iTRAQ-based comparative proteomic analysis of embryogenic and non-embryogenic tissues of Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr)

Plant Cell, Tissue and Organ Culture

Volumn 120, Issue 2, 2015, Pages 655-669

  Zhao, Jian ^a   Wang, Beibei ^a   Wang, Xiaoqi ^a   Zhang, Yan ^a   Dong, Mingliang ^a   Zhang, Jinfeng ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

iTRAQ; Prince Rupprecht s larch; Proteome analysis; Somatic embryogenesis; Totipotency

Indexed keywords

ANIMAL CELL CULTURE; CELL PROLIFERATION; TISSUE;

GTPASE-ACTIVATING PROTEIN; HISTOLOGICAL OBSERVATIONS; ITRAQ; PROLIFERATING CELL NUCLEAR ANTIGENS; PROTEOME ANALYSIS; SOMATIC EMBRYOGENESIS; TOTIPOTENCY; TRIOSEPHOSPHATE ISOMERASE;

PROTEINS;

EID: 84925482228     PISSN: 01676857     EISSN: 15735044     Source Type: Journal    
DOI: 10.1007/s11240-014-0633-y     Document Type: Article

References (89)

1. Agati G, Azzarello E, Pollastri S, Tattini M (2012) Flavonoids as antioxidants in plants: location and functional significance. Plant Sci 196:67–76
2. Almeida AM, Parreira JR, Santos R, Duque AS, Francisco R, Tome DF, Ricardo CP, Coelho AV, Fevereiro P (2012) A proteomics study of the induction of somatic embryogenesis in Medicago truncatula using 2DE and MALDI-TOF/TOF. Physiol Plant 146:236–249
3. Arnold SV, Sabala I, Bozhkov P, Dyachok J, Filonova L (2002) Developmental pathways of somatic embryogenesis. Plant Cell Tissue Organ Cult 69:233–249
4. Barna B, Smigocki A, Baker J (2008) Transgenic production of cytokinin suppresses bacterially induced hypersensitive response symptoms and increases antioxidative enzyme levels in Nicotiana spp. Phytopathology 98:1242–1247
5. Bian F, Zheng C, Qu F, Gong X, You C (2009) Proteomic analysis of somatic embryogenesis in Cyclamen persicum Mill. Plant Mol Biol Rep 28:22–31
6. Boutilier K, Offringa R, Sharma VK, Kieft H, Ouellet T, Zhang L, Hattori J, Liu CM, van Lammeren André AM, Miki Brian LA (2002) Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell Online 14:1737–1749
7. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
8. Buer CS, Muday GK, Djordjevic MA (2007) Flavonoids are differentially taken up and transported long distances in Arabidopsis. Plant Physiol 145:478–490
9. Bunney TD, van Walraven HS, de Boer AH (2001) 14-3-3 protein is a regulator of the mitochondrial and chloroplast ATP synthase. Proc Natl Acad Sci 98:4249–4254
10. Cabiscol E, Piulats E, Echave P, Herrero E, Ros J (2000) Oxidative stress promotes specific protein damage in Saccharomyces cerevisiae. J Biol Chem 275:27393–27398
11. Carrari F (2006) Metabolic regulation underlying tomato fruit development. J Exp Bot 57:1883–1897
12. Champagne A, Boutry M (2013) Proteomics of nonmodel plant species. Proteomics 13:663–673
13. Chivasa S, Tome DF, Hamilton JM, Slabas AR (2011) Proteomic analysis of extracellular ATP-regulated proteins identifies ATP synthase beta-subunit as a novel plant cell death regulator. Mol Cell Proteomics 10(M110):003905
14. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
15. Correia S, Vinhas R, Manadas B, Lourenco AS, Verissimo P, Canhoto JM (2012) Comparative proteomic analysis of auxin-induced embryogenic and nonembryogenic tissues of the solanaceous tree Cyphomandra betacea (Tamarillo). J Proteome Res 11:1666–1675
16. Cyr R, Bustos M, Guiltinan MJ, Fosket D (1987) Developmental modulation of tubulin protein and mRNA levels during somatic embryogenesis in cultured carrot cells. Planta 171:365–376
17. de Castro RD (2000) Cell division and subsequent radicle protrusion in tomato seeds are inhibited by osmotic stress but DNA synthesis and formation of microtubular cytoskeleton are not. Plant Physiol 122:327–336
18. Dudits D, Bogre L, Gyorgyey J (1991) Molecular and cellular approaches to the analysis of plant embryo development from somatic cells in vitro. J Cell Sci 99:475–484
19. 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
20. Feher A, Pasternak TP, Dudits D (2003) Transition of somatic plant cells to an embryogenic state. Plant Cell Tissue Organ Cult 74:201–228
