Proteomic analysis of embryo development in rice (Oryza sativa)

Planta

Volumn 235, Issue 4, 2012, Pages 687-701

  Xu, Hong ^a   Zhang, Weiping ^a   Gao, Yi ^a   Zhao, Yong ^a   Guo, Lin ^a   Wang, Jianbo ^a  

^a WUHAN UNIVERSITY   (China)

Author keywords

Embryo development; Nano LC MS MS; Proteome; Rice; Two dimensional gel electrophoresis (2 DE)

Indexed keywords

VEGETABLE PROTEIN;

ARTICLE; CHEMISTRY; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT SEED; PROTEOMICS; RICE;

ORYZA SATIVA; PLANT PROTEINS; PROTEOMICS; SEEDS;

ORYZA SATIVA;

EID: 84858861182     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-011-1535-4     Document Type: Article

References (75)

1. Abbasi FM, Komatsu S (2004) A proteomic approach to analyze salt responsive proteins in rice leaf sheath. Proteomics 4: 2072-2081.
2. Agrawal GK, Rakwal R, Yonekura M, Kubo A, Saji H (2002) Proteome analysis of differentially displayed proteins as a tool for investigating ozone stress in rice (Oryza sativa L.) seedlings. Proteomics 2: 947-959.
3. Ahsan N, Lee DG, Lee SH, Kang KY, Lee JJ, Kim PJ, Yoon HS, Kim JS, Lee BH (2007) Excess copper induced physiological and proteomic changes in germinating rice seeds. Chemosphere 67: 1182-1193.
4. Ali N, Probert R, Hay F, Davies H, Stuppy W (2007) Post-dispersal embryo growth and acquisition of desiccation tolerance in Anemone nemorosa L. seeds. Seed Sci Res 17: 155-163.
5. Anderson NL, Anderson NG (1998) Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 19: 1853-1861.
6. Andriotis VME, Kruger NJ, Pike MJ, Smith AM (2010) Plastidial glycolysis in developing Arabidopsis embryos. New Phytol 185: 649-662.
7. Balbuena TS, Silveira V, Junqueira M, Dias LL, Santa-Catarina C, Shevchenko A, Floh EI (2009) Changes in the 2-DE protein profile during zygotic embryogenesis in the Brazilian pine (Araucaria angustifolia). Proteomics 72: 337-352.
8. Battaglia M, Olvera-Carrillo Y, Garciarrubio A, Campos F, Covarrubias AA (2008) The enigmatic LEA proteins and other hydrophilins. Plant Physiol 148: 6-24.
9. Bechtel DB, Pomeranz Y (1978) Ultrastructure of the mature ungerminated rice (Oryza sativa) caryopsis. The starchy endosperm. Am J Bot 65: 684-691.
10. Bies-Ethève N, Gaubier-Comella P, Debures A, Lasserre E, Jobet E, Raynal M, Cooke R, Delseny M (2008) Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana. Plant Mol Biol 67: 107-124.
11. Bosch M, Mayer CD, Cookson A, Donnison IS (2011) Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes. J Exp Bot 62: 3545-3561.
12. Bradford MM (1976) A rapid and sensitive method for quantitation of microgram quantities of protein utilizing the principle of protein-dye-binding. Anal Biochem 72: 248-254.
13. Breviario D (2008) Plant tubulin genes: regulatory and evolutionary aspects. Plant Cell Monogr 11: 207-232.
14. Candiano G, Bruschi M, Musante L, Santucci L, Ghiggeri GM, Carnemolla B, Orecchia P, Zardi L, Righetti PG (2004) Blue silver: a very sensitive colloidal coomassie G-250 staining for proteome analysis. Electrophoresis 25: 1327-1333.
15. Carrari F, Fernie AR (2006) Metabolic regulation underlying tomato fruit development. J Exp Bot 57: 1883-1897.
16. Chen Q, Yang L, Ahmad P, Wan X, Hu X (2011) Proteomic profiling and redox status alteration of recalcitrant tea (Camellia sinensis) seed in response to desiccation. Planta 233: 583-592.
