Advertisement

Karyotyping of Yeast Strains by Pulsed-Field Gel Electrophoresis

  • John R. Johnston
Part of the Methods in Molecular Biology™ book series (MIMB, volume 53)

Abstract

Pulsed-field (gradient) gel electrophoresis (now abbreviated to PFGE or PF) was first described by Schwartz and Cantor (1) and Carle and Olson (2) in 1984. It allows separation of DNA molecules in the size range 50 kb to approx 10 Mb in agarose gels to which electric fields are applied in different directions. The chromosomes of Saccharomyces cerevisiae lie within the approximate size range of 200 kb to 3 Mb and can therefore be separated by this method to provide “electrophoretic karyotyping” of both laboratory-bred (3) and industrial (4), strains of this and related species. Several other yeasts of various genera, such as Candida albicans and Schizosaccharomyces pombe, have also been karyotyped by this method (4, 5, 6, 7, 8).

Keywords

Schizosaccharomyces Pombe Fume Cupboard Agarose Block Cell Wall Lytic Enzyme Chromosome Length Polymorphism 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Schwartz, D. C. and Cantor, C. R. (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67–75.PubMedCrossRefGoogle Scholar
  2. 2.
    Carle, G. F. and Olson, M. V. (1984) Separation of chromosomal DNA molecules from yeast by orthogonal field alternation gel electrophoresis. Nucleic Acids Res. 12, 5647–5664.PubMedCrossRefGoogle Scholar
  3. 3.
    Carle, G. F. and Olson, M. V. (1985) An electrophoretic karyotype for yeast. Proc. Natl. Acad. Sci. USA 82, 3756–3760.PubMedCrossRefGoogle Scholar
  4. 4.
    Johnston, J. R. and Mortimer, R. K. (1986) Electrophoretic karyotyping of laboratory and commercial strains of Saccharomyces and other yeasts. Int. J. Syst. Bacteriol. 36, 569–572.CrossRefGoogle Scholar
  5. 5.
    DeJonge, P., Dejonge, F. C. M., Meijers, R., Steensma, H. J., and Scheffers, W. A. (1986) Orthogonal field alternation gel electrophoresis banding patterns of DNA from yeasts. Yeast 2, 193–204.CrossRefGoogle Scholar
  6. 6.
    Vollrath, D. and Davis, R. W. (1987) Resolution of DNA molecules greater than 5 megabases by contour-clamped homogeneous electric fields. Nucleic Acids Res. 15, 7865–7876.PubMedCrossRefGoogle Scholar
  7. 7.
    Smith, C., Matsumoto, T., Niwa, O., Kleo, S., Fan, J. B., Yanagida, M., and Cantor, C. R. (1987) An electrophoretic karyotype for Schizosaccharomyces pombe by pulsed field gel electrophoresis. Nucleic Acids Res. 15, 4481–4489.PubMedCrossRefGoogle Scholar
  8. 8.
    Johnston, J. R., Contopoulou, C. R., and Mortimer, R. K. (1988) Karyotyping of yeast strains of several genera by field inversion gel electrophoresis. Yeast 4, 191–198.PubMedCrossRefGoogle Scholar
  9. 9.
    Anand, R. and Southern, E. M. (1990) Pulsed field gel electrophoresis, in Gel Electrophoresis of Nucleic Acids, A Practical Approach, 2nd ed., (Rickwood, D. and Hames, B. D., eds.), IRL, Oxford, pp. 101–123.Google Scholar
  10. 10.
    Eby, M. J. (1990) Pulsed-field separations: continued evolution. Biotechnology 8, 243–245.PubMedCrossRefGoogle Scholar
  11. 11.
    Carle, G. F., Frank, M., and Olson, M. V. (1986) Electrophoretic separation of large DNA molecules by inversion of the electric field. Science 232, 65–68.PubMedCrossRefGoogle Scholar
  12. 12.
    Heller, C. and Pohl, F. M. (1990) Field inversion gel electrophoresis with different pulse time ramps. Nucleic Acids Res. 18, 6299–6304.PubMedCrossRefGoogle Scholar
  13. 13.
    Chu, G., Vollrath, D., and Davis, R. W. (1986) Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science 234, 1582–1585.PubMedCrossRefGoogle Scholar
  14. 14.
