Comparative proteomics analysis of developing peanut aerial and subterranean pods identifies pod swelling related proteins

Journal of Proteomics

Volumn 91, Issue , 2013, Pages 172-187

  Zhu, Wei ^a,b   Zhang, Erhua ^a   Li, Haifen ^a   Chen, Xiaoping ^a   Zhu, Fanghe ^a   Hong, Yanbin ^a   Liao, Boshou ^b   Liu, Shengyi ^b   Liang, Xuanqiang ^a  

^a INSTITUTE OF ANIMAL SCIENCE   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Aerial and subterranean pods; Peanut; Plant proteome; Pod development

Indexed keywords

LIGNIN; MESSENGER RNA; PROTEASOME; PROTEIN; TRANSCRIPTOME; UBIQUITIN;

ARTICLE; BIOSYNTHESIS; CATABOLISM; DEVELOPMENTAL STAGE; FATTY ACID SYNTHESIS; GENE EXPRESSION; GLYCOLYSIS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; OXIDATIVE STRESS; PEANUT; PHOTOSYNTHESIS; POD; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SYNTHESIS; PROTEOMICS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEED DEVELOPMENT; SEED YIELD; SOIL; TWO DIMENSIONAL ELECTROPHORESIS;

AERIAL AND SUBTERRANEAN PODS; PEANUT; PLANT PROTEOME; POD DEVELOPMENT;

ARACHIS HYPOGAEA; DARKNESS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; LIGHT; OXIDATIVE STRESS; PHOTOSYNTHESIS; PLANT PROTEINS; PROTEOME; PROTEOMICS; RNA, MESSENGER; SEEDS;

EID: 84881520623     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.07.002     Document Type: Article

References (88)