17. Chen S, Harmon AC (2006) Advances in plant proteomics. Proteomics 6: 5504-5516.
18. Chugh A, Khurana P (2002) Gene expression during somatic embryogenesis-recent advances. Curr Sci 86: 715-730.
19. Cordova-Tellez L, Burris JS (2002) Embryo drying rates during the acquisition of desiccation tolerance in maize seed. Crop Sci 42: 1989-1995.
20. Dai WG, Dong LC, Song YQ (2007) Nanosizing of a drug/carrageenan complex to increase solubility and dissolution rate. Int J Pharm 342: 201-207.
21. De Smet I, Lau S, Mayer U, Jürgens G (2010) Embryogenesis-the humble beginnings of plant life. Plant J 61: 959-970.
22. Egerton-Warburton LM, Balsamo RA, Close TJ (1997) Temporal accumulation and ultrastructural localization of dehydrins in Zea mays. Physiol Plant 101: 545-555.
23. Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G (2006) Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol 142: 839-854.
24. Farré EM, Geigenberger P, Willmitzer L, Trethewey RN (2000) A possible role for pyrophosphate in the coordination of cytosolic and plastidial carbon metabolism within the potato tuber. Plant Physiol 123: 681-688.
25. Farré EM, Tiessen A, Roessner U, Geigenberger P, Trethewey RN, Willmitzer L (2001) Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids, and sugar alcohols in potato tubers using a nonaqueous fractionation method. Plant Physiol 127: 685-700.
26. Fernie AR, Carrari F, Sweetlove LJ (2004) Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport. Curr Opin Plant Biol 7: 254-261.
27. Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN, Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18: 1157-1161.
28. Franco OL, Pelegrini PB, Gomes CP, Souza A, Costa FT, Domont G, Quirino BF, Eira MT, Mehta A (2009) Proteomic evaluation of coffee zygotic embryos in two different stages of seed development. Plant Physiol Biochem 47: 1046-1050.
29. Gallardo K, Firnhaber C, Zuber H, Héricher D, Belghazi M, Henry C, Küster H, Thompson R (2007) A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: evidence for metabolic specialization of maternal and filial tissues. Mol Cell Proteomics 6: 2165-2179.
30. Garay-Arroyo A, Colmenero-Flores JM, Garciarrubio A, Covarrubias AA (2000) Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. J Biol Chem 275: 5668-5674.
31. Gaubier P, Raynal M, Hull G, Huestis GM, Grellet F, Arenas C, Pagès M, Delseny M (1993) Two different Em-like genes are expressed in Arabidopsis thaliana seeds during maturation. Mol Gen Genet 238: 409-418.
32. Guillaumie S, San-Clemente H, Deswarte C, Martinez Y, Lapierre C, Murigneux A, Barriere Y, Pichon M, Goffner D (2007) Maizewall. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. Plant Physiol 143: 339-363.
33. Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720-1730.
34. Hajduch M, Casteel JE, Hurrelmeyer KE, Song Z, Agrawal GK, Thelen JJ (2006) Proteomic analysis of seed filling in Brassica napus: developmental characterization of metabolic isozymes using high-resolution two-dimensional gel electrophoresis. Plant Physiol 141: 32-46.
35. Harada JJ, DeLisle AJ, Baden CS, Crouch ML (1989) Unusual sequence of an abscisic acid inducible mRNA which accumulates late in Brassica napus seed development. Plant Mol Biol 12: 395-401.
36. Hewezi T, Petitprez M, Gentzbittel L (2006) Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays. Planta 223: 948-964.
