Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1992 Apr;174(7):2078–2086. doi: 10.1128/jb.174.7.2078-2086.1992

Determination of genome size, macrorestriction pattern polymorphism, and nonpigmentation-specific deletion in Yersinia pestis by pulsed-field gel electrophoresis.

T S Lucier 1, R R Brubaker 1
PMCID: PMC205823  PMID: 1551830

Abstract

Of 16 restriction endonucleases known to hydrolyze rare 6- or 8-base recognition sequences that were tested, only SpeI, NotI, AscI, and SfiI generated fragments of chromosomal DNA from Yersinia pestis, the causative agent of bubonic plague, of sufficient length to permit physical analysis by pulsed-field gel electrophoresis (PFGE). Of the individual bands detected after single-dimensional PFGE of these digests, the largest sum was obtained with SpeI (3,575.6 +/- 114.6 kb). Of these 41 bands, 3 were found to contain comigrating fragments, as judged by the results of two-dimensional SpeI-ApaI PFGE; addition of these fragments and the three plasmids of the species yielded a refined estimate of 4,397.9 +/- 134.6 kb for the genome. This size was similar for eight strains of diverse geographical origin that exhibited distinct DNA macrorestriction patterns closely related to their biotypes. The high-frequency chromosomal deletion known to exist in nonpigmented mutants (unable to assimilate Fe3+ at 37 degrees C or store hemin at 26 degrees C) was shown by two-dimensional PFGE analysis with SpeI and ApaI or with SfiI and SpeI to be 92.5 and 106 kb in size, respectively. The endpoints of this deletion were precise, and its size was more than sufficient to encode the eight known peptides reported to be absent in nonpigmented mutants. This deletion had not occurred (but was able to do so) in a rare mutant capable of hemin storage but not iron transport.

Full text

PDF
2086

Images in this article

2082Image
on p.2082
2082Image
on p.2082
2083Image
on p.2083
2084Image
on p.2084
2084Image
on p.2084
2084Image
on p.2084
2084Image
on p.2084

