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. 1995 Oct;177(20):5784–5789. doi: 10.1128/jb.177.20.5784-5789.1995

Heterogeneity of genome sizes among natural isolates of Escherichia coli.

U Bergthorsson 1, H Ochman 1
PMCID: PMC177399  PMID: 7592324

Abstract

Comparisons of the genetic maps of Escherichia coli K-12 and Salmonella typhimurium LT2 suggest that the size and organization of bacterial chromosomes are highly conserved. Employing pulsed-field gel electrophoresis, we have estimated the extent of variation in genome size among 14 natural isolates of E. coli. The BlnI and NotI restriction fragment patterns were highly variable among isolates, and genome sizes ranged from 4,660 to 5,300 kb, which is several hundred kilobases larger than the variation detected between enteric species. Genome size differences increase with the evolutionary genetic distance between lineages of E. coli, and there are differences in genome size among the major subgroups of E. coli. In general, the genomes of natural isolates are larger than those of laboratory strains, largely because of the fact that laboratory strains were derived from the subgroup of E. coli with the smallest genomes.

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Selected References

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  1. Anderson D. G., McKay L. L. Simple and rapid method for isolating large plasmid DNA from lactic streptococci. Appl Environ Microbiol. 1983 Sep;46(3):549–552. doi: 10.1128/aem.46.3.549-552.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Anderson P., Roth J. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc Natl Acad Sci U S A. 1981 May;78(5):3113–3117. doi: 10.1073/pnas.78.5.3113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Anderson R. P., Roth J. R. Tandem genetic duplications in phage and bacteria. Annu Rev Microbiol. 1977;31:473–505. doi: 10.1146/annurev.mi.31.100177.002353. [DOI] [PubMed] [Google Scholar]
  4. Arbeit R. D., Arthur M., Dunn R., Kim C., Selander R. K., Goldstein R. Resolution of recent evolutionary divergence among Escherichia coli from related lineages: the application of pulsed field electrophoresis to molecular epidemiology. J Infect Dis. 1990 Feb;161(2):230–235. doi: 10.1093/infdis/161.2.230. [DOI] [PubMed] [Google Scholar]
  5. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Blum G., Ott M., Lischewski A., Ritter A., Imrich H., Tschäpe H., Hacker J. Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect Immun. 1994 Feb;62(2):606–614. doi: 10.1128/iai.62.2.606-614.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brenner D. J., Fanning G. R., Skerman F. J., Falkow S. Polynucleotide sequence divergence among strains of Escherichia coli and closely related organisms. J Bacteriol. 1972 Mar;109(3):953–965. doi: 10.1128/jb.109.3.953-965.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Böhm H., Karch H. DNA fingerprinting of Escherichia coli O157:H7 strains by pulsed-field gel electrophoresis. J Clin Microbiol. 1992 Aug;30(8):2169–2172. doi: 10.1128/jcm.30.8.2169-2172.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Carlson C. R., Kolstø A. B. A small (2.4 Mb) Bacillus cereus chromosome corresponds to a conserved region of a larger (5.3 Mb) Bacillus cereus chromosome. Mol Microbiol. 1994 Jul;13(1):161–169. doi: 10.1111/j.1365-2958.1994.tb00411.x. [DOI] [PubMed] [Google Scholar]
