Two-Dimensional Reference Map of Schizosaccharomyces pombe Proteins (Update)

  • Kim, Sun-Kyung (Laboratory of Protein Chemistry, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Won, Mi-Sun (Genome Research Center, Korea Research Institute of Biotechnology & Bioscience) ;
  • Sun, Nam-Kyu (Korea Food & Drug Administration) ;
  • Jang, Jae-Won (Laboratory of Protein Chemistry, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Lee, Seung-Hee (Laboratory of Protein Chemistry, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Shin, Hee-Young (Laboratory of Protein Chemistry, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Song, Kyung-Bin (Laboratory of Protein Chemistry, College of Agriculture and Life Sciences, Chungnam National University)
  • Published : 2006.10.31

Abstract

Based on the first 2D reference map of the fission yeast Schizosaccharomyces pombe protein reported previously, we expanded and updated the map using narrower pI ranges. In this paper, 240 protein spots were identified on our reference map. In the pI 4-7 range, 144 spots corresponding to 86 different proteins were identified. In the pI 6-9 range, 43 spots corresponding to 35 different proteins were identified. Fifty-three new spots corresponding to 39 different proteins were further identified in the pI 5-6 range.

Keywords

References

  1. Aravind, L., H. Watanabe, D. J. Lipman, and E. V. Koonin. 2000. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc. Natl. Acad. Sci. USA 97: 11319-11324
  2. Arcangioli, B. and R. De Lahondes. 2000. Fission yeast switches mating type by a replication-recombination couples process. EMBO J. 19: 1389-1396 https://doi.org/10.1093/emboj/19.6.1389
  3. Berkelman, T. and T. Stenstedt. 1998. 2-D Electrophoresis, pp. 27-55. Amersham Biosciences, Uppsala, Sweden
  4. Boucherie, H., F. Sagliocco, R. Joubert, I. Maillet, J. Labarre, and M. Perrot. 1996. Two-dimensional gel protein database of Saccharomyces cerevisiae. Electrophoresis 17: 1683-1699 https://doi.org/10.1002/elps.1150171106
  5. Chikashige, Y., D. Q. Ding, Y. Imai, M. Yamamoto, T. Haraguchi, and Y. Hiraoka. 1997. Meiotic nuclear reorganization: Switching the position of centromeres and telomeres in the fission yeast Schizosaccharomyces pombe. EMBO J. 16: 193-202 https://doi.org/10.1093/emboj/16.1.193
  6. Cordwell, S. J., A. S. Nouwens, N. M. Verrills, D. J. Basseal, and B. J. Walsh. 2000. Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels. Electrophoresis 21: 1094-1103 https://doi.org/10.1002/(SICI)1522-2683(20000401)21:6<1094::AID-ELPS1094>3.0.CO;2-0
  7. Dalgaard, J. Z. and A. J. S. Klar. 2000. Swi1 and swi3 perform imprinting, pausing, and termination of DNA replication in S. pombe. Cell 102: 745-751 https://doi.org/10.1016/S0092-8674(00)00063-5
  8. Damerval, C., D. De Vienne, M. Zivy, and H. Thiellement. 1986. Technical improvements in two-dimensional electrophoresis analyzed by immobilized pH gradient two-dimensional gel electrophoresis. Electrophoresis 16: 1935-1945 https://doi.org/10.1002/elps.11501601320
  9. Davis, L. and G. R. Smith, 2001. Meiotic recombination and chromosome segregation in Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 98: 8395-8402
  10. Garrels, J. I., B. Futcher, R. Kobayashi, and G. I. Latter. 1994. Protein identifications for a Saccharomyces cerevisiae protein database. Electrophoresis 15: 1466-1486 https://doi.org/10.1002/elps.11501501210
  11. Garrels, J. I., C. S. McLaughlin, J. R. Warner, and B. Futcher. 1997. Proteome studies of Saccharomyces cerevisiae: Identification and characterization of abundant proteins. Electrophoresis 18: 1347-1360 https://doi.org/10.1002/elps.1150180810
  12. Goffeau, A., B. G. Barrell, J. Bussey, R. W. Davis, et al. 1996. Life with 6000 genes. Science 274: 546-567 https://doi.org/10.1126/science.274.5287.546
  13. Gorg, A., W. Postel, and S. Gunther. 1988. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9: 531-546 https://doi.org/10.1002/elps.1150090913
  14. Guerreiro, N., J. W. Redmond, B. G. Rolfe, and M. A. Djordjevic. 1997. New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins. Mol. Plant Microbe Inv. 10: 506-516 https://doi.org/10.1094/MPMI.1997.10.4.506
  15. Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19: 1720-1730 https://doi.org/10.1128/MCB.19.3.1720
  16. Hagan, I. M. 1998. The fission yeast microtubule cytoskeleton. J. Cell Sci. 111: 1603-1612
