Chapter 19 : Horizontal Transfer, Genomic Diversity, and Genomic Differentiation

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Horizontal Transfer, Genomic Diversity, and Genomic Differentiation, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817749/9781555812713_Chap19-1.gif /docserver/preview/fulltext/10.1128/9781555817749/9781555812713_Chap19-2.gif


The genome of an individual cellular organism or a DNA virus is best defined as a single example of a set of unique and uniquely placed DNA sequences. Two techniques that have provided detailed bases of comparison among strains, as well as among those of many other bacterial species, are multilocus enzyme electrophoresis (MLEE) and restriction fragment length polymorphism (RFLP, also referred to as restriction analysis). Multilocus sequence typing (MLST) technique has been particularly useful in epidemiological studies of pathogenic bacteria such as , , , and . A major difference between prokaryotic and eukaryotic recombination processes lies in the great phylogenetic distances crossed (very infrequently, to be sure, but with evolutionarily important effects) in prokaryotic horizontal transfer. Many types of antibiotic resistance are coded by plasmids, and conjugative plasmids facilitate horizontal gene transfer. The rates of horizontal transfer among the various bacteria in the same colon have not been investigated to any important extent; they would be worth knowing. The two sizeable hypervariable regions constitute genomic differentiation both in their site-specific dynamics of horizontal transfer and the resulting distinct local patterns of high variation. It summarizes Woese's view that horizontal transfer preceded vertical transfer and that horizontal transfer was the engine of evolution in supramolecular aggregates, which preceded cells, whose eventual achievement of sufficient complexity led to heredity and Darwinian evolution.

Citation: Milkman R. 2004. Horizontal Transfer, Genomic Diversity, and Genomic Differentiation, p 297-318. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch19