21. Forward BS, Misra S (2000) Characterization and expression of the Douglas-fir luminal binding protein (PmBiP). Planta 212:41–51
22. Frydman J (2001) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70:603–647
23. Gaj MD, Zhang S, Harada JJ, Lemaux PG (2005) Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis. Planta 222:977–988
24. Gallardo K, Le Signor C, Vandekerckhove J, Thompson RD, Burstin J (2003) Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol 133:664–682
25. Gazzarrini S, Tsuchiya Y, Lumba S, Okamoto M, McCourt P (2004) The transcription factor FUSCA3 controls developmental timing in Arabidopsis through the hormones gibberellin and abscisic acid. Dev Cell 7:373–385
26. Gijzen M (2001) A class I chitinase from soybean seed coat. J Exp Bot 52:2283–2289
27. Greenbaum D, Colangelo C, Williams K, Gerstein M (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 4:117
28. Hackenberg T, Juul T, Auzina A, Gwizdz S, Malolepszy A, Van Der Kelen K, Dam S, Bressendorff S, Lorentzen A, Roepstorff P, Lehmann Nielsen K, Jorgensen JE, Hofius D, Breusegem FV, Petersen M, Andersen SU (2013) Catalase and NO CATALASE ACTIVITY1 promote autophagy-dependent cell death in Arabidopsis. Plant Cell 25:4616–4626
29. Helleboid S (2000) Three major somatic embryogenesis related proteins in Cichorium identified as PR proteins. J Exp Bot 51:1189–1200
30. Imin N, Nizamidin M, Daniher D, Nolan KE, Rose RJ, Rolfe BG (2005) Proteomic analysis of somatic embryogenesis in Medicago truncatula. Explant cultures grown under 6-benzylaminopurine and 1-naphthaleneacetic acid treatments. Plant Physiol 137:1250–1260
31. Jo L, Dos Santos AL, Bueno CA, Barbosa HR, Floh EI (2013) Proteomic analysis and polyamines, ethylene and reactive oxygen species levels of Araucaria angustifolia (Brazilian pine) embryogenic cultures with different embryogenic potential. Tree Physiol 34:94–104
32. Kambiranda D, Katam R, Basha SM, Siebert S (2013) iTRAQ-based quantitative proteomics of developing and ripening muscadine grape berry. J Proteome Res 13:555–569
33. Karami O, Aghavaisi B, Mahmoudi Pour A (2009) Molecular aspects of somatic-to-embryogenic transition in plants. J Chem Biol 2:177–190
34. Kasprzewska A (2003) Plant chitinases-regulation and function. Cell Mol Biol Lett 8:809–824
35. Kitamiya E, Suzuki S, Sano T, Nagata T (2000) Isolation of two genes that were induced upon the initiation of somatic embryogenesis on carrot hypocotyls by high concentrations of 2,4-D. Plant Cell Rep 19:551–557
36. Koizumi N (1996) Isolation and responses to stress of a gene that encodes a luminal binding protein in Arabidopsis thaliana. Plant Cell Physiol 37:862–865
37. Koizumi K, Naramoto S, Sawa S, Yahara N, Ueda T, Nakano A, Sugiyama M, Fukuda H (2005) VAN3 ARF-GAP-mediated vesicle transport is involved in leaf vascular network formation. Development 132:1699–1711
38. Laohavisit A, Davies JM (2011) Annexins. New Phytol 189:40–53
39. Larsson E, Sitbon F, Ljung K, Arnold SV (2008) Inhibited polar auxin transport results in aberrant embryo development in Norway spruce. New Phytol 177:356–366
40. Lelu-Walter M-A, Pâques LE (2009) Simplified and improved somatic embryogenesis of hybrid larches (Larix × eurolepis and Larix × marschlinsii). Perspectives for breeding. Ann For Sci 66:104
41. Lippert D, Zhuang J, Ralph S, Ellis DE, Gilbert M, Olafson R, Ritland K, Ellis B, Douglas CJ, Bohlmann J (2005) Proteome analysis of early somatic embryogenesis in Picea glauca. Proteomics 5:461–473
42. Lyngved R, Renaut J, Hausman J-F, Iversen T-H, Hvoslef-Eide AK (2008) Embryo-specific Proteins in Cyclamen persicum Analyzed with 2-D DIGE. J Plant Growth Regul 27:353–369
43. Maga G, Hubscher U (2003) Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J Cell Sci 116:3051–3060
44. Mahmood T, Jan A, Kakishima M, Komatsu S (2006) Proteomic analysis of bacterial-blight defense-responsive proteins in rice leaf blades. Proteomics 6:6053–6065
45. Malerba M, Contran N, Tonelli M, Crosti P, Cerana R (2008) Role of nitric oxide in actin depolymerization and programmed cell death induced by fusicoccin in sycamore (Acer pseudoplatanus) cultured cells. Physiol Plant 133:449–457