  10. Daniels D. L. The complete AvrII restriction map of the Escherichia coli genome and comparisons of several laboratory strains. Nucleic Acids Res. 1990 May 11;18(9):2649–2651. doi: 10.1093/nar/18.9.2649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Drake J. W. A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7160–7164. doi: 10.1073/pnas.88.16.7160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. DuBose R. F., Dykhuizen D. E., Hartl D. L. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1988 Sep;85(18):7036–7040. doi: 10.1073/pnas.85.18.7036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Guttman D. S., Dykhuizen D. E. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics. 1994 Dec;138(4):993–1003. doi: 10.1093/genetics/138.4.993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. HORIUCHI T., HORIUCHI S., NOVICK A. The genetic basis of hyper-synthesis of beta-galactosidase. Genetics. 1963 Feb;48:157–169. doi: 10.1093/genetics/48.2.157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hacker J., Bender L., Ott M., Wingender J., Lund B., Marre R., Goebel W. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb Pathog. 1990 Mar;8(3):213–225. doi: 10.1016/0882-4010(90)90048-u. [DOI] [PubMed] [Google Scholar]
  16. Hall B. G., Sharp P. M. Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates. Mol Biol Evol. 1992 Jul;9(4):654–665. doi: 10.1093/oxfordjournals.molbev.a040751. [DOI] [PubMed] [Google Scholar]
  17. Harsono K. D., Kaspar C. W., Luchansky J. B. Comparison and genomic sizing of Escherichia coli O157:H7 isolates by pulsed-field gel electrophoresis. Appl Environ Microbiol. 1993 Sep;59(9):3141–3144. doi: 10.1128/aem.59.9.3141-3144.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hartl D. L., Medhora M., Green L., Dykhuizen D. E. The evolution of DNA sequences in Escherichia coli. Philos Trans R Soc Lond B Biol Sci. 1986 Jan 29;312(1154):191–204. doi: 10.1098/rstb.1986.0001. [DOI] [PubMed] [Google Scholar]
  19. Heath J. D., Perkins J. D., Sharma B., Weinstock G. M. NotI genomic cleavage map of Escherichia coli K-12 strain MG1655. J Bacteriol. 1992 Jan;174(2):558–567. doi: 10.1128/jb.174.2.558-567.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Heath J. D., Weinstock G. M. Tandem duplications of the lac region of the Escherichia coli chromosome. Biochimie. 1991 Apr;73(4):343–352. doi: 10.1016/0300-9084(91)90099-m. [DOI] [PubMed] [Google Scholar]
  21. Herzer P. J., Inouye S., Inouye M., Whittam T. S. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J Bacteriol. 1990 Nov;172(11):6175–6181. doi: 10.1128/jb.172.11.6175-6181.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Karch H., Meyer T., Rüssmann H., Heesemann J. Frequent loss of Shiga-like toxin genes in clinical isolates of Escherichia coli upon subcultivation. Infect Immun. 1992 Aug;60(8):3464–3467. doi: 10.1128/iai.60.8.3464-3467.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Krawiec S., Riley M. Organization of the bacterial chromosome. Microbiol Rev. 1990 Dec;54(4):502–539. doi: 10.1128/mr.54.4.502-539.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Liu S. L., Hessel A., Cheng H. Y., Sanderson K. E. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella paratyphi B. J Bacteriol. 1994 Feb;176(4):1014–1024. doi: 10.1128/jb.176.4.1014-1024.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Liu S. L., Hessel A., Sanderson K. E. Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6874–6878. doi: 10.1073/pnas.90.14.6874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Liu S. L., Hessel A., Sanderson K. E. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2. Mol Microbiol. 1993 Nov;10(3):655–664. doi: 10.1111/j.1365-2958.1993.tb00937.x. [DOI] [PubMed] [Google Scholar]
  27. Liu S. L., Sanderson K. E. Rearrangements in the genome of the bacterium Salmonella typhi. Proc Natl Acad Sci U S A. 1995 Feb 14;92(4):1018–1022. doi: 10.1073/pnas.92.4.1018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Louarn J., Cornet F., François V., Patte J., Louarn J. M. Hyperrecombination in the terminus region of the Escherichia coli chromosome: possible relation to nucleoid organization. J Bacteriol. 1994 Dec;176(24):7524–7531. doi: 10.1128/jb.176.24.7524-7531.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Mikkola R., Kurland C. G. Is there a unique ribosome phenotype for naturally occurring Escherichia coli? Biochimie. 1991 Jul-Aug;73(7-8):1061–1066. doi: 10.1016/0300-9084(91)90148-t. [DOI] [PubMed] [Google Scholar]