Key Concept Ranking

Restriction Fragment Length Polymorphism
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Amor, K.,, D. E. Heinrichs,, E. Frirdich,, K. Ziebell,, R. Johnson,, and C. Whitfield. 2000. Distribution of core oligosaccharide types in lipopolysaccharides from Escherichia coli . Infect. Immun. 68: 1116 1124.
2. Barcus, V. A.,, J. B. Titheradge,, and N. E. Murray. 1995. The diversity of alleles at the hsd locus in natural populations of Escherichia coli . Genetics 140: 1187 1197.
3. Berlyn, M. K. B. 1998. Linkage Map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol Biol. Rev. 62: 814 984.
4. Box, G. E. P.,, and M. E. Muller. 1958. A note on the generation of random normal deviates. Ann. Math. Stat. 29: 610 611.
5. Crameri, A.,, S.-A. Raillard,, E. Bermudez,, and W. P. C. Stemmer. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391: 288 291.
6. Crow, J. F.,, and M. Kimura. 1970. An Introduction to Population Genetics Theory. Harper & Row Publishers, New York, N.Y.
7. Hayes, J. M. 2000. Lipids as a common interest of microorganisms and geochemists. Proc. Natl. Acad. Sci. USA 97: 14033 14034.
8. Kudva, I. T.,, P. S. Evans,, N. T. Perna,, T.J. Barrett,, F. M. Ausubel,, F. R. Blattner,, and S. B. Calderwood. 2002. Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions. J. Bacteriol. 184: 1873 1879.
9. Lan, R.,, and P. R. Reeves. 2000. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8: 396 401.
10. Li, Q.,, and P. R. Reeves. 2000. Genetic variation of dTDP-1-rhamnose pathway genes in Salmonella enterica . Microbiology 146: 2291 2307.
11. Milkman, R. 1978. Selection differentials and selection coefficients. Genetics 88: 391 403.
12. Milkman, R., 1999. Gene transfer in Escherichia coli, p. 291 309. In R. L. Charlebois (ed.), Organization of the Prokaryotic Genome. American Society for Microbiology, Washington, D.C.
13. Milkman, R.,, and M. McKane Bridges. 1990. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126: 505 517.
14. Milkman, R.,, E. A. Raleigh,, M. McKane,, D. Cryderman,, P. Bilodeau,, and K. McWeeny. 1999. Molecular evolution of the Escherichia coli chromosome. V. Recombination patterns among strains of diverse origin. Genetics 153: 539 554.
15. Milkman, R.,, E. B. Jaeger,, and R. D. McBride. 2003. Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination. Genetics 163: 475 483.
16. Ochman, H.,, and R. K. Selander. 1984. Standard reference strains of E. coli from natural populations. J. Bacteriol. 157: 690 693.
17. Perna, N. T.,, G. Plunkett III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E.J. Grotbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch,, and F. R Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529 533.
18. Reeves, P. 1993. Evolution of Salmonella O antigen variation by interspecific gene transfer on a large scale. Trends Genet. 9: 17 22.
19. Rudd, K. E. 1998. Linkage map of Escherichia coli K-12, edition 10: the physical map. Microbiol. Mol. Biol. Rev. 62: 985 1019.
20. Spratt, B. G. 1999. Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr. Opin. Microbiol. 2: 312 316.
21. Vaisvila, R.,, R. D. Morgan,, J. Postal,, and E. A. Raleigh. 2001. Discovery and distribution of superintegrons among pseudomonads. Mol. Microbiol. 42: 587 601.
22. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221 271.
23. Woese, C. R. 2002. On the evolution of cells. Proc. Natl. Acad. Sci. USA 99: 8742 8747.
24. Atwood, K. C.,, L. K. Schneider,, and F. J. Ryan. 1951. Selective mechanisms in bacteria. Cold Spring Harbor Symp. Quant. Biol. 16: 345 355.
25. Avise, J. 1989. Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution 43: 1192 1208.
26. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D.J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli . Science 277: 1453 1474.
27. Crawford, I. P. 1989. Evolution of a biosynthetic pathway: the tryptophan paradigm. Annu. Rev. Microbiol. 43: 567 600.
28. Darwin, C. 1859. On the Origin of Species, p. 484. Harvard University Press, Cambridge, Mass.
29. Dykhuizen, D. E.,, and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173: 7257 7268.
30. Hall, R. M., and CM. Collis. 1995. Mobile genetic cassettes and integrons: capture and spread of genes by site-specific recombination. Mol. Microbiol. 15: 593 600.
31. Heinemann, J.,, and G. Sprague. 1989. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340: 205 209.
32. Herzer, P. J.,, S. Inouye,, M. Inouye,, and T. Whittam. 1990. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli . J. Bacteriol. 172: 6175 6181.
33. Hobbs, M.,, and P. R. Reeves. 1994. The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters. Mol. Microbiol. 12: 855 856.
34. Kohara, Y.,, K. Akiyama,, and K. Isono. 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.
35. Madigan, M. T.,, J. M. Martinko,, and J. Parker. 2002. Brock's Biology of Microorganisms, 10th ed. Prentice-Hall, Upper Saddle Raver, N.J.
36. Masters, M., 1996. Generalized transduction, p. 2421 2441. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.
37. Mayr, E. 1963. Animal Species and Evolution, p. 19. The Belknap Press of Harvard University Press, Cambridge, Mass.
38. Mayr, E. 2001. What Evolution IS. Basic Books, New York, N.Y.
39. McKane, M.,, and R. Milkman. 1995. Transduction, restriction and recombination patterns in Escherichia coli . Genetics 139: 35 43.
40. Milkman, R. 1973. Electrophoretic variation in Escherichia coli from diverse natural sources. Science 182: 1024 1026.
41. Milkman, R., 1996. Recombinational exchange among clonal populations, p. 2663 2684. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.
42. Milkman, R. 1997. Recombination and population structure in Escherichia coli . Genetics 146: 745 750.
43. Salyers, A. A.,, and D. D. Whitt. 2001. Microbiology. Fitzgerald Science Press, Bethesda, Md.
44. Selander, R. K.,, J. Li,, and K. Nelson,. 1996. Evolutionary genetics of Salmonella enterica, p. 2691 2707. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.
45. Smith, L. M.,, R.J. Kaiser,, J. Z. Sanders,, and L. E. Hood. 1987. The synthesis and use of fluorescent oligonucleotides DNA sequence analysis. Methods Enzymol. 155: 260 301.
46. Whittam, T. S., 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708 2720. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error