R.C., Hansman, D., Linares, J., Tomasz, A., Maynard Smith, J. and Spratt, B.G. (1989) Horizontal transfer of a penicillin-binding protein gene in a penicillin-resistant clinical isolate of Streptococcus pneumoniae. Proc. Natl. Acad. Sci. USA 86: 8842–8846. ArticlePubMedCAS Google Scholar
Dykhuizen, D.E. and Green, L. (1991) Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173: 7257–7268. PubMedCAS Google Scholar
Feinberg, A.P. and Vogelstein, B. (1983) A technique for radiolabeling DNA restriction endonuclease fragments of high specific activity. Anal. Biochem. 132: 6–13 ArticlePubMedCAS Google Scholar
Filipski, J., Salinas, J. and Rodier, F. (1989) Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences. J. Mol. Biol. 206: 563–566. ArticlePubMedCAS Google Scholar
Finlay, B.B. and Falkow, S. (1989) Salmonella as an intracellular parasite. Mol. Microbiol. 3: 1833–1841. ArticlePubMedCAS Google Scholar
Fitts, R. (1985) Development of a DNA-DNA hybridization test for the presence of Salmonella in foods. Foods Technol. 39: 95–102. CAS Google Scholar
Galán, J.E. and Curtiss III, R. (1991) Distribution of the invA, -B, -C, and -D genes of Salmonella typhimurium among other Salmonella serovars: invA mutants of Salmonella typhi are deficient for entry into mammalian cells. Infect. Immun. 59: 2901–2908. PubMed Google Scholar
Groisman, E.A., Fields, P.I. and Heffron, F. (1990) Molecular biology of Salmonella pathogenesis In: B.H. Iglewski and V.L. Clark (eds): Molecular Basis of Bacterial Pathogenesis, Vol. XL Academic Press, San Diego, pp. 251–272. Google Scholar
Groisman, E.A., Chiao, E., Lipps, C.J. and Heffron, F. (1992a) Salmonella typhimurium phoP virulence gene is a transcriptional regulator. Proc. Natl. Acad. Sci. USA 86: 7077–7081. Article Google Scholar
Groisman, E.A., Saier, Jr., M.H. and Ochman, H. (1992b) Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome. EMBO J. 11: 1309–1316. PubMedCAS Google Scholar
Groisman, E.A., Parra-Lopez, C., Salcedo, M., Lipps, C.J. and Heffron, F. (1992c) Resistance to host antimicrobial peptides is necessary for Salmonella virulence. Proc. Natl. Acad. Sci. USA 89: 11939–11943. ArticlePubMedCAS Google Scholar
Groisman, E. A. and Ochman, H. (1993a) Cognate genes govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri. EM BO J. 12: 3779–3787. CAS Google Scholar
Groisman, E.A., Sturmoski, M.A., Solomon, F.R., Lin, R. and Ochman, H. (1993b) Molecular, functional, and evolutionary analysis of sequences specific to Salmonella. Proc. Natl. Acad. Sci. USA 90: 1033–1037. ArticlePubMedCAS Google Scholar
Heinemann, J.A. (1991) Genetics of gene transfer between species. Trends Genet. 7: 171–175. Google Scholar
Hoyer, L.L., Hamilton, A.C., Steenbergen, S.M. and Vimr, E.R. (1992) Cloning, sequencing and distribution of the Salmonella typhimurium LT2 sialidase gene, nanH, provides evidence for interspecies gene transfer. Mol. Microbiol. 6: 873–884. ArticlePubMedCAS Google Scholar
Ikemura, T., Wada, K.-W. and Aota, S.-I. (1990) Giant G + C% mosaic structures of the human genome found by arrangement of Genbank human DNA sequences according to genetic positions. Genomics 8: 207–216. ArticlePubMedCAS Google Scholar
Jensen, R.A. (1985) Biochemical pathways in prokaryotes can be traced backward through evolutionary time. Mol. Biol. Evol. 2: 92–108. PubMedCAS Google Scholar
Kohara, Y., Akiyama, K. and Isono, K. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50: 495–508. ArticlePubMedCAS Google Scholar
Kohring, G.-W. and Mayer, F. (1987) In situ distribution of EcoRI methylase and restriction endonuclease in cells of Escherichia coli. FEBS Lett. 216: 207–210. ArticlePubMedCAS Google Scholar
