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Plant Proteomics pp 361–377Cite as

Seed Proteomics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1072))

Abstract

Rather than providing a single specific protocol, the inclusive area of seed proteomics is reviewed; methods are described and compared and primary literature citations are provided. The limitations and challenges of proteomics as an approach to study seed biology are emphasized. The proteomic analysis of seeds encounters some specific problems that do not impinge on analyses of other plant cells, tissues, or organs. There are anatomic considerations. Seeds comprise the seed coat, the storage organ(s), and the embryonic axis. Are these to be studied individually or as a composite? The physiological status of the seeds must be considered; developing, mature, or germinating? If mature, are they quiescent or dormant? If mature and quiescent, then orthodox or recalcitrant? The genetic uniformity of the population of seeds being compared must be considered. Finally, seeds are protein-rich and the extreme abundance of the storage proteins results in a study-subject with a dynamic range that spans several orders of magnitude. This represents a problem that must be dealt with if the study involves analysis of proteins that are of “normal” to low abundance. Several different methods of prefractionation are described and the results compared.

“Seeds of every generation between our hands. And the promise to teach you the little I have learned so far”—Brooke Fraser.

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Abbreviations

DIGE:

Difference in gel electrophoresis

LC:

Liquid chromatography

MS:

Mass spectrometry

PAGE:

Polyacrylamide gel electrophoresis

SSP:

Seed storage proteins

References

  1. Kanei M, Horiguch G, Tsukaya H (2012) Stable establishment of cotyledon identity during embryogenesis in Arabidopsis by ANGUSTIFOA3 and HANABA TARANU. Development 139:2436–2446

    Article  PubMed  CAS  Google Scholar 

  2. Li J, Berger F (2012) Endosperm: food for humankind and fodder for scientific discoveries. New Phytol 195:290–305

    Article  PubMed  Google Scholar 

  3. Miernyk JA, Hajduch M (2011) Seed proteomics. J Proteomics 74:389–400

    Article  PubMed  CAS  Google Scholar 

  4. Miernyk JA, Petrova A, Olmedilla A et al (2011) Using proteomics to study sexual reproduction in angiosperms. Sex Plant Reprod 24:9–22

    Article  PubMed  CAS  Google Scholar 

  5. Herridge RP, Herridge RP, Day RC et al (2011) Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery. Plant Methods 7:3

    Article  PubMed  Google Scholar 

  6. Chibani K, Ali-Rachedi S, Job C et al (2006) Proteomic analysis of seed dormancy in Arabidopsis. Plant Physiol 142:1493–1510

    Article  PubMed  CAS  Google Scholar 

  7. Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171:501–523

    Article  PubMed  CAS  Google Scholar 

  8. Finkelstein R, Reeves W, Ariizumi T et al (2008) Molecular aspects of seed dormancy. Annu Rev Plant Biol 59:387–415

    Article  PubMed  CAS  Google Scholar 

  9. Balbuena TS, Jo L, Pieruzzi FP et al (2011) Differential proteome analysis of mature and germinated embryos of Araucaria angustifolia. Phytochemistry 72:302–311

    Article  PubMed  CAS  Google Scholar 

  10. Hortin GL, Sviridov D (2010) The dynamic range problem in the analysis of the plasma proteome. J Proteomics 73:629–636

    Article  PubMed  CAS  Google Scholar 

  11. Armirotti A, Damonte G (2010) Achievements and perspectives of top-down proteomics. Proteomics 10:3566–3576

    Article  PubMed  CAS  Google Scholar 

  12. Jacob RJ (2010) Bioinformatics for LC-MS/MS-based proteomics. Methods Mol Biol 658:61–91

    Article  PubMed  CAS  Google Scholar 

  13. May C, Brosseron F, Chartowski P et al (2011) Instruments and methods in proteomics. Methods Mol Biol 696:3–26

    Article  PubMed  CAS  Google Scholar 

  14. Thelen JJ, Miernyk JA (2012) The proteomic future: where mass spectrometry should be taking us. Biochem J 444:169–181

    Article  PubMed  CAS  Google Scholar 

  15. Rabilloud T (2012) The whereabouts of 2D gels in quantitative proteomics. Meth Mol Biol 893:25–35

    Article  CAS  Google Scholar 

  16. Nikolov M, Schmidt C, Urlaub H (2012) Quantitative mass spectrometry-based proteomics: an overview. Meth Mol Biol 893:85–100