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allardet-Servent A., Bourg G., Ramuz M., Pages M., Bellis M., Roizes G. DNA polymorphism in strains of the genus Brucella. J Bacteriol. 1988 Oct;170(10):4603–4607. doi: 10.1128/jb.170.10.4603-4607.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. BURROWS T. W., JACKSON S. The pigmentation of Pasteurella pestis on a defined medium containing haemin. Br J Exp Pathol. 1956 Dec;37(6):570–576. [PMC free article] [PubMed] [Google Scholar]
  4. BURROWS T. W., JACKSON S. The virulence-enhancing effect of iron on nonpigmented mutants of virulent strains of Pasteurella pestis. Br J Exp Pathol. 1956 Dec;37(6):577–583. [PMC free article] [PubMed] [Google Scholar]
  5. Birch A., Häusler A., Rüttener C., Hütter R. Chromosomal deletion and rearrangement in Streptomyces glaucescens. J Bacteriol. 1991 Jun;173(11):3531–3538. doi: 10.1128/jb.173.11.3531-3538.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Birch A., Häusler A., Vögtli M., Krek W., Hütter R. Extremely large chromosomal deletions are intimately involved in genetic instability and genomic rearrangements in Streptomyces glaucescens. Mol Gen Genet. 1989 Jun;217(2-3):447–458. doi: 10.1007/BF02464916. [DOI] [PubMed] [Google Scholar]
  7. Brubaker R. R. Factors promoting acute and chronic diseases caused by yersiniae. Clin Microbiol Rev. 1991 Jul;4(3):309–324. doi: 10.1128/cmr.4.3.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brubaker R. R. Mutation rate to nonpigmentation in Pasteurella pestis. J Bacteriol. 1969 Jun;98(3):1404–1406. doi: 10.1128/jb.98.3.1404-1406.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Brubaker R. R. The genus Yersinia: biochemistry and genetics of virulence. Curr Top Microbiol Immunol. 1972;57:111–158. doi: 10.1007/978-3-642-65297-4_4. [DOI] [PubMed] [Google Scholar]
  10. Carniel E., Antoine J. C., Guiyoule A., Guiso N., Mollaret H. H. Purification, location, and immunological characterization of the iron-regulated high-molecular-weight proteins of the highly pathogenic yersiniae. Infect Immun. 1989 Feb;57(2):540–545. doi: 10.1128/iai.57.2.540-545.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Carniel E., Mazigh D., Mollaret H. H. Expression of iron-regulated proteins in Yersinia species and their relation to virulence. Infect Immun. 1987 Jan;55(1):277–280. doi: 10.1128/iai.55.1.277-280.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Carniel E., Mercereau-Puijalon O., Bonnefoy S. The gene coding for the 190,000-dalton iron-regulated protein of Yersinia species is present only in the highly pathogenic strains. Infect Immun. 1989 Apr;57(4):1211–1217. doi: 10.1128/iai.57.4.1211-1217.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Crosa J. H. Genetics and molecular biology of siderophore-mediated iron transport in bacteria. Microbiol Rev. 1989 Dec;53(4):517–530. doi: 10.1128/mr.53.4.517-530.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. DEVIGNAT R. Variétés de l'espèce Pasteurella pestis; nouvelle hypothèse. Bull World Health Organ. 1951;4(2):247–263. [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Ferber D. M., Brubaker R. R. Plasmids in Yersinia pestis. Infect Immun. 1981 Feb;31(2):839–841. doi: 10.1128/iai.31.2.839-841.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. GIRARD G. Plague. Annu Rev Microbiol. 1955;9:253–276. doi: 10.1146/annurev.mi.09.100155.001345. [DOI] [PubMed] [Google Scholar]
  18. HERTMAN I., BEN-GURION R. A study on pesticin biosynthesis. J Gen Microbiol. 1959 Aug;21:135–143. doi: 10.1099/00221287-21-1-135. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Iteman I., Baril C., Saint Girons I., Carniel E. Pulse field electrophoresis of the chromosome of the pathogenic yersiniae. Contrib Microbiol Immunol. 1991;12:198–202. [PubMed] [Google Scholar]
  21. Knapp S., Hacker J., Then I., Müller D., Goebel W. Multiple copies of hemolysin genes and associated sequences in the chromosomes of uropathogenic Escherichia coli strains. J Bacteriol. 1984 Sep;159(3):1027–1033. doi: 10.1128/jb.159.3.1027-1033.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Lawlor K. M., Payne S. M. Aerobactin genes in Shigella spp. J Bacteriol. 1984 Oct;160(1):266–272. doi: 10.1128/jb.160.1.266-272.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Leblond P., Demuyter P., Simonet J. M., Decaris B. Genetic instability and associated genome plasticity in Streptomyces ambofaciens: pulsed-field gel electrophoresis evidence for large DNA alterations in a limited genomic region. J Bacteriol. 1991 Jul;173(13):4229–4233. doi: 10.1128/jb.173.13.4229-4233.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Leblond P., Francou F. X., Simonet J. M., Decaris B. Pulsed-field gel electrophoresis analysis of the genome of Streptomyces ambofaciens strains. FEMS Microbiol Lett. 1990 Oct;60(1-2):79–88. doi: 10.1016/0378-1097(90)90349-u. [DOI] [PubMed] [Google Scholar]