Krane, D.E., Hartl, D.L. and Ochman, H. (1991) Rapid determination of the nucleotide content and its application to the study of genome organization. Nucleic Acids Res. 19: 5181–5185. ArticlePubMedCAS Google Scholar
Krawiec, S. and Riley, M. (1990) Organization of the bacterial chromosome. Microbiol. Rev. 54: 502–539. PubMedCAS Google Scholar
Kroll, J.S. and Moxon, E.R. (1990) Capsulation in distantly related strains of Haemophilus influenzae type B: genetic drift and gene transfer at the capsulation locus. J. Bacteriol. 172: 1374–1379. PubMedCAS Google Scholar
Lawrence, J.G., Ochman, H. and Hartl, D.L. (1991) Molecular and evolutionary relationships among enteric bacteria. J. Gen Microbiol. 137: 1911–1921. ArticlePubMedCAS Google Scholar
Levin, B.R. and Svanborg Eden, C. (1990) Selection and evolution of virulence in bacteria: an ecumenical excursion and modest suggestion. Parasitology 100: S103–S115. ArticlePubMed Google Scholar
Maynard Smith, J., Dowson, C.G. and Spratt, B.G. (1991) Localized sex in bacteria. Nature 349: 29–31. Article Google Scholar
Maynard Smith, J., Smith, N.H., O’Rourke, M. and Spratt, B.G. (1993) How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90: 4384–4389. Article Google Scholar
Mazodier, P. and Davies, J. (1991) Gene transfer between distantly related bacteria. Ann. Rev. Genet. 25: 147–171. ArticlePubMedCAS Google Scholar
Miller, J. H. (1972) Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. Google Scholar
Miller, S.L, Kukra, A.M. and Mekalanos, J.J. (1989) A two-component regulatory system (phoP phoQ) controls Salmonella typhimurium virulence. Proc. Natl. Acad. Sci. USA 86: 5054–5058. ArticlePubMedCAS Google Scholar
Miller, J.H. (1992) A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. Google Scholar
Muto, A. and Osawa, S. (1987) The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84: 166–169. ArticlePubMedCAS Google Scholar
Normore, W.M. and Brown, J.R. (1970) G + C composition in bacteria. In: H.A. Sober (ed.): Handbook of Biochemistry: Selected Data for Molecular Biology. CRC Press, Cleveland, pp. 24–74. Google Scholar
Ochman, H., Whittam, T.S., Caugant, D.A. and Seiander, R.K. (1983) Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. J. Gen. Microbiol. 129: 2715–2726. PubMedCAS Google Scholar
Ochman, H. and Wilson, A.C. (1987) Evolutionary history of enteric bacteria. In: F.C. Neidhardt, J.L. Ingraham, K.B. Low, B. Magasanik, M. Schaechter, and H.E. Umbarger (eds): Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Vol. 2. American Society of Microbiology Publications, Washington, DC, pp. 1649–1654. Google Scholar
Ochman, H. and Wilson, A.C. (1988) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26: 74–86. Article Google Scholar
Parra-Lopez, C., Baer, M.T. and Groisman, E.A. (1993) Molecular genetic analysis of a locus required for resistance to antimicrobial peptides in Salmonella typhimurium. EM BO J. 12: 4053–4062. CAS Google Scholar
Radman, M. and Wagner, R. (1986) Mismatch repair in Escherichia coli. Ann. Rev. Genet. 20: 523–538. ArticleCAS Google Scholar
Rayssiguier, C., Thaler, D.S. and Radman, M. (1989) The barrier of recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396–401. ArticlePubMedCAS Google Scholar
Reeves, P. (1993) Evolution of Salmonella O antigen variation by interspecific gene transfer on a large scale. Trends Genet. 9: 17–22. ArticlePubMedCAS Google Scholar
Riley, M. and Krawiec, S. (1987) Genome organization. In: F.C. Neidhardt, J.L. Ingraham, K.B. Low, B. Magasanik, M. Schaechter, and H.E. Umbarger (eds): Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Vol. 2. American Society for Microbiology Publications, Washington, DC, pp. 967–981. Google Scholar
Riley, M. and Sanderson, K.E. (1990) Comparative genetics of Escherichia coli and Salmonella typhimurium. In:M. Riley and K. Drlica (eds): The Bacterial Chromosome. American Society for Microbiology Publications, Washington, DC, pp. 85–95. Google Scholar
