Proteomic variation is as large within as between strawberry varieties

Journal of Proteome Research

Volumn 6, Issue 8, 2007, Pages 3011-3020

  Alm, Rikard ^a   Ekefjärd, Andreas ^b   Krogh, Morten ^a   Häkkinen, Jari ^a   Emanuelsson, Cecilia ^a  

^a LUND UNIVERSITY   (Sweden)

^b Ludesi   (Sweden)

Author keywords

Allergen; Biological variation; DIGE; External validity; Growth conditions; Intraspecific; Phenotypic plasticity; Proteomics; Variety

Indexed keywords

ALLERGEN;

AMINO ACID SEQUENCE; ARTICLE; DOWN REGULATION; INTRASPECIFIC VARIATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PHENOTYPE; PLANT BREEDING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SYNTHESIS; PROTEOMICS; STRAWBERRY; TWO DIMENSIONAL GEL ELECTROPHORESIS; VARIETAS;

ALLERGENS; ANTIGENIC VARIATION; ANTIGENS, PLANT; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FRAGARIA; PROTEOME; SPECIES SPECIFICITY;

FRAGARIA X ANANASSA;

EID: 34548162709     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0700450     Document Type: Article

References (43)

1. Alonso-Blanco, C.; Mendez-Vigo, B.; Koornneef, M. From phenotypic to molecular polymorphisms involved in naturally occurring variation of plant development. Int. J. Dev. Biol. 2005, 49 (5-6), 717-732.
2. Kaczmarska, E.; Hortyn'ski, J. The application of RAPD markers for genetic studies on Fragaria x Fragaria duch. (strawberry) with due consideration for permanent flowering. Electron. J. Pol. Agric. Univ. 2002, 5, (1).
3. Kellogg, E. A. Evolution of developmental traits. Curr. Opin. Plant Biol. 2004, 7 (1), 92-98.
4. Jimenez-Bermudez, S.; Redondo-Nevado, J.; Munoz-Blanco, J.; Caballero, J. L.; Lopez-Aranda, J. M.; Valpuesta, V.; Pliego-Alfaro, F.; Quesada, M. A.; Mercado, J. A. Manipulation of Strawberry Fruit Softening by Antisense Expression of a Pectate Lyase Gene. Plant Physiol. 2002, 128, 751-759.
5. Salentijn, E. M.; Aharoni, A.; Schaart, J. G.; Boone, M. J.; Krens, F. A. Differential gene expresson analysis of strawberry cultivars that differ in fruit-firmness. Physiol. Plant. 2003, 118, 571-578.
6. Aharoni, A.; Keizer, L. C.; Bouwmeester, H. J.; Sun, Z.; Alvarez-Huerta, M.; Verhoeven, H. A.; Blaas, J.; van Houwelingen, A. M.; De Vos, R. C.; van der Voet, H.; Jansen, R. C.; Guis, M.; Mol, J.; Davis, R. W.; Schena, M.; van Tunen, A. J.; O'Connell, A. P. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 2000, 12 (5), 647-662.
7. Aharoni, A.; Giri, A. P.; Verstappen, F. W.; Bertea, C. M.; Sevenier, R.; Sun, Z.; Jongsma, M. A.; Schwab, W.; Bouwmeester, H. J. Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 2004, 16 (11), 3110-3131.
8. Raab, T.; Lopez-Raez, J. A.; Klein, D.; Caballero, J. L.; Moyano, E.; Schwab, W.; Munoz-Blanco, J. FaQR, required for the biosynthesis of the strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone, encodes an enone oxidoreductase. Plant Cell 2006, 18 (4), 1023-1037.
9. Wein, M.; Lavid, N.; Lunkenbein, S.; Lewinsohn, E.; Schwab, W.; Kaldenhoff, R. Isolation, cloning and expression of a multifunctional O-methyltransferase capable of forming 2,5-dimethyl-4-methoxy-3(2H)-furanone, one of the key aroma compounds in strawberry fruits. Plant J. 2002, 31 (6), 755-765.
