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Biochemistry (Moscow)

, Volume 74, Issue 5, pp 480–490 | Cite as

Proteome analysis of the moss Physcomitrella patens (Hedw.) B.S.G.

  • A. Yu. SkripnikovEmail author
  • N. B. Polyakov
  • E. V. Tolcheva
  • V. V. Velikodvorskaya
  • S. V. Dolgov
  • I. A. Demina
  • M. A. Rogova
  • V. M. Govorun
Article

Abstract

The sequencing of the moss Physcomitrella patens genome has facilitated studies of the plant proteome. To develop a proteome reference map based on the genome sequence, we conducted 2D electrophoreses of proteins extracted from moss protoplasts, protonemata, and gametophores grown under standard conditions on Petri dishes. On silver-stained gels, depending on the developmental stage of the moss, we resolved from 500 to 600 protein spots that were then excised and digested by trypsin, and 212 proteins were identified by PMF-MALDI-TOF. To enhance the proteome coverage, we performed 1D SDS-PAGE with subsequent separation of tryptic peptides derived from digested gel band slices by LC-ESI-MS/MS. The proposed approach allowed us to identify 186 proteins had not been determined by 2D PMF-MALDI-TOF. Proteins identified by both methods were categorized using a system of clusterization of orthologous genes as metabolism (26%), cellular processes and signaling (16%), and information storage and processing (7%). Proteome analysis by differential gel electrophoresis revealed moderate differences between filamentous protonemata and leafy shoots. Surprisingly, protoplasts isolated from protonema filaments displayed significant differences in protein composition compared with both protonemata and gametophores.

Key words

proteomics 2D electrophoresis MALDI-TOF LC-ESI-MS/MS Physcomitrella patens protoplasts DiGE 