1. Chen X.P., Zhu W., Azam S., Li H.Y., Zhu F.H., Li H.F., et al. Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnol J 2013, 11:115-127.
2. Moctezuma E., Feldman L.J. The role of amyloplasts during gravity perception in gynophores of the peanut plant. Ann Bot 1999, 84:709-714.
3. Feng Q.L., Stalker H.T., Pattee H.E., Isleib T.G. Arachis hypogaea plant recovery through in vitro culture of peg tips. Peanut Sci 1995, 22:129-135.
4. Moctezuma E. The peanut gynophore: a developmental and physiological perspective. Can J Bot 2003, 81:183-190.
5. Ziv M., Zamskj E. Geotropic responses and pod development in gynophore explants of peanut (Arachis hypogaea L.) cultured in vitro. Ann Bot 1975, 39:579-583.
6. Zamski E., Ziv M. Pod formation and its geotropic orientation in the peanut, Aruchis hypogaea L., in relation to light and mechanical stimulus. Ann Bot 1976, 40:63l-636l.
7. Thompson L.K., Ziv M., Deitzer G.F. Photocontrol of peanut (Arachis hypogaea L.) embryo and ovule development in vitro. Plant Physiol 1985, 78:370-373.
8. Shushu D.D., Cutter E.G. Growth of the gynophore of the peanut Arachis hypogaea L. intact and decapitated gynophores. Can J Bot 1990, 68:955-964.
9. Jacobs W. Auxin relationships in an intercalary meristem: further studies on the gynophore of Arachis hypogaea L. Am J Bot 1951, 38:307-310.
10. Moctezuma E., Feldman L.J. IAA redistributes to the upper side of gravistimulated peanut (Arachis hypogaea) gynophores. Plant Physiol 1996, 111:S73.
11. Ziv M., Kahana O. The role of the peanut (Araschis hypogaea) ovular tissue in the photo-morphogenetic response of the embryo. Plant Sci 1988, 57:159-164.
12. Shlamovitz N., Ziv M., Zamski E. Light, dark and growth regulator involvement in groundnut (Arachis hypogaea L.) pod development. Plant Growth Regul 1995, 16:37-42.
13. Moctezuma E. Changes in auxin patterns in developing gynophores of the peanut plant (Arachis hypogaea L.). Ann Bot 1999, 83:235-242.
14. Thompson L.K., Burgess C.L., Skinner E.N. Localization of phytochrome during peanut (Arachis hypogaea) gynophore and ovule development. Am J Bot 1992, 79:828-832.
15. Underwood C.V., Taylor H.M., Hoveland C.S. Soil physical factors affecting peanut pod development. Agron J 1971, 63:953-954.
16. Haegeman A., Jacob J., Vanholme B., Kyndt T., Mitreva M., Gheysen G. Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: the first transcriptome analysis of an Anguinid nematode. Mol Biochem Parasitol 2009, 167:32-40.
17. Bi Y.P., Liu W., Xia H., Su L., Zhao Z.C., Wan S.B., et al. EST sequencing and gene expression profiling of cultivated peanut (Arachis hypogaea). Genome 2010, 53:832-839.
18. Tirumalaraju S.V., Jain M., Gallo M. Differential gene expression in roots of nematode-resistant and -susceptible peanut (Arachis hypogaea L.) cultivars in response to early stages of peanut root-knot nematode (Meloidogyne arenaria) parasitization. Plant Physiol 2011, 168:481-492.
19. Payton P., Kottapalli K.R., Rowland D., Faircloth W., Guo B.Z., Burow M., et al. Gene expression profiling in peanut using high density oligonucleotide microarrays. BMC Genomics 2009, 10:265-276.
20. Zhang J., Liang S., Duan J., Wang J., Chen S., Cheng Z., et al. De novo assembly and characterization of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 2012, 13:90.
21. Guo B.Z., Chen X.P., Dang P., Scully B.T., Liang X.Q., Holbrook C.C., et al. Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection. BMC Dev Biol 2008, 8:12-28.
22. Wang T., Chen X.P., Li H.F., Liu H.Y., Hong Y.B., Yang Q.L., et al. Transcriptome identification of the resistance-associated genes (RAGs) to Aspergillus flavus infection in pre-harvested peanut (Arachis hypogaea). Funct Plant Biol 2012, 10.1071/FP12143.
23. Chi X., Yang Q., Chen X., Wang J., Pan L., Chen M., et al. Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS One 2011, 6(11):e27530.
24. Wang T., Zhang E.H., Chen X.P., Li L., Liang X.Q. Identification of seed proteins associated with resistance to pre-harvested aflatoxin contamination in peanut (Arachis hypogaea L.). BMC Plant Biol 2010, 10:267-278.
25. Yang Q.S., Wu J.H., Li C.Y., Wei Y.R., Sheng O., Hu C.H., et al. Quantitative proteomic analysis reveals that antioxidation mechanisms contribute to cold tolerance in plantain (Musa paradisiaca L.) seedlings. Mol Cell Proteomics 2012, 11:1853-1869.
26. Dam S., Laursen B.S., Urnfeit J.H., Jochimsen B., Stærfeldt H.H., Friis C., et al. The proteome of seed development in the model legume Lotus japonicus. Plant Physiol 2009, 149:1325-1340.
27. Pedersen G.N., Dam S., Laursen B.S., Siegumfeldt A.L., Nielsen K., Goffard N., et al. Proteome analysis of pod and seed development in the model legume Lotus japonicus. J Proteome Res 2010, 9:5715-5726.
28. Gallardo K., Signor C.L., Vandekerckhove J., Thompson R.D., Burstin J., et al. Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol 2003, 133:664-682.
29. Gallardo K., Firnhaber C., Zuber H., Hericher D., Belghazi M., Henry C., et al. A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. Mol Cell Proteomics 2007, 6:2165-2179.
30. Hajduch M., Ganapathy A., Stein J.W., Thelen J.J. A systematic proteomic study of seed filling in soybean establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. Plant Physiol 2005, 137:1397-1419.
31. Finnie C., Melchior S., Roepstorff P., Svensson B. Proteome analysis of grain filling and seed maturation in barley. Plant Physiol 2002, 129:1308-1319.
32. Faurobert M., Mihr C., Bertin N., Pawlowski T., Negroni L., Sommerer N., et al. Major proteome variations associated with berry tomato pericarp development and ripening. Plant Physiol 2007, 143:1327-1346.
33. Giribaldi M., Perugini L., Sauvage F.X., Schubert A. Analysis of protein changes during grape berry ripening by 2-DE and MALDI-TOF. Proteomics 2007, 7:3l54-3170.
34. Zhang E.H., Chen X.P., Liang X.Q. Resolubilization of TCA precipitated plant proteins for 2-D electrophoresis. Electrophoresis 2011, 32:696-698.
35. Yan X.J., Wait R., Berkeiman T., Harry R.A., Westbrook J.A., Wheeler C.H., et al. A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry. Electrophoresis 2000, 21:3666-3672.
36. Chang S., Puryear J., Cairney J. A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Report 1993, 11:113-116.
37. Parry M.A.J., Andralojc P.J., Mitchell R.A.C., Madgwick P.J., Keys A.J. Manipulation of Rubisco: the amount, activity, function and regulation. J Exp Bot 2003, 54:1321-1333.
38. Portis J.A.R., Li C., Wang D., Salvucci M.E. Regulation of Rubisco activase and its interaction with Rubisco. J Exp Bot 2008, 59:1597-1604.
39. Bassi R., Sandona D., Croce R. Novel aspects of chlorophyll a/b-binding proteins. Physiol Plant 1997, 100:769-779.
40. Mayfield S.P., Bennoun P., Rochaix J.D. Expression of the nuclear encoded OEE1 protein is required for oxygen evolution and stability of photosystem II particles in Chlamydomonas reinhardtii. EMBO J 1987, 6:313-318.
41. Mayfield S.P., Rahire M., Frank G., Zuber H., Rochaix J.D. Expression of the nuclear OEE2 gene is required for high levels of photosynthetic oxygen evolution in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 1987, 84:749-753.
42. Ubbink M., Ejdeback M., Karlsson B.G., Bendall D.S. The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics. Structure 1998, 6:323-335.
43. Halpin C., Knight M.E., Foxon G.A., Campbell M.M., Boudet A.M., Boon J.J., et al. Manipulation of lignin quality by down regulation of cinnamyl alcohol dehydrogenase. Plant J 1994, 6:339-350.
44. Kim S.J., Kim M.R., Bedgar D.L., Moinuddin S.G.A., Cardenas C.L., Davin L.B., et al. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc Natl Acad Sci U S A 2004, 101:1455-1460.
45. Zubieta C., Kota P., Ferrer J.L., Dixon R.A., Noel J.P. Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase. Plant Cell 2002, 14:1265-1277.
46. Moon J., Parry G., Estelle1 M. The ubiquitin-proteasome pathway and plant development. Plant Cell 2004, 16:3181-3195.
47. Feng S., Shen Y., Sullivan J.A., Rubio V., Xiong Y., Sun T.P., et al. Arabidopsis CAND1, an unmodified CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasome-mediated protein degradation. Plant Cell 2004, 16:1870-1882.
48. Hellmann H., Estelle M. Plant development: regulation by protein degradation. Science 2002, 297:793-797.
49. Doherty F.J., Dawson S., Mayer R.J. The ubiquitinproteasome pathway of intracellular proteolysis. Essays Biochem 2002, 38:51-63.
50. Kurepa J., Smalle J.A. Structure, function and regulation of plant proteasomes. Biochimie 2008, 90:324-335.
51. Ozga J.A., Reinecke D.M. Hormonal interactions in fruit development. J Plant Growth Regul 2003, 22:73-81.
52. Clough R.C., Beebe E.T.J., Lohman K.N., Marita J.M., Walker J.M., Gatz C., et al. Sequences within both the N- and C-terminal domains of phytochrome A are required for Pfr ubiquitination and degradation. Plant J 1999, 17:155-167.
53. Osterlund M.T., Hardtke C.S., Wei N., Deng X.W. Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 2000, 405:462-466.
54. Vierstra R.D. The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends Plant Sci 2003, 8:1360-1385.
55. Suzuki G., Yanagawa Y., Kwok S.F., Matsui M., Deng X.W. Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant that acts together with COP1 and the COP9 signalosome in repressing photomorphogenesis. Genes Dev 2002, 16:554-559.
56. Santner A., Estelle M. The ubiquitin-proteasome system regulates plant hormone signaling. Plant J 2010, 61:1029-1040.
57. Kepinski S., Leyser O. Ubiquitination and auxin signaling: a degrading story. Plant Cell 2002, 14:S81-S95.
58. Dharmasiri S., Estelle M. The role of regulated protein degradation in auxin response. Plant Mol Biol 2002, 49:401-409.
59. Ramos J.A., Zenser N., Leyser O., Callis J. Rapid degradation of auxin/indoleacetic acid proteins requires conserved amino acids of domain II and is proteasome dependent. Plant Cell 2001, 13:2349-2360.