10. Ostergaard, O.; Melchior, S.; Roepstorff, P.; Svensson, B. Initial proteome analysis of mature barley seeds and malt. Proteomics 2002, 2 (6), 733-739.
11. Jorge, I.; Navarro, R. M.; Lenz, C.; Ariza, D.; Jorrin, J. Variation in the holm oak leaf proteome at different plant developmental stages, between provenances and in response to drought stress. Proteomics 2006, 6 (Suppl. 1), S207-214.
12. Carpentier, S.; Witters, E.; Laukens, K.; Deckers, P.; Swennen, R.; Panis, B. Preparation of protein extracts from recalcitrant plant tissues: An evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 2005, 5 (10), 2497-2507.
13. Hjerno, K.; Alm, R.; Canback, B.; Matthiesen, R.; Trajkovski, K.; Bjork, L.; Roepstorff, P.; Emanuelsson, C. S. Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colourless strawberry mutant. Proteomics 2006, 6 (5), 1574-1587.
14. Hannum, S. M. Potential impact of strawberries on human health: a review of the science. Crit. Rev. Food Sci. Nutr. 2004, 44 (1), 1-17.
15. Vieths, S.; Scheurer, S.; Ballmer-Weber, B. Current understanding of cross-reactivity of food allergens and pollen. Ann. N. Y. Acad. Sci. 2002, 964, 47-68.
16. Aalberse, R. C.; Akkerdaas, J.; van Ree, R. Cross-reactivity of IgE antibodies to allergens. Allergy 2001, 56 (6), 478-490.
17. Breiteneder, H.; Ebner, C. Molecular and biochemical classification of plant-derived food allergens. J. Allergy Clin. Immunol. 2000, 106 (1 Pt 1), 27-36.
18. Mills, E.; Madsen, C.; Shewry, P.; Wichers, H. Food allergens of plant origin - their milecular and evolutionary relationships. Trends Food Sci. Technol. 2003, 14, 145-156.
19. Eriksson, N. E.; Moller, C.; Werner, S.; Magnusson, J.; Bengtsson, U.; Zolubas, M. Self-reported food hypersensitivity in Sweden, Denmark, Estonia, Lithuania, and Russia. J. Invest. Allergol. Clin. Immunol. 2004, 14 (1), 70-79.
20. Sultan, S. E. Phenotypic plasticity for plant development, function and life history. Trends Plant Sci. 2000, 5 (12), 537-542.
21. Karlsson, A. L.; Alm, R.; Ekstrand, B.; Fjelkner-Modig, S.; Schiott, A.; Bengtsson, U.; Bjork, L.; Hjerno, K.; Roepstorff, P.; Emanuelsson, C. S. Bet v 1 homologues in strawberry identified as IgE-binding proteins and presumptive allergens. Allergy 2004, 59 (12), 1277-1284.
22. Lilley, K. S.; Friedman, D. B. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 2004, 1 (4), 401-409.
23. Wu, T. L. Two-dimensional difference gel electrophoresis. Methods Mol. Biol. 2006, 328, 71-95.
24. Kendall, M. G. A New Measure of Rank Correlation. Biometrika 1938, 30 (1-2), 81-93.
25. Jonckheere, A. A distribution-free K sample test against ordered alternatives. Biometrika 1954, 41, 133-145.
26. Krogh, M.; Liu, Y.; Bengtsson, S.; Valastro, B.; James, P. Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects. J. Proteome Res. 2006, submitted for publication.
27. Levander, F.; Rognvaldsson, T.; Samuelsson, J.; James, P. Automated methods for improved protein identification by peptide mass fingerprinting. Proteomics 2004, 4 (9), 2594-2601.
28. Samuelsson, J.; Dalevi, D.; Levander, F.; Rognvaldsson, T. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics 2004, 20 (18), 3628-3635.
29. Higdon, R.; Hogan, J. M.; Belle, G. V.; Kolker, E. Randomized sequence databases for tandem mass spectrometry peptide and protein identification. OMICS: J. Integr. Biol. 2005, 9 (4), 364-379.
30. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
31. Levander, F.; Krogh, M.; Warell, K.; Garden, P.; James, P.; Hakkinen, J. Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 2007, 7 (5), 668-674.
32. Alm, R.; Johansson, P.; Hjerno, K.; Emanuelsson, C.; Ringner, M.; Hakkinen, J. Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra. J. Proteome Res. 2006, 5 (4), 785-792.
33. Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 2002, 13 (4), 378-386.
34. Resing, K. A.; Meyer-Arendt, K.; Mendoza, A. M.; Aveline-Wolf, L. D.; Jonscher, K. R.; Pierce, K. G.; Old, W. M.; Cheung, H. T.; Russell, S.; Wattawa, J. L.; Goehle, G. R.; Knight, R. D.; Ann, N. G. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 2004, 76 (13), 3556-3568.
35. Musidlowska-Persson, A.; Alm, R.; Emanuelsson, C. Cloning and sequencing of the Bet v 1-homologous allergen Fra a 1 in strawberry (Fragaria ananassa) shows the presence of an intron and little variability in amino acid sequence. Mol. Immunol. 2007, 44 (6), 1245-1252.
36. Mogensen, J. E.; Wimmer, R.; Larsen, J. N.; Spangfort, M. D.; Otzen, D. E. The major birch allergen, Bet v 1, shows affinity for a broad spectrum of physiological ligands. J. Biol. Chem. 2002, 277 (26), 23684-23692.
37. Bolhaar, S. T.; van de Weg, W. E.; van Ree, R.; Gonzalez-Mancebo, E.; Zuidmeer, L.; Bruijnzeel-Koomen, C. A.; Fernandez-Rivas, M.; Jansen, J.; Hoffmann-Sommergruber, K.; Knulst, A. C.; Gilissen, L. J. In vivo assessment with prick-to-prick testing and double-blind, placebo-controlled food challenge of allergenicity of apple cultivars. J. Allergy Clin. Immunol. 2005, 116 (5), 1080-1086.
38. Marzban, G.; Puehringer, H.; Dey, R.; Brynda, S.; Ma, Y.; Martinelli, A.; Zaccarini, M.; van der Weg, E.; Housley, Z.; Kolarich, D. Localisation and distribution of the major allergens in apple fruits. Plant Sci. 2005, 169 (2), 387-394.
39. Sancho, A. I.; Foxall, R.; Browne, T.; Dey, R.; Zuidmeer, L.; Marzban, G.; Waldron, K. W.; vanRee, R.; Hoffmann-Sommergruber, K.; Laimer, M.; Mills, E. N. C. Effect of postharvest storage on the expression of the apple allergen Mal d 1. J. Agric. Food Chem. 2006, 54 (16), 5917-5923.
40. Molloy, M. P.; Brzezinski, E. E.; Hang, J.; McDowell, M. T.; VanBogelen, R. A. Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003, 3 (10), 1912-1919.
41. Jorge, I.; Navarro, R. M.; Lenz, C.; Ariza, D.; Porras, C.; Jorrin, J. The holm oak leaf proteome: analytical and biological variability in the protein expression level assessed by 2-DE and protein identification tandem mass spectrometry de novo sequencing and sequence similarity searching. Proteomics 2005, 5 (1), 222-234.
42. Asirvatham, V. S.; Watson, B. S.; Sumner, L. W. Analytical and biological variances associated with proteomic studies of Medicago truncatula by two-dimensional polyacrylamide gel electrophoresis. Proteomics 2002, 2 (8), 960-968.
43. Newman, J. R.; Ghaemmaghami, S.; Ihmels, J.; Breslow, D. K.; Noble, M.; DeRisi, J. L.; Weissman, J. S. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441 (7095), 840-846.