  26. Lee J. J., Smith H. O. Sizing of the Haemophilus influenzae Rd genome by pulsed-field agarose gel electrophoresis. J Bacteriol. 1988 Sep;170(9):4402–4405. doi: 10.1128/jb.170.9.4402-4405.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Levene S. D., Zimm B. H. Separations of open-circular DNA using pulsed-field electrophoresis. Proc Natl Acad Sci U S A. 1987 Jun;84(12):4054–4057. doi: 10.1073/pnas.84.12.4054. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lipson L. G. Plague in San Francisco in 1900. The United States Marine Hospital Service Commission to study the existence of plague in San Francisco. Ann Intern Med. 1972 Aug;77(2):303–310. doi: 10.7326/0003-4819-77-2-303. [DOI] [PubMed] [Google Scholar]
  29. MARMUR J., FALKOW S., MANDEL M. NEW APPROACHES TO BACTERIAL TAXONOMY. Annu Rev Microbiol. 1963;17:329–372. doi: 10.1146/annurev.mi.17.100163.001553. [DOI] [PubMed] [Google Scholar]
  30. McClelland M., Jones R., Patel Y., Nelson M. Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Res. 1987 Aug 11;15(15):5985–6005. doi: 10.1093/nar/15.15.5985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. McDougall S., Neilands J. B. Plasmid- and chromosome-coded aerobactin synthesis in enteric bacteria: insertion sequences flank operon in plasmid-mediated systems. J Bacteriol. 1984 Jul;159(1):300–305. doi: 10.1128/jb.159.1.300-305.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Pendrak M. L., Perry R. D. Characterization of a hemin-storage locus of Yersinia pestis. Biol Met. 1991;4(1):41–47. doi: 10.1007/BF01135556. [DOI] [PubMed] [Google Scholar]
  33. Perez-Casal J. F., Crosa J. H. Aerobactin iron uptake sequences in plasmid ColV-K30 are flanked by inverted IS1-like elements and replication regions. J Bacteriol. 1984 Oct;160(1):256–265. doi: 10.1128/jb.160.1.256-265.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Perry R. D., Pendrak M. L., Schuetze P. Identification and cloning of a hemin storage locus involved in the pigmentation phenotype of Yersinia pestis. J Bacteriol. 1990 Oct;172(10):5929–5937. doi: 10.1128/jb.172.10.5929-5937.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Römling U., Grothues D., Bautsch W., Tümmler B. A physical genome map of Pseudomonas aeruginosa PAO. EMBO J. 1989 Dec 20;8(13):4081–4089. doi: 10.1002/j.1460-2075.1989.tb08592.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Schaffer H. E., Sederoff R. R. Improved estimation of DNA fragment lengths from Agarose gels. Anal Biochem. 1981 Jul 15;115(1):113–122. doi: 10.1016/0003-2697(81)90533-9. [DOI] [PubMed] [Google Scholar]
  37. Sikkema D. J., Brubaker R. R. Outer membrane peptides of Yersinia pestis mediating siderophore-independent assimilation of iron. Biol Met. 1989;2(3):174–184. doi: 10.1007/BF01142557. [DOI] [PubMed] [Google Scholar]
  38. Sikkema D. J., Brubaker R. R. Resistance to pesticin, storage of iron, and invasion of HeLa cells by Yersiniae. Infect Immun. 1987 Mar;55(3):572–578. doi: 10.1128/iai.55.3.572-578.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Smith C. L., Condemine G. New approaches for physical mapping of small genomes. J Bacteriol. 1990 Mar;172(3):1167–1172. doi: 10.1128/jb.172.3.1167-1172.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Staggs T. M., Perry R. D. Identification and cloning of a fur regulatory gene in Yersinia pestis. J Bacteriol. 1991 Jan;173(2):417–425. doi: 10.1128/jb.173.2.417-425.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Straley S. C., Brubaker R. R. Localization in Yersinia pestis of peptides associated with virulence. Infect Immun. 1982 Apr;36(1):129–135. doi: 10.1128/iai.36.1.129-135.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Surgalla M. J., Beesley E. D. Congo red-agar plating medium for detecting pigmentation in Pasteurella pestis. Appl Microbiol. 1969 Nov;18(5):834–837. doi: 10.1128/am.18.5.834-837.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Une T., Brubaker R. R. In vivo comparison of avirulent Vwa- and Pgm- or Pstr phenotypes of yersiniae. Infect Immun. 1984 Mar;43(3):895–900. doi: 10.1128/iai.43.3.895-900.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Wee S., Neilands J. B., Bittner M. L., Hemming B. C., Haymore B. L., Seetharam R. Expression, isolation and properties of Fur (ferric uptake regulation) protein of Escherichia coli K 12. Biol Met. 1988;1(1):62–68. doi: 10.1007/BF01128019. [DOI] [PubMed] [Google Scholar]
  46. Zahorchak R. J., Brubaker R. R. Effect of exogenous nucleotides on Ca2+ dependence and V antigen synthesis in Yersinia pestis. Infect Immun. 1982 Dec;38(3):953–959. doi: 10.1128/iai.38.3.953-959.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES