Label-free quantitative proteomics to investigate strawberry fruit proteome changes under controlled atmosphere and low temperature storage

Journal of Proteomics

Volumn 120, Issue , 2015, Pages 44-57

  Li, Li ^a   Luo, Zisheng ^b   Huang, Xinhong ^a   Zhang, Lu ^a   Zhao, Pengyu ^a   Ma, Hongyuan ^a   Li, Xihong ^a   Ban, Zhaojun ^c,d   Liu, Xia ^a  

^a TIANJIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c Jinan Fruit Research Institute   (China)

^d XINJIANG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Controlled atmosphere; Fruit; LC MS MS; Storage; Strawberry; Volatiles

Indexed keywords

ASCORBIC ACID; PROTEOME; VOLATILE AGENT; VEGETABLE PROTEIN;

ACIDITY; ARTICLE; CARBOHYDRATE METABOLISM; CONTROLLED ATMOSPHERE; ENERGY METABOLISM; INVESTIGATIVE PROCEDURES; LOW TEMPERATURE; METABOLOMICS; NONHUMAN; POSTHARVEST PERIOD; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN SYNTHESIS; PROTEOMICS; QUANTITATIVE ANALYSIS; QUANTITATIVE STUDY; ROOM TEMPERATURE; SENESCENCE; STORAGE TEMPERATURE; STRAWBERRY; STRESS; TRANSCRIPTOMICS; ATMOSPHERE; COLD; COMPARATIVE STUDY; FOOD ANALYSIS; FOOD STORAGE; FRAGARIA; FRUIT; GENE EXPRESSION PROFILING; HEAT SHOCK RESPONSE; METABOLISM; PHYSIOLOGY; PROCEDURES;

FRAGARIA X ANANASSA;

ATMOSPHERE; COLD TEMPERATURE; FOOD ANALYSIS; FOOD STORAGE; FRAGARIA; FRUIT; GENE EXPRESSION PROFILING; HEAT-SHOCK RESPONSE; PLANT PROTEINS; PROTEOME;

EID: 84924916478     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.02.016     Document Type: Article

References (71)

1. Ruelland E., Vaultier M.N., Zachowski A., Hurry V. Cold signalling and cold acclimation in plants. Adv Bot Res 2009, 49:35-150.
2. Baginsky S., Hennig L., Zimmermann P., Gruissem W. Gene expression analysis, proteomics, and network discovery. Plant Physiol 2010, 152:402-410.
3. Cox J., Mann M. Is proteomics the new genomics?. Cell 2007, 130:395-398.
4. Palma J.M., Corpas F.J., del Rio L.A. Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening. J Proteomics 2011, 74:1230-1243.
5. Bianco L., Lopez L., Scalone A.G., Di Carli M., Desiderio A., Benvenuto E., et al. Strawberry proteome characterization and its regulation during fruit ripening and in different genotypes. J Proteomics 2009, 72:586-607.
6. Deytieux C., Geny L., Lapaillerie D., Claverol S., Bonneu M., Donèche B. Proteome analysis of grape skins during ripening. J Exp Bot 2007, 58:1851-1862.
7. Herndl A., Marzban G., Kolarich D., Hahn R., Boscia D., Hemmer W., et al. Mapping of Malus domestica allergens by 2-D electrophoresis and IgE-reactivity. Electrophoresis 2007, 28:437-448.
8. Hjernø K., Alm R., Canbäck B., Matthiesen R., Trajkovski K., Björk L., et al. Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant. Proteomics 2006, 6:1574-1587.
9. Pedreschi R., Hertog M., Robben J., Noben J.P., Nicolaï B. Physiological implications of controlled atmosphere storage of 'Conference' pears (Pyrus communis L.): a proteomic approach. Postharvest Biol Technol 2008, 50:110-116.
10. Rocco M., D'Ambrosio C., Arena S., Faurobert M., Scaloni A., Marra M. Proteomic analysis of tomato fruits from two ecotypes during ripening. Proteomics 2006, 6:3781-3791.
11. Shulaev V., Sargent D.J., Crowhurst R.N., Mockler T.C., Folkerts O., Delcher A.L., et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet 2010, 43:109-116.
12. Li L., Song J., Kalt W., Forney C., Tsao R., Pinto D., et al. Quantitative proteomic investigation employing stable isotope labeling by peptide dimethylation on proteins of strawberry fruit at different ripening stages. J Proteomics 2013, 94:219-239.
13. Alm R., Ekefjärd A., Krogh M., Häkkinen J., Emanuelsson C. Proteomic variation is as large within as between strawberry varieties. J Proteome Res 2007, 6:3011-3020.
14. Mitcham E. Strawberry. Agriculture Handbook 2004, 66. U.S. Dept. of Agriculture, Beltsville Area, (Agricultural Research Service). K. Gross, C. Wang, M. Saltveit (Eds.).
15. Mitcham E.J., Crisosto C.H., Kader A.A. Strawberry: recommendations for maintaining postharvest quality http://postharvest.ucdavis.edu/PFfruits/Strawberry/.
16. Zapata S., Dufour J.-P. Ascorbic, Dehydroascorbic and isoascorbic acid simultaneous determinations by reverse phase ion interaction HPLC. J Food Sci 1992, 57:506-511.
17. Elias J.E., Gygi S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207.
18. Li N., Wu S., Zhang C., Chang C., Zhang J., Ma J., et al. PepDistiller: a quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics. Proteomics 2012, 12:1720-1725.
19. Chang C., Zhang J., Han M., Ma J., Zhang W., Wu S., et al. SILVER: An efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. Bioinformatics 2014, 30:586-587.
20. Azodanlou R., Darbellay C., Luisier J.L., Villettaz J.C., Amadò R. Changes in flavour and texture during the ripening of strawberries. Eur Food Res Technol 2004, 218:167-172.
21. Jackman R.L., Stanley D.W. Perspectives in the textural evaluation of plant foods. Trends Food Sci Technol 1995, 6:187-194.
22. Caner C., Aday M., Demir M. Extending the quality of fresh strawberries by equilibrium modified atmosphere packaging. Eur Food Res Technol 2008, 227:1575-1583.
23. 2 atmospheres. J Food Sci 2008, 73:S339-S344.
24. Wright K.P., Kader A.A. Effect of slicing and controlled-atmosphere storage on the ascorbate content and quality of strawberries and persimmons. Postharvest Biol Technol 1997, 10:39-48.
25. Veltman R.H., Sanders M.G., Persijn S.T., Peppelenbos H.W., Oosterhaven J. Decreased ascorbic acid levels and brown core development in pears (Pyrus communis L. cv. Conference). Physiol Plant 1999, 107:39-45.
26. 2 and controlled atmosphere (CA) on the ascorbic and dehydroascorbic acid content of some berry fruits. Postharvest Biol Technol 1997, 11:47-55.
27. Azodanlou R., Darbellay C., Luisier J.L., Villettaz J.C., Amado R. Quality assessment of strawberries (Fragaria species). J Agric Food Chem 2003, 51:715-721.
28. Li L., Luo Z., Huang X., Zhang L., Zhao P., Ma H., et al. Data in support of comparative analysis of strawberry proteome in response to controlled atmosphere and low temperature storage using a label-free quantification. Data in Brief 2015, (in press).
29. Yun Z., Jin S., Ding Y., Wang Z., Gao H., Pan Z., et al. Comparative transcriptomics and proteomics analysis of citrus fruit, to improve understanding of the effect of low temperature on maintaining fruit quality during lengthy post-harvest storage. J Exp Bot 2012, 63:2873-2893.
30. Ogundiwin E.A., Peace C.P., Gradziel T.M., Parfitt D.E., Bliss F.A., Crisosto C.H. A fruit quality gene map of Prunus. BMC Genomics 2009, 10.
31. Yun Z., Li W., Pan Z., Xu J., Cheng Y., Deng X. Comparative proteomics analysis of differentially accumulated proteins in juice sacs of ponkan (Citrus reticulata) fruit during postharvest cold storage. Postharvest Biol Technol 2010, 56:189-201.
32. Bowler C., Van Montagu M., Inze D. Superoxide dismutase and stress tolerance. Annu Rev Plant Physiol Plant Mol Biol 1992, 43:83-116.
33. Bae M.S., Cho E.J., Choi E.Y., Park O.K. Analysis of the Arabidopsis nuclear proteome and its response to cold stress. Plant J 2003, 36:652-663.
34. 2 concentrations. J Am Soc Hortic Sci 1990, 115:111-114.
35. Holtgrefe S., Gohlke J., Starmann J., Druce S., Klocke S., Altmann B., et al. Regulation of plant cytosolic glyceraldehyde 3-phosphate dehydrogenase isoforms by thiol modifications. Physiol Plant 2008, 133:211-228.
36. Song J., Forney C.F. Flavour volatile production and regulation in fruit. Can J Plant Sci 2008, 88:537-550.
37. Bood K.G., Zabetakis I. The biosynthesis of strawberry flavor (II): biosynthetic and molecular biology studies. J Food Sci 2002, 67:2-8.
38. Ulrich D., Hoberg E., Rapp A., Kecke S. Analysis of strawberry flavour - discrimination of aroma types by quantification of volatile compounds. Eur Food Res Technol 1997, 205:218-223.
39. Raab T., López-Ráez J.A., Klein D., Caballero J.L., Moyano E., Schwab W., et al. 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, 18:1023-1037.
40. Vogt T. Phenylpropanoid biosynthesis. Mol Plant 2010, 3:2-20.
41. Griesser M., Hoffmann T., Bellido M.L., Rosati C., Fink B., Kurtzer R., et al. Redirection of flavonoid biosynthesis through the down-regulation of an anthocyanidin glucosyltransferase in ripening strawberry fruit. Plant Physiol 2008, 146:1528-1539.
42. Foyer C.H., Noctor G. Redox homeostasis and antioxidant signaling: a metabolic interface between stress perception and physiological responses. Plant Cell 2005, 17:1866-1875.
43. Toivonen P.M.A. Postharvest storage procedures and oxidative stress. HortScience 2004, 39:938-942.
44. Koehler G., Wilson R.C., Goodpaster J.V., Sønsteby A., Lai X., Witzmann F.A., et al. Proteomic study of low-temperature responses in strawberry cultivars (Fragaria×ananassa) that differ in cold tolerance. Plant Physiol 2012, 159:1787-1805.
45. Gupta A.S., Heinen J.L., Holaday A.S., Burke J.J., Allen R.D. Increased resistance to oxidative stress in transgenic plants that overexpress chloroplastic Cu/Zn superoxide dismutase. Proc Natl Acad Sci U S A 1993, 90:1629-1633.
46. Haque M., Yoshida Y., Hasunuma K. ROS resistance in Pisum sativum cv. Alaska: the involvement of nucleoside diphosphate kinase in oxidative stress responses via the regulation of antioxidants. Planta 2010, 232:367-382.
47. Tripathi B.N., Bhatt I., Dietz K.J. Peroxiredoxins: a less studied component of hydrogen peroxide detoxification in photosynthetic organisms. Protoplasma 2009, 235:3-15.
48. Vega-García M.O., López-Espinoza G., Ontiveros J.C., Caro-Corrales J.J., Vargas F.D., López-Valenzuela J.A. Changes in protein expression associated with chilling injury in tomato fruit. J Am Soc Hortic Sci 2010, 135:83-89.
49. Giraldo E., Díaz A., Corral J.M., García A. Applicability of 2-DE to assess differences in the protein profile between cold storage and not cold storage in nectarine fruits. J Proteomics 2012, 75:5774-5782.
50. Wang Y., Wisniewski M., Meilan R., Cui M., Webb R., Fuchigami L. Overexpression of cytosolic ascorbate peroxidase in tomato confers tolerance to chilling and salt stress. J Am Soc Hortic Sci 2005, 130:167-173.
51. Toledo T.T., Nogueira S.B., Cordenunsi B.R., Gozzo F.C., Pilau E.J., Lajolo F.M., et al. Proteomic analysis of banana fruit reveals proteins that are differentially accumulated during ripening. Postharvest Biol Technol 2012, 70:51-58.
52. Hartl F.U. Molecular chaperones in cellular protein folding. Nature 1996, 381:571-580.
53. Sanchez-Bel P., Egea I., Sanchez-Ballesta M.T., Sevillano L., Del Carmen Bolarin M., Flores F.B. Proteome changes in tomato fruits prior to visible symptoms of chilling injury are linked to defensive mechanisms, uncoupling of photosynthetic processes and protein degradation machinery. Plant Cell Physiol 2012, 53:470-484.
54. van der Hoorn R.A. Plant proteases: from phenotypes to molecular mechanisms. Annu Rev Plant Biol 2008, 59:191-223.
55. Thornberry N.A., Lazebnik Y. Caspases: enemies within. Science 1998, 281:1312-1316.
56. Woltering E.J. Death proteases come alive. Trends Plant Sci 2004, 9:469-472.
57. Rodrigues S.P., Ventura J.A., Aguilar C., Nakayasu E.S., Choi H., Sobreira T.J.P., et al. Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants. J Proteomics 2012, 75:3191-3198.
58. Pedreschi R., Vanstreels E., Carpentier S., Hertog M., Lammertyn J., Robben J., et al. Proteomic analysis of core breakdown disorder in Conference pears (Pyrus communis L.). Proteomics 2007, 7:2083-2099.
59. Bolhaar S.T.H.P., Van De Weg W.E., Van Ree R., Gonzalez-Mancebo E., Zuidmeer L., Bruijnzeel-Koomen C.A.F.M., et al. 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, 116:1080-1086.
60. Weiss J., Egea-Cortines M. Transcriptomic analysis of cold response in tomato fruits identifies dehydrin as a marker of cold stress. J Appl Genet 2009, 50:311-319.
61. Yang Z., Zhang T., Bolshoy A., Beharav A., Nevo E. Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel. Mol Ecol 2009, 18:2063-2075.
62. Yang S., Oetiker J. Molecular biology of ethylene biosynthesis and its application in horticulture. J Jpn Soc Hortic Sci 1998, 67:1209-1214.
63. Vierstra R.D. The ubiquitin-26S proteasome system at the nexus of plant biology. Nat Rev Mol Cell Biol 2009, 10:385-397.
64. Khatoon A., Rehman S., Oh M.W., Woo S.H., Komatsu S. Analysis of response mechanism in soybean under low oxygen and flooding stresses using gel-base proteomics technique. Mol Biol Rep 2012, 39:10581-10594.
65. Kamauchi S., Wadahama H., Iwasaki K., Nakamoto Y., Nishizawa K., Ishimoto M., et al. Molecular cloning and characterization of two soybean protein disulfide isomerases as molecular chaperones for seed storage proteins. FEBS J 2008, 275:2644-2658.
66. Mithoe S.C., Menke F.L.H. Phosphoproteomics perspective on plant signal transduction and tyrosine phosphorylation. Phytochemistry 2011, 72:997-1006.
67. +-ATPase activity in the plasma membrane of suspension-cultured sugar beet cells under cold stress. FEBS Lett 1999, 456:22-26.
68. +-ATPases activity, membrane integrity, and apoplastic pH during papaya fruit ripening. Postharvest Biol Technol 2008, 48:242-247.
69. Luo H., Bao Y., Jiang J., Zhang L., Song L., Jiang L., et al. Proteome changes of fresh-cut Zizania latifolia during refrigerated (1°C) storage. Eur Food Res Technol 2012, 1-11.
70. Valluru R., Lammens W., Claupein W., Van den Ende W. Freezing tolerance by vesicle-mediated fructan transport. Trends Plant Sci 2008, 13:409-414.
71. Minami A., Fujiwara M., Furuto A., Fukao Y., Yamashita T., Kamo M., et al. Alterations in detergent-resistant plasma membrane microdomains in Arabidopsis thaliana during cold acclimation. Plant Cell Physiol 2009, 50:341-359.