60. Smalle J., Kurepa J., Yang P., Emborg T.J., Babyichuk E., Kushnir S., et al. The pleiotropic role of the 26S proteasome subunit RPN10 in Arabidopsis thaliana growth and development supports a substrate specific function in abscisic acid signaling. Plant Cell 2003, 15:965-980.
61. Fu X.D., Richards D.E., Ait-Ali T., Hynes L.W., Ougham H., Peng J., et al. Gibberellin mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor. Plant Cell 2002, 14:3191-3200.
62. Smalle J., Kurepa J., Yang P., Babiychuk E., Kushnir S., Durski A., et al. Cytokinin growth responses in Arabidopsis involve the 26S proteasome subunit RPN12a. Plant Cell 2002, 14:17-32.
63. Farras R., Ferrando A., Jasik J., Kleinow T., Okresz L., Tiburcio A., et al. SKP1-SnRK protein kinase interactions mediate proteasomal binding of a plant SCF ubiquitin ligase. EMBO J 2001, 20:2742-2756.
64. Yanagawa Y., Hasezawa S., Kumagai F., Oka M., Fujimuro M., Naito T., et al. Cell cycle dependent dynamic change of 26S proteasome distribution in tobacco BY-2 cells. Plant Cell Physiol 2002, 43:604-613.
65. Dewitte W., Murray J.A.H. The plant cell cycle. Annu Rev Plant Biol 2003, 54:235-264.
66. Smalle J., Vierstra R.D. The ubiqutin 26S proteasome proteolytic pathway. Annu Rev Plant Biol 2004, 55:555-590.
67. Woo H.R., Chung K.M., Park J.H., Oh S.A., Ahn T., Hong S.H., et al. ORE9, an F-Box protein that regulates leaf senescence in Arabidopsis. Plant Cell 2001, 13:1779-1790.
68. Kim M., Ahn J.W., Jin U.H., Choi D., Paek K.H., Pai H.S. Activation of the programmed cell death pathway by inhibition of proteasome function in plants. J Biol Chem 2003, 278:19406-19415.
69. Asada K. Production and scavenging of reactive oxygen species in chloroplasts and their functions. Plant Physiol 2006, 141:391-396.
70. Liszkay A.K. Singlet oxygen production in photosynthesis. J Exp Bot 2005, 56:337-346.
71. Gechev T.S., Breusegem F.V., Stone J.M., Denev I., Laloi C. Reactive oxygen species as signals that modulate plant stress responses and programmed cell death. Bioessays 2006, 28:1091-1101.
72. Bhattacharjee S. Reactive oxygen species and oxidative burst: Role in stress, senescence and signal transduction in plant. Curr Sci 2005, 89:1113-1121.
73. Davletova S., Rizhsky L., Liang H., Zhong S.Q., Oliver D.J., Coutu J., et al. Cytosolic ascorbate peroxidase is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell 2005, 17:268-281.
74. Asada K. Ascorbate peroxidase-a hydrogen peroxide-scavenging enzyme in plants. Physiol Plant 1992, 85:235-241.
75. Ryan C.A. Proteolytic enzymes and their inhibitors in plant. Annu Rev Plant Physiol 1977, 24:173-196.
76. Olmeda G.F., Sakedo G., Monge S.R., Gomez L., Royo J., Carbonero P. Plant proteinaceous inhibitors of proteinases. Oxf Surv Plant Cell Mol Biol 1987, 4:275-334.
77. Putzai A., Grant G., Stewart J.C., Watt W.B. Isolation of soybean trypsin inhibitors by affinity chromatography on anhydro trypsin-Sepharose 4B. Anal Biochem 1988, 172:108-112.
78. Sin S.F., Yeung E.C., Chye M.L. Downregulation of Solanum americanum genes encoding proteinase inhibitor II causes defective seed development. Plant J 2006, 45:58-70.
79. Baumgartmer B., Chrispeels M.J. Partial characterization of a protease inhibitor which inhibits the major endopeptidase present in the cotyledons of mung bean. Plant Physiol 1976, 58:1-6.
80. Poerio E., Carranzo L., Garzillo A.M., Buonocore V. A trypsin inhibitor from the water-soluble fraction of wheat kernel. Phytochemistry 1989, 28:1307-1311.
81. Welham T., Domoney C. Temporal and spatial activity of a promoter from a pea enzyme inhibitor gene and its exploitation for seed quality improvement. Plant Sci 2000, 159:289-299.
82. Solomon M., Belenghi B., Delledonne M., Menachem E., Levinea A. The involvement of cysteine proteases and protease inhibitor genes in the regulation of programmed cell death in plants. Plant Cell 1999, 11:431-443.
83. Eason J.R., Ryan D.J., Pinkney T.T., Donoghue E.M. Programmed cell death during flower senescence: isolation and characterization of cysteine proteinases from Sandersonia aurantiaca. Funct Plant Biol 2002, 29:1055-1064.
84. Misset O., Opperdoes F.R. Simultaneous purification of hexokinase, class-I fructose-bisphosphate aldolase, triosephosphate isomerase and phosphoglycerate kinase from Trypanosoma brucei. Eur J Biochem 1984, 144:475-483.
85. Gothel S.F., Marahiel M.A. Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 1999, 55:423-436.
86. Beers E.P., Woffenden B.J., Zhao C.G. Plant proteolytic enzymes: possible roles during programmed cell death. Plant Mol Biol 2000, 44:399-415.
87. Agrawal G.K., Thelen J.J. Large scale identification and quantitative profiling of phosphoproteins expressed during seed filling in oilseed rape. Mol Cell Proteomics 2006, 5:2044-2059.
88. Feng H.Z., Chen Q.G., Feng J., Zhang J., Yang X.H., Zuo J.R. Functional characterization of the Arabidopsis eukaryotic translation initiation factor 5A-2 that plays a crucial role in plant growth and development by regulating cell division, cell growth, and cell death. Plant Physiol 2007, 144:1531-1545.