    Chu, G. (1989) Pulsed field electrophoresis in contour-clamped homogeneous electric fields for the resolution of DNA by size or topology. Electrophoresis 10, 290–295.PubMedCrossRefGoogle Scholar
  15. 15.
    Meese, E. and Meltzer, P. S. (1990) A modified CHEF system for PFGE analysis. Technique 2, 26–42.Google Scholar
  16. 16.
    Southern, E. M., Anand, R., Brown, W. R., and Fletcher, D. S. (1987) A model for the separation of large DNA molecules by crossed field gel electrophoresis. Nucleic Acids Res. 15, 5925–5943.PubMedCrossRefGoogle Scholar
  17. 17.
    Serwer, P. (1987) Gel electrophoresis with discontinuous rotation of the gel: an alternative to gel electrophoresis with changing direction of the electric field. Electrophoresis 8, 301–304.CrossRefGoogle Scholar
  18. 18.
    Gardiner, K. and Patterson, D. (1989) Transverse alternating field electrophoresis and applications to mammalian genome mapping. Electrophoresis 10, 296–302.PubMedCrossRefGoogle Scholar
  19. 19.
    Birren, B. W., Hood, L., and Lai, E. (1989) Pulsed field gel electrophoresis: studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system. Electrophoresis 10, 302–309.PubMedCrossRefGoogle Scholar
  20. 20.
    Sutherland, J. C., Emrick, A. B., and Trunk, J. (1989) Separation of chromosomal length DNA molecules: pneumatic apparatus for rotating gels during electrophoresis. Electrophoresis 10, 315–317.PubMedCrossRefGoogle Scholar
  21. 21.
    Gunderson, K. and Chu, G. (1991) Pulsed-field electrophoresis of megabase-sized DNA. Mol. Cell. Biol. 11, 3348–3354.PubMedGoogle Scholar
  22. 22.
    Chu, G. and Gunderson, K. (1991) Separation of large DNA by a variable-angle contour-clamped homogeneous electric field apparatus. Anal. Biochem. 194, 439–446.PubMedCrossRefGoogle Scholar
  23. 23.
    Nagy, A. and Choo, K. H. (1991) Pulsed field gel electrophoresis using a double-decker gel system. Nucleic Acids Res. 18, 5317.CrossRefGoogle Scholar
  24. 24.
    Zhang, T. Y., Smith, C. L., and Cantor, C. R. (1991) Secondary pulsed field gel electrophoresis: a new method for faster separation of larger DNA molecules. Nucleic Acids Res. 19, 1291–1296.PubMedCrossRefGoogle Scholar
  25. 25.
    Gardner, D. C. J., Heale, S. M., Stateva, L. I., and Oliver, S. G. (1993) Treatment of yeast cell with wall lytic enzymes is not required to prepare chromosomes for pulsed-field gel analysis. Yeast 9, 1053–1055.PubMedCrossRefGoogle Scholar
  26. 26.
    Kwan, H., Li, C., Chiu, S., and Cheng, S. (1991) A simple method to prepare intact yeast chromosomal DNA for pulsed field gel electrophoresis. Nucleic Acids Res. 19, 1347.PubMedCrossRefGoogle Scholar
  27. 27.
    Mortimer, R. K., Game, J. C., Bell, M., and Contopoulou, C. R. (1990) Use of pulsed-field gel electrophoresis to study the chromosomes of Saccharomyces and other yeasts. Methods: A companion to Methods Enzymol. 1(2), 169–179.CrossRefGoogle Scholar
  28. 28.
    Mortimer, R. K. and Johnston, J. R. (1986) Genealogy of principal strains of the yeast genetic stock center. Genetics 113, 35–43.PubMedGoogle Scholar
  29. 29.
    Johnston, J. R., Curran, L., and Mortimer, R. K. (1991) Chromosome length polymorphisms in ancestral diploid strain EM93 of S. cerevisiae. Abstr. Gen. Soc. Amer. Yeast Gen. Mol. Biol., San Francisco, p. 115.Google Scholar
  30. 30.
    Johnston, J. R. (1987) Electrophoretic karyotyping of strains of Saccharomyces and other yeasts. Found. Biotechnol. Ind. Ferment. Res. 5, 43–55.Google Scholar

Copyright information

© Humana Press Inc.,Totowa, NJ 1996

Authors and Affiliations

  • John R. Johnston
    • 1
  1. 1.Department of Bioscience and BiotechnologyUniversity of StratcylydeGlasgowScotland

Personalised recommendations