46. Marsoni M, Bracale M, Espen L, Prinsi B, Negri AS, Vannini C (2008) Proteomic analysis of somatic embryogenesis in Vitis vinifera. Plant Cell Rep 27:347–356
47. Mélida H, Caparrós-Ruiz D, Álvarez J, Acebes JL, Encina A (2011) Deepening into the proteome of maize cells habituated to the cellulose biosynthesis inhibitor dichlobenil. Plant Signal Behav 6:143
48. Moss SE, Morgan RO (2004) The annexins. Genome Biol 5:219
49. Nagata T, Ishida S, Hasezawa S, Takahashi Y (1994) Genes involved in the dedifferentiation of plant cells. Int J Dev Biol 38:321–327
50. Neilson KA, Mariani M, Haynes PA (2011) Quantitative proteomic analysis of cold-responsive proteins in rice. Proteomics 11:1696–1706
51. Pan Z, Guan R, Zhu S, Deng X (2009) Proteomic analysis of somatic embryogenesis in Valencia sweet orange (Citrus sinensis Osbeck). Plant Cell Rep 28:281–289
52. Peer WA, Murphy AS (2007) Flavonoids and auxin transport: modulators or regulators? Trends Plant Sci 12:556–563
53. Pourcel L, Irani NG, Koo AJ, Bohorquez-Restrepo A, Howe GA, Grotewold E (2013) A chemical complementation approach reveals genes and interactions of flavonoids with other pathways. Plant J 74:383–397
54. Proust J, Houlné G, Schantz M-L, Shen W-H, Schantz R (1999) Regulation of biosynthesis and cellular localization of Sp32 annexins in tobacco BY2 cells. Plant Mol Biol 39:361–372
55. Pullman GS, Buchanan M (2003) Loblolly pine (Pinus taeda L.): stage-specific elemental analyses of zygotic embryo and female gametophyte tissue. Plant Sci 164:943–954
56. Pullman G, Johnson S, Peter G, Cairney J, Xu N (2003) Improving loblolly pine somatic embryo maturation: comparison of somatic and zygotic embryo morphology, germination, and gene expression. Plant Cell Rep 21:747–758
57. Ramachandran S, Christensen HE, Ishimaru Y, Dong CH, Chao-Ming W, Cleary AL, Chua NH (2000) Profilin plays a role in cell elongation, cell shape maintenance, and flowering in Arabidopsis. Plant Physiol 124:1637–1647
58. Randazzo PA, Andrade J, Miura K, Brown MT, Long YQ, Stauffer S, Roller P, Cooper JA (2000) The Arf GTPase-activating protein ASAP1 regulates the actin cytoskeleton. Proc Natl Acad Sci 97:4011–4016
59. Rawe VY, Payne C, Schatten G (2006) Profilin and actin-related proteins regulate microfilament dynamics during early mammalian embryogenesis. Hum Reprod 21:1143–1153
60. Roberts MR, Salinas J, Collinge DB (2002) 14-3-3 proteins and the response to abiotic and biotic stress. Plant Mol Biol 50:1031–1039
61. Robles P, Fleury D, Candela H, Cnops G, Alonso-Peral MM, Anami S, Falcone A, Caldana C, Willmitzer L, Ponce MR, Van Lijsebettens M, Micol JL (2010) The RON1/FRY1/SAL1 gene is required for leaf morphogenesis and venation patterning in Arabidopsis. Plant Physiol 152:1357–1372
62. Rode C, Lindhorst K, Braun HP, Winkelmann T (2012) From callus to embryo: a proteomic view on the development and maturation of somatic embryos in Cyclamen persicum. Planta 235:995–1011
63. Rose JK, Bashir S, Giovannoni JJ, Jahn MM, Saravanan RS (2004) Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J 39:715–733
64. Schmidt E, Guzzo F, Toonen M, De Vries S (1997) A leucine-rich repeat containing receptor-like kinase marks somatic plant cells competent to form embryos. Development 124:2049–2062
65. Schwarzerova K, Vondrakova Z, Fischer L, Borikova P, Bellinvia E, Eliasova K, Havelkova L, Fiserova J, Vagner M, Opatrny Z (2010) The role of actin isoforms in somatic embryogenesis in Norway spruce. BMC Plant Biol 10:89
66. Sghaier B, Kriaa W, Bahloul M, Novo JVJ, Drira N (2009) Effect of ABA, arginine and sucrose on protein content of date palm somatic embryos. Sci Hortic 120:379–385
67. Sghaier-Hammami B, Drira N, Jorrin-Novo JV (2009) Comparative 2-DE proteomic analysis of date palm (Phoenix dactylifera L.) somatic and zygotic embryos. J Proteomics 73:161–177
68. Sharifi G, Ebrahimzadeh H, Ghareyazie B, Gharechahi J, Vatankhah E (2012) Identification of differentially accumulated proteins associated with embryogenic and non-embryogenic calli in saffron (Crocus sativus L.). Proteome Sci 10:3