Rudd, K. (1993) Maps, genes, sequences and computers: an Escherichia coli case study. ASM News 50: 335–341. Google Scholar
Sanderson, K.E. and Roth, J.R. (1988) Linkage map of Salmonella typhimurium, edition VII. Microbiol. Rev. 52: 485–532. PubMedCAS Google Scholar
Sanger, F., Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA 74: 5463–5467. ArticlePubMedCAS Google Scholar
Sasakawa, C., Komatsu, K., Tobe, T., Suzuki, T. and Yoshikawa, M. (1993) Eight genes in region 5 that form an operon are essential for invasion of epithelial cells by Shigella flexneri 2a. J. Bacteriol. 175: 2334–2346. PubMedCAS Google Scholar
Seiander, R.K., Caugant, D.A. and Whittam, T.S. (1987) Genetic structure and variation in natural populations of Escherichia coli. In: F.C. Neidhardt, J.L. Ingraham. K.B. Low, B. Magasanik, M. Schaechter and H.E. Umbarger (eds): Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Vol. 2. American Society for Microbiology, Washington, DC, pp. 1625–1648. Google Scholar
Seiander, R.K., Beltran, P. and Smith, N.H. (1991) Evolutionary genetics of Salmonella. In: R.K. Selander, A.G. Clark and T.S. Whittam (eds): Evolution at the Molecular Level. Sinauer Associates Inc., Sunderland, Massachusetts, pp. 25–57. Google Scholar
Sharp, P.M. (1991) Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position and concerted evolution. J. Mol. Evol. 33: 23–33. ArticlePubMedCAS Google Scholar
Smith, M.W., Feng, D.-W. and Doolittle, R.F. (1992) Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17: 489–493. ArticlePubMedCAS Google Scholar
Spratt, B.G., Bowler, L.D., Zhang, Q.-Y., Zhou, J. and Maynard Smith, J. (1992) Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species. J. Mol. Evol. 34: 115–125. ArticlePubMedCAS Google Scholar
Sueoka, N. (1961) Variation and heterogeneity of base composition of deoxy-ribonucleic acids: a compilation of old and new data. J. Mol. Biol. 3: 31–40. ArticleCAS Google Scholar
Tabata, S., Higashitani, A., Takanami, M., Akiyama, K., Kohara, Y., Nishimura, Y., Nishimura, A., Yasuda, S. and Hirota, Y. (1989) Construction of an ordered cosmid collection of the Escherichia coli K-12 W3110 chromosome. J. Bacteriol. 171: 1214–1218. PubMedCAS Google Scholar
Turpin, P.E., Maycroft, K.A., Rowlands, C.L. and Wellington, E.M.H. (1993) Viable but unculturable Salmonellas in soil. J. Applied Bacteriol. 74: 421–427. ArticleCAS Google Scholar
Van Vliet, F., Boyen, A. and Glansdorff, N. (1988) On interspecies gene transfer: the case of the argf gene in E. coli. Ann. Inst. Pasteur. Microbiol. 139: 493–496. ArticlePubMed Google Scholar
Venkatesan, M.M., Buyusse, J.M. and Oaks, E.V. (1992) Surface presentation of Shigella flexneri invasion plasmid antigens requires products of the spa locus. J. Bacteriol. 174: 1990–2001. PubMedCAS Google Scholar
Wada, K., Wada, Y., Ishibashi, F., Gojobori, T. and Ikemura, T. (1992) Codon usage tabulated from the Genbank genetic sequence data. Nucleic Acids Res. 18: 2367–2413. Article Google Scholar
Wakabayashi, S., Matsubara, H. and Webster, D.A. (1986) Primary sequence of a dimeric bacterial haemoglobin from Vitreoscilla. Nature 322: 481–483. ArticleCAS Google Scholar
Whittam, T.S. and Ake, S. (1992) Genetic polymorphisms and recombination in natural populations of Escherichia coli. In: N. Takahata and A.G. Clark (eds): Mechanisms of Molecular Evolution. Japan Scientific Society Press, pp. 223–246. Google Scholar
Yura, T., Mori, H., Nagai, H., Nagata, T., Ishihama, A., Fujita, N., Isono, K., Mizobuchi, K. and Nakata, A. (1992) Systematic sequencing of the Escherichia coli genome: analysis of the 0–2.4 min region. Nucleic Acids Res. 20: 3305–3308. ArticlePubMedCAS Google Scholar