37. Hoekstra FA, Golovina EA, Tetteroo FA, Wolkers WF (2001) Induction of desiccation tolerance in plant somatic embryos: how exclusive is the protective role of sugars? Cryobiology 43: 140-150.
38. Hollung K, Espelund M, Jakobsen KS (1994) Another Lea B19 gene (group 1 Lea) from barley containing a single 20 amino acid hydrophilic motif. Plant Mol Biol 25: 559-564.
39. Hsing YC, Chen ZY, Shih MD, Hsieh JS, Chow TY (1995) Unusual sequences of group 3 LEA mRNA inducible by maturation or drying in soybean seeds. Plant Mol Biol 29: 863-868.
40. Ichihara K, Kobayashi N, Saito K (2003) Lipid synthesis and acyl-CoA synthetase in developing rice seeds. Lipids 38: 881-884.
41. Itoh J, Nonomura K, Ikeda K, Yamaki S, Inukai Y, Yamagishi H, Kitano H, Nagato Y (2005) Rice plant development: from zygote to spikelet. Plant Cell Physiol 46: 23-47.
42. Joosen R, Cordewener J, Supena ED, Vorst O, Lammers M, Maliepaard C, Zeilmaker T, Miki B, America T, Custers J, Boutilier K (2007) Combined transcriptome and proteome analysis identifies pathways and markers associated with the establishment of rapeseed microspore-derived embryo development. Plant Physiol 144: 155-172.
43. Katz E, Fon M, Lee YJ, Phinney BS, Sadka A, Blumwald E (2007) The citrus fruit proteome: insights into citrus fruit metabolism. Planta 226: 989-1005.
44. Kaufmann K, Smaczniak C, de Vries S, Angenent GC, Karlova R (2011) Proteomics insights into plant signaling and development. Proteomics 11: 744-755.
45. Kersten B, Bürkle L, Kuhn EJ, Giavalisco P, Konthur Z, Lueking A, Walter G, Eickhoff H, Schneider U (2002) Large-scale plant proteomics. Plant Mol Biol 48: 133-141.
46. Kim HS, Lee JH, Kim JJ, Kim CH, Jun SS, Hong YN (2005) Molecular and functional characterization of CaLEA6, the gene for a hydrophobic LEA protein from Capsicum annuum. Gene 344: 115-123.
47. Koga K, Minohata T (2011) An approach for identification of phosphoproteins using the G-electrode-loading method in two-dimensional gel electrophoresis. Proteomics 11: 1545-1549.
48. Komatsu S, Abbasi F, Kobori E, Fujisawa Y, Kato H, Iwasaki Y (2005) Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins. Proteomics 5: 3932-3941.
49. Kopczak SD, Haas NA, Hussey PJ, Silflow CD, Snustad DP (1992) The small genome of Arabidopsis contains at least six expressed alpha-tubulin genes. Plant Cell 4: 539-547.
50. Laux T, Würschum T, Breuninger H (2004) Genetic regulation of embryonic pattern formation. Plant Cell 16: S190-S202.
51. Lee JM, Williams ME, Tingey SV, Rafalski JA (2002) DNA array profiling of gene expression changes during maize embryo development. Funct Integr Genomics 2: 13-27.
52. Lu TC, Meng LB, Yang CP, Liu GF, Liu GJ, Ma W, Wang BC (2008) A shotgun phosphoproteomics analysis of embryos in germinated maize seeds. Planta 228: 1029-1041.
53. Lyngved R, Renaut J, Hausman JF, Iversen TH, Hvoslef-Eide AK (2008) Embryo-specific proteins in Cyclamen persicum analyzed with 2-D DIGE. J Plant Growth Regul 27: 353-369.
54. Martin SW, Glover BJ, Davies JM (2005) Lipid microdomains-plant membranes get organized. Trends Plant Sci 10: 263-265.
55. Mayer U, Torres-Ruiz RA, Berleth T, Miseéra S, Jürgens G (1991) Mutations affecting body organization in the Arabidopsis embryo. Nature 353: 402-407.
56. Minic Z, Jamet E, San-Clemente H, Pelletier S, Renou JP, Rihouey C, Okinyo DP, Proux C, Lerouge P, Jouanin L (2009) Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes. BMC Plant Biol 9: 6.