Abbreviations

DiGE

differential gel electrophoresis

DTT

dithiothreitol

KOG

EuKaryotic Orthologous Groups

LC-ESI-MS/MS

liquid chromatography-electrospray ionization-tandem mass spectrometry

MALDI-TOF

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

PAGE

polyacrylamide gel electrophoresis

PMF

peptide mass fingerprinting

RuBisCo

ribulose bisphosphate carboxylase

SDS

sodium dodecyl sulfate

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References

  1. 1.
    Rossignol, M., Peltier, J. B., Mock, H. P., Matros, A., Maldonado, A. M., and Jorrin, J. V. (2006) Proteomics, 6, 5529–5548.PubMedCrossRefGoogle Scholar
  2. 2.
    Espagne, C., Martinez, A., Valot, B., Meinnel, T., and Giglione, C. (2007) Proteomics, 7, 3788–3799.PubMedCrossRefGoogle Scholar
  3. 3.
    Lloyd, C. (1995) Curr. Biol., 5, 1085–1087.PubMedCrossRefGoogle Scholar
  4. 4.
    Batygina, T. B. (1999) Russ. J. Plant Physiol., 46, 774–788.Google Scholar
  5. 5.
    Rensing, S. A., Lang, D., Zimmer, A. D., Terry, A., Salamov, A., Shapiro, H., Nishiyama, T., Perroud, P. F., Lindquist, E. A., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., et al. (2008) Science, 319, 64–69.PubMedCrossRefGoogle Scholar
  6. 6.
    Sarnighausen, E., Wurtz, V., Heintz, D., van Dorsselaer, A., and Reski, R. (2004) Phytochemistry, 65, 1589–1607.PubMedCrossRefGoogle Scholar
  7. 7.
    Cho, S. H., Hoang, Q. T., Kim, Y. Y., Shin, H. Y., Ok, S. H., Bae, J. M., and Shin, J. S. (2006) Plant Cell Rep., 25, 475–488.PubMedCrossRefGoogle Scholar
  8. 8.
    Ashton, N. W., and Cove, D. J. (1977) Mol. Gen. Genet., 154, 87–95.CrossRefGoogle Scholar
  9. 9.
    Trouiller, B., Schaefer, D. G., Charlot, F., and Nogue, F. (2006) Nucleic Acids Res., 34, 232–242.PubMedCrossRefGoogle Scholar
  10. 10.
    Grimsley, N. H., Ashton, N. W., and Cove, D. J. (1977) Mol. Gen. Genet., 154, 97–100.CrossRefGoogle Scholar
  11. 11.
    O’Farrel, P. H. (1975) J. Biol. Chem., 250, 4007–4021.Google Scholar
  12. 12.
    Blum, H., Beier, H., and Gross, H. J. (1987) Electrophoresis, 8, 93–99.CrossRefGoogle Scholar
  13. 13.
    Laemmli, U. K. (1970) Nature, 227, 680–685.PubMedCrossRefGoogle Scholar
  14. 14.
    Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., and Mann, M. (2006) Nature Protocols, 1, 2856–2860.PubMedCrossRefGoogle Scholar
  15. 15.
    Savizky, A., and Golay, M. J. E. (1964) Anal. Chem., 36, 1627–1639.CrossRefGoogle Scholar
  16. 16.
    Cormen, T. H., Leiserson, C. E., Rivest, R. L., and Stein, C. (2001) Introduction to Algorithms, McGraw-Hill, Columbus.Google Scholar
  17. 17.
    Bradford, M. M. (1976) Anal. Biochem., 72, 248–254.PubMedCrossRefGoogle Scholar
  18. 18.
    Kiraga, J., Mackiewicz, K., Mackiewicz, D., Kowalczuk, M., Biecek, P., Polak, N., Smolarczyk, K., Dudek, M. R., and Cebrat, S. (2007) BMC Genomics, 8, 163.PubMedCrossRefGoogle Scholar
  19. 19.
    Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) Science, 278, 631–637.PubMedCrossRefGoogle Scholar
  20. 20.
    Feller, U., Anders, I., and Mae, T. (2008) J. Exp. Bot., 59, 1615–1624.PubMedCrossRefGoogle Scholar
  21. 21.
    Cove, D., Bezanilla, M., Harries, P., and Quatrano, R. (2006) Annu. Rev. Plant Biol., 57, 497–520.PubMedCrossRefGoogle Scholar
  22. 22.
    Schaefer, D. G. (2001) Curr. Opin. Plant Biol., 4, 143–150.PubMedCrossRefGoogle Scholar
  23. 23.
    Mittmann, F., Brucker, G., Zeidler, M., Repp, A., Abts, T., and Hartmann, E. (2004) Proc. Natl. Acad. Sci. USA, 101, 13939–13944.PubMedCrossRefGoogle Scholar
  24. 24.
    Sytnik, K. M., and Kordyum, E. L. (1994) in Modern Problems of Space Sell Phytobiology (Ugolev, A. M., ed.) [in Russian], Nauka, Moscow, pp. 243–249.Google Scholar
  25. 25.
    Wagner, T. A., and Sack, F. D. (1998) Planta, 205, 352–358.PubMedCrossRefGoogle Scholar
  26. 26.
    Cove, D. J., Quatrano, R. S., and Hartmann, E. (1996) Development, 122, 371–379.PubMedGoogle Scholar
  27. 27.
    Kern, V. D., and Sack, F. D. (1999) Planta, 209, 299–307.PubMedCrossRefGoogle Scholar
  28. 28.
    Hartmann, E., and Jenkins, G. I. (1984) in The Experimental Biology of Bryophytes (Dyer, A. F., and Duckett, J. D., eds.) Academic Press, New York-London, pp. 203–228.Google Scholar
  29. 29.
    Siminis, C. I., Kanellis, A. K., and Roubelakis-Angelakis, K. A. (1994) Plant Physiol., 105, 1375–1383.PubMedGoogle Scholar
  30. 30.
    Hohe, A., and Reski, R. (2005) Plant Cell Rep., 23, 513–521.PubMedCrossRefGoogle Scholar
  31. 31.
    Hartmann, E., and Weber, M. (1990) in Bryophyte Development: Physiology and Biochemistry (Chopra, R. N., and Bhatla, S. C., eds.) CRC Press, Boca Raton, Ann Arbor, Boston, pp. 33–54.Google Scholar
  32. 32.
    Schaefer, D., and Zryd, J.-P. (2001) Plant Physiol., 127, 1430–1438.PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2009

Authors and Affiliations

  • A. Yu. Skripnikov
    • 1
    • 2
    Email author
  • N. B. Polyakov
    • 1
  • E. V. Tolcheva
    • 1
  • V. V. Velikodvorskaya
    • 1
  • S. V. Dolgov
    • 3
  • I. A. Demina
    • 4
  • M. A. Rogova
    • 4
  • V. M. Govorun
    • 1
    • 4
  1. 1.Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
  2. 2.Biology FacultyLomonosov Moscow State UniversityMoscowRussia
  3. 3.Branch of Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesPushchino, Moscow RegionRussia
  4. 4.Scientific Research Institute of Physicochemical MedicineMoscowRussia

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