  17. Hesketh, A. R., G.. Chandra, A. D. Shaw, J. J. Rowland, D. B. Kell, and M. J. Bibb. 2002. Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor. Mol. Microbiol. 46: 917-932 https://doi.org/10.1046/j.1365-2958.2002.03219.x
  18. Kahn, P. 1995. From genome to proteome: Looking at a cell's proteins. Science 270: 369-370 https://doi.org/10.1126/science.270.5235.369
  19. Karaginnis, J. and P. G. Young. 2001. Intracellular pH homeostasis during cell-cycle progression and growth state transition in Schizosaccharomyces pombe. J. Cell Sci. 114: 2929-2941
  20. Kaufer, N. F. and J. Potashkin. 2000. Analysis of the splicing machinery in fission yeast: A comparison with budding yeast and mammals. Nucleic Acids Res. 28: 3003-3010 https://doi.org/10.1093/nar/28.16.3003
  21. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685 https://doi.org/10.1038/227680a0
  22. Len, A. C. L., S. J. Cordwell, D. W. S. Harty, and N. A. Jacques. 2003. Cellular and extracellular proteome analysis of Streptococcus mutans grown in a chemostat. Proteomics 3: 627-646 https://doi.org/10.1002/pmic.200300391
  23. Naresh, A., S. Saini, and J. Singh. 2003. Identification of uhp1, a ubiquitinated histone-like protein, as a target/mediator of rhp6 in mating-type silencing in fission yeast. J. Biol. Chem. 278: 9185-9194 https://doi.org/10.1074/jbc.M212732200
  24. Nawrocki, A., M. R. Larsen, A. V. Podtelejnikov, O. N. Jensen, et al. 1998. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification. Electrophoresis 19: 1024-1035 https://doi.org/10.1002/elps.1150190618
  25. Norbeck, J. and A. Blomberg. 1997. Two-dimensional electrophoretic separation of yeast proteins using a nonlinear wide range (pH 3-10) immobilized pH gradient in the first dimension; reproducibility and evidence for isoelectric focusing of alkaline (pl>7) proteins. Yeast 13: 1519-1534 https://doi.org/10.1002/(SICI)1097-0061(199712)13:16<1519::AID-YEA211>3.0.CO;2-U
  26. Pardo, M. and P. Nurse. 2003. Equatorial retention of the contractile actin ring by microtubules during cytokinesis. Science 300: 1569-1573 https://doi.org/10.1126/science.1084671
  27. Parker, K. C., J. I. Garrels, W. Hines, E. M. Butler, A. H. Z McKee, D. Patterson, and S. Martin. 1998. Identification of yeast proteins from two-dimensional gels: Working out spot cross-contamination. Electrophoresis 19: 1920-1932 https://doi.org/10.1002/elps.1150191110
  28. Parrot, M., F. Sagliocco, T. Mini, and C. Monrlbot. 1999. Two-dimensional gel protein database of Saccharomyces cerevisiae. Microbial Proteomes 1999: 2280-2298
  29. Peng, J., J. E. Elias, C. C. Thoreen, L. J. Licklider, and S. P. Gygi. 2003. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LCMS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2: 43-50 https://doi.org/10.1021/pr025556v
  30. Sagliocco, F., J. Guillemot, C. Monribot, J. Capdevielle, M. Perrot, E. Ferran, P. Ferrara, and H. Boucherie. 1996. Identification of proteins of the yeast protein map using genetically manipulated strains and peptide-mass fingerprinting. Yeast 12: 1519-1534 https://doi.org/10.1002/(SICI)1097-0061(199612)12:15<1519::AID-YEA47>3.0.CO;2-M
  31. Shevchenko, A., O. N. Jensen, A. V. Podtelejnikov, F. Sagliocco, et al. 1996. Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci USA 93: 14440-14445
  32. Singh, J., V. Goel, and A. J. S. Klar. 1998. A novel function of the DNA repair gene rhp6 in mating-type silencing by chromatin remodeling in fission yeast. Mol. Cell. Biol. 18: 5511-5522 https://doi.org/10.1128/MCB.18.9.5511
  33. Sun, N., J. Jang, S. Lee, S. Kim, et al. 2005. The first two-dimensional reference map of the fission yeast, Schizosaccharomyces pombe proteins. Proteomics 5: 1574-1579 https://doi.org/10.1002/pmic.200401053
  34. Vas, A., W. Mok, and J. Leatherwood. 2001. Control of DNA rereplication via cdc2 phosphorylation sites in the origin recognition complex. Mol. Cell. Biol. 21: 5767-5777 https://doi.org/10.1128/MCB.21.17.5767-5777.2001
  35. Wood, V., R. Gwilliam, M.-A. Rajandream, M. Lyne, et al. 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880 https://doi.org/10.1038/nature724
  36. Wildgruber, R., A. Harder, C. Obermaier, G. Boguth, et al. 2001. Towards higher resolution: Two-dimensional electrophoresis of Saccharomyces cerevisiae proteins using overlapping narrow immobilized pH gradients. Electrophoresis 21: 2610-2616 https://doi.org/10.1002/1522-2683(20000701)21:13<2610::AID-ELPS2610>3.0.CO;2-H
  37. URL: http://www.ibgc.u-bordeauw2.fr/YPM
  38. URL: http://www.Proteome.com
  39. URL: http://expasy.hcuge.ch/ch2d.ch2d-top.html
  40. URL: http://yeast-2dpage.gmm.gu.se