  30. Mikkola R., Kurland C. G. Selection of laboratory wild-type phenotype from natural isolates of Escherichia coli in chemostats. Mol Biol Evol. 1992 May;9(3):394–402. doi: 10.1093/oxfordjournals.molbev.a040731. [DOI] [PubMed] [Google Scholar]
  31. Milkman R., Bridges M. M. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics. 1990 Nov;126(3):505–517. doi: 10.1093/genetics/126.3.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Médigue C., Rouxel T., Vigier P., Hénaut A., Danchin A. Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol. 1991 Dec 20;222(4):851–856. doi: 10.1016/0022-2836(91)90575-q. [DOI] [PubMed] [Google Scholar]
  33. Ochman H., Selander R. K. Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984 Feb;157(2):690–693. doi: 10.1128/jb.157.2.690-693.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Ochman H., Wilson A. C. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol. 1987;26(1-2):74–86. doi: 10.1007/BF02111283. [DOI] [PubMed] [Google Scholar]
  35. Okada N., Sasakawa C., Tobe T., Talukder K. A., Komatsu K., Yoshikawa M. Construction of a physical map of the chromosome of Shigella flexneri 2a and the direct assignment of nine virulence-associated loci identified by Tn5 insertions. Mol Microbiol. 1991 Sep;5(9):2171–2180. doi: 10.1111/j.1365-2958.1991.tb02147.x. [DOI] [PubMed] [Google Scholar]
  36. Ott M. Dynamics of the bacterial genome: deletions and integrations as mechanisms of bacterial virulence modulation. Zentralbl Bakteriol. 1993 Jun;278(4):457–468. doi: 10.1016/s0934-8840(11)80817-0. [DOI] [PubMed] [Google Scholar]
  37. Perkins J. D., Heath J. D., Sharma B. R., Weinstock G. M. SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655. Nucleic Acids Res. 1992 Mar 11;20(5):1129–1137. doi: 10.1093/nar/20.5.1129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Perkins J. D., Heath J. D., Sharma B. R., Weinstock G. M. XbaI and BlnI genomic cleavage maps of Escherichia coli K-12 strain MG1655 and comparative analysis of other strains. J Mol Biol. 1993 Jul 20;232(2):419–445. doi: 10.1006/jmbi.1993.1401. [DOI] [PubMed] [Google Scholar]
  39. Riley M., Anilionis A. Evolution of the bacterial genome. Annu Rev Microbiol. 1978;32:519–560. doi: 10.1146/annurev.mi.32.100178.002511. [DOI] [PubMed] [Google Scholar]
  40. Sanderson K. E. Genetics of the Enterobacteriaceae. A. Genetic homology in the Enterobacteriaceae. Adv Genet. 1971;16:35–51. doi: 10.1016/s0065-2660(08)60353-3. [DOI] [PubMed] [Google Scholar]
  41. Sanderson K. E., Roth J. R. Linkage map of Salmonella typhimurium, edition VII. Microbiol Rev. 1988 Dec;52(4):485–532. doi: 10.1128/mr.52.4.485-532.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Smith C. L., Econome J. G., Schutt A., Klco S., Cantor C. R. A physical map of the Escherichia coli K12 genome. Science. 1987 Jun 12;236(4807):1448–1453. doi: 10.1126/science.3296194. [DOI] [PubMed] [Google Scholar]
  43. Sonti R. V., Roth J. R. Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources. Genetics. 1989 Sep;123(1):19–28. doi: 10.1093/genetics/123.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Starlinger P. DNA rearrangements in procaryotes. Annu Rev Genet. 1977;11:103–126. doi: 10.1146/annurev.ge.11.120177.000535. [DOI] [PubMed] [Google Scholar]
  45. Tschäpe H., Prager R., Bender L., Ott M., Blum G., Hacker J. Dissection of pathogenetic determinants and their genomic positions for the evaluation of epidemic strains and infection routes. Zentralbl Bakteriol. 1993 Apr;278(2-3):425–435. doi: 10.1016/s0934-8840(11)80859-5. [DOI] [PubMed] [Google Scholar]

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