57. Parker KC, Garrels JI, Hines W, Butler EM, McKee AH, Patterson D, Martin S (1998) Identification of yeast proteins from two-dimensional gels: working out spot cross-contamination. Electrophoresis 19: 1920-1932.
58. Sengupta S, Majumder AL (2009) Insight into the salt tolerance factors of a wild halophytic rice, Porteresia coarctata: a physiological and proteomic approach. Planta 229: 911-929.
59. Sghaier-Hammami B, Drira N, Jorrín-Novo JV (2009) Comparative 2-DE proteomic analysis of date palm (Phoenix dactylifera L.) somatic and zygotic embryos. Proteomics 73: 161-177.
60. Spencer MW, Casson SA, Lindsey K (2007) Transcriptional profiling of the Arabidopsis embryo. Plant Physiol 143: 924-940.
61. Sulpice R, Trenkamp S, Steinfath M, Usadel B, Gibon Y, Witucka-Wall H, Pyl ET, Tschoep H, Steinhauser MC, Guenther M, Hoehne M, Rohwer JM, Altmann T, Fernie AR, Stitt M (2010) Network analysis of enzyme activities and metabolite levels and their relationship to biomass in a large panel of Arabidopsis accessions. Plant Cell 22: 2872-2893.
62. Takáč T, Pechan T, Samaj J (2011) Differential proteomics of plant development. J Proteomics 74: 577-588.
63. Tunnacliffe A, Wise MJ (2007) The continuing conundrum of the LEA proteins. Naturwissenschaften 94: 791-812.
64. Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, Meinke D (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135: 1206-1220.
65. Vicient CM, Gruber V, Delseny M (2001) The Arabidopsis AtEm1 promoter is active in Brassica napus L. and is temporally and spatially regulated. J Exp Bot 52: 1587-1591.
66. Vierstra RD (2003) The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends Plant Sci 8: 135-142.
67. West M, Harada JJ (1993) Embryogenesis in higher plants: an overview. Plant Cell 5: 1361-1369.
68. Williams BA, Tsang A (1994) Analysis of multiple classes of abscisic acid responsive genes during embryogenesis in Zea mays. Dev Genet 15: 415-424.
69. Winkelmann T, Heintz D, van Dorsselaer A, Serek M, Braun HP (2006) Proteomic analyses of somatic and zygotic embryos of Cyclamen persicum Mill. reveal new insights into seed and germination physiology. Planta 224: 508-519.
70. Wise MJ, Tunnacliffe A (2004) POPP the question: what do LEA proteins do? Trends Plant Sci 9: 13-17.
71. Xu SB, Li T, Deng ZY, Chong K, Xue Y, Wang T (2008) Dynamic proteomic analysis reveals a switch between central carbon metabolism and alcoholic fermentation in rice filling grains. Plant Physiol 148: 908-925.
72. Yang P, Li X, Wang X, Chen H, Chen F, Shen S (2007a) Proteomic analysis of rice (Oryza sativa) seeds during germination. Proteomics 7: 3358-3368.
73. Yang Q, Wang Y, Zhang J, Shi W, Qian C, Peng X (2007b) Identification of aluminum-responsive proteins in rice roots by a proteomic approach: cysteine synthase as a key player in Al response. Proteomics 7: 737-749.
74. Zamboni A, Di Carli M, Guzzo F, Stocchero M, Zenoni S, Ferrarini A, Tononi P, Toffali K, Desiderio A, Lilley KS, Pè ME, Benvenuto E, Delledonne M, Pezzotti M (2010) Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks. Plant Physiol 154: 1439-1459.
75. Zegzouti H, Jones B, Marty C, Lelièvre JM, Latché A, Pech JC, Bouzayen M (1997) ER5, a tomato cDNA encoding an ethylene-responsive LEA-like protein: characterization and expression in response to drought, ABA and wounding. Plant Mol Biol 35: 847-854.