69. Sieburth LE, Muday GK, King EJ, Benton G, Kim S, Metcalf KE, Meyers L, Seamen E, Van Norman JM (2006) SCARFACE encodes an ARF-GAP that is required for normal auxin efflux and vein patterning in Arabidopsis. Plant Cell 18:1396–1411
70. Spielbauer G, Li L, Romisch-Margl L, Do PT (2013) Chloroplast-localized 6-phosphogluconate dehydrogenase is critical for maize endosperm starch accumulation. J Exp Bot 64:2231–2242
71. Staiger CJ, Poulter NS, Henty JL, Franklin-Tong VE, Blanchoin L (2010) Regulation of actin dynamics by actin-binding proteins in pollen. J Exp Bot 61:1969–1986
72. Stasolla C (2003) Recent advances in conifer somatic embryogenesis: improving somatic embryo quality. Plant Cell Tissue Organ Cult 74:15–35
73. Steward F (1958) Growth and organized development of cultured cells. III. Interpretations of the growth from free cell to carrot plant. Am J Bot 45:709–713
74. Sun L, Wu Y, Zou HD, Su SZ, Li SP, Shan XH, Xi JH, Yuan YP (2012) Comparative proteomic analysis of the H99 inbred maize (Zea mays L.) line in embryogenic and non-embryogenic callus during somatic embryogenesis. Plant Cell Tissue Organ Cult 113:103–119
75. Sun T, Li S, Ren H (2013) Profilin as a regulator of the membrane-actin cytoskeleton interface in plant cells. Front Plant Sci 4:512
76. Sweetlove LJ, Heazlewood JL, Herald V, Holtzapffel R, Day DA, Leaver CJ, Millar AH (2002) The impact of oxidative stress on Arabidopsis mitochondria. Plant J 32:891–904
77. Teyssier C, Maury S, Beaufour M, Grondin C, Delaunay A, Le Mette C, Ader K, Cadene M, Label P, Lelu-Walter MA (2014) In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses. Physiol Plant 150:271–291
78. van Hengel AJ (2001) N-acetylglucosamine and glucosamine-containing arabinogalactan proteins control somatic embryogenesis. Plant Physiol 125:1880–1890
79. 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
80. Witke W, Sutherland JD, Sharpe A, Arai M, Kwiatkowski DJ (2001) Profilin I is essential for cell survival and cell division in early mouse development. Proc Natl Acad Sci 98:3832–3836
81. Wiweger M, Farbos I, Ingouff M, Lagercrantz U, Arnold SV (2003) Expression of Chia4-Pa chitinase genes during somatic and zygotic embryo development in Norway spruce (Picea abies): similarities and differences between gymnosperm and angiosperm class IV chitinases. J Exp Bot 54:2691–2699
82. Xu H, Zhang W, Gao Y, Zhao Y, Guo L, Wang J (2012) Proteomic analysis of embryo development in rice (Oryza sativa). Planta 235:687–701
83. Yang QS, Wu JH, Li CY, Wei YR, Sheng O, Hu CH, Kuang RB, Huang YH, Peng XX, McCardle JA, Chen W, Yang Y, Rose JK, Zhang S, Yi GJ (2012) Quantitative proteomic analysis reveals that antioxidation mechanisms contribute to cold tolerance in plantain (Musa paradisiaca L.; ABB Group) seedlings. Mol Cell Proteomics 11:1853–1869
84. Yang Y, Qiang X, Owsiany K, Zhang S, Thannhauser TW, Li L (2011) Evaluation of different multidimensional LC–MS/MS pipelines for isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis of potato tubers in response to cold storage. J Proteome Res 10:4647–4660
85. Zhang Z, Henderson C, Gurr SJ (2004) Blumeria graminis secretes an extracellular catalase during infection of barley: potential role in suppression of host defence. Mol Plant Pathol 5:537–547
86. Zhang J, Ma H, Chen S, Ji M, Perl A, Kovacs L, Chen S (2009) Stress response proteins’ differential expression in embryogenic and non-embryogenic callus of Vitis vinifera L. cv. Cabernet Sauvignon—a proteomic approach. Plant Sci 177:103–113
87. Zi J, Zhang JY, Wang QH, Zhou BJ, Zhong JY, Zhang CL, Qiu XM, Wen B, Zhang SY, Fu XQ, Lin L, Liu SQ (2013) Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One 8:e74229
88. Zimmerman JL (1993) Somatic embryogenesis: a model for early development in higher plants. Plant Cell 5:1411–1423
89. Zuo J, Niu QW, Frugis G, Chua NH (2002) The WUSCHEL gene promotes vegetative-to-embryonic transition in Arabidopsis. Plant J 30:349–359