    Article  CAS  Google Scholar 

  17. Weber H, Borisjuk L, Wobus U (2005) Molecular physiology of legume seed development. Annu Rev Plant Biol 56:253–279

    Article  PubMed  CAS  Google Scholar 

  18. Hajduch M, Matusova R, Houston N et al (2011) Comparative proteomics of seed maturation in oilseeds reveals differences in intermediary metabolism. Proteomics 11:1619–1629

    Article  PubMed  CAS  Google Scholar 

  19. Rajjou L, Duval M, Gallardo K et al (2012) Seed germination and vigor. Annu Rev Plant Biol 63:507–533

    Article  PubMed  CAS  Google Scholar 

  20. Moïse JA, Han S, Gudynaitę-Savitch L et al (2005) Seed coats: structure, development, composition, and biotechnology. In Vitro Cell Dev Biol Plant 41:620–644

    Article  Google Scholar 

  21. Houston NL, Hajduch M, Thelen JJ (2009) Quantitative proteomics of seed filling in castor: comparison with soybean and rapeseed reveals differences between photosynthetic and nonphotosynthetic seed metabolism. Plant Physiol 151:857–868

    Article  PubMed  CAS  Google Scholar 

  22. Campos FAP, Nogueira FCS, Cardoso K et al (2010) Proteome analysis of castor bean seeds. Pure Appl Chem 82:259–267

    Article  CAS  Google Scholar 

  23. Bewley JD (1997) Seed germination and dormancy. Plant Cell 9:1055–1066

    Article  PubMed  CAS  Google Scholar 

  24. Miernyk JA, Trelease RN (1981) Role of malate synthase in citric acid synthesis by maturing cotton embryos: a proposal. Plant Physiol 67:875–881

    Article  PubMed  CAS  Google Scholar 

  25. Miernyk JA, Dennis DT (1992) A developmental analysis of the enolase isozymes of Ricinus communis. Plant Physiol 99:748–750

    Article  PubMed  CAS  Google Scholar 

  26. Hajduch M, Casteel JE, Hurrelmeyer KE et al (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

    Article  PubMed  CAS  Google Scholar 

  27. Linkies A, Graeber K, Knight C et al (2010) The evolution of seeds. New Phytol 186:817–831

    Article  PubMed  CAS  Google Scholar 

  28. Berjak P, Pammenter NW (2008) From Avicennia to Zizania: seed recalcitrance in perspective. Ann Bot 101:213–228

    Article  PubMed  Google Scholar 

  29. Baskin CC, Baskin JM (1998) Seeds. Ecology, Biogeography, and Evolution of Dormancy and Germination. Academic, San Diego, p 666

    Google Scholar 

  30. Bewley JD, Black M (1994) Seeds. NY, Plenum Press, Physiology of Development and Germination. Second Ed., p 445

    Book  Google Scholar 

  31. Harlan JR (1992) Crops and Man. Am Soc Agron. Am Soc Crop Sci, Madison, WI, p 294

    Google Scholar 

  32. Arc E, Galland M, Cueff G et al (2011) Reboot the system thanks to protein post-translational modifications and proteome diversity: how quiescent seeds restart their metabolism to prepare seedling establishment. Proteomics 11:1606–1618

    Article  PubMed  CAS  Google Scholar 

  33. Weitbrecht K, Müller K, Leubner-Metzger G (2011) First off the mark: early seed germination. J Exp Bot 62:3289–3309

    Article  PubMed  CAS  Google Scholar 

  34. Kim HT, Tae C, Ung-Kyu R et al (2011) Mobilization of storage proteins in soybean seed (Glycine max L.) during germination and seedling growth. Biochim Biophys Acta 1814:1178–1187

    Article  PubMed  CAS  Google Scholar 

  35. Finnie C, Andersen B, Shahpiri A et al (2011) Proteomes of the barley aleurone layer: a model system for plant signalling and protein secretion. Proteomics 11:1595–1605

    Article  PubMed  CAS  Google Scholar 

  36. Müntz K, Belozersky MA, Dunaevsky YE et al (2001) Stored proteinases and the initiation of storage protein mobilization in seeds during germination and seedling growth. J Exp Bot 52:1741–1752

    Article  PubMed  Google Scholar 

  37. Graham IA (2008) Seed storage oil mobilization. Annu Rev Plant Biol 59:115–142

    Article  PubMed  CAS  Google Scholar 

  38. Natarajan S, Xu C, Bae H et al (2007) Proteomic and genomic characterization of Kunitz trypsin inhibitors in wild and cultivated soybean genotypes. J Plant Physiol 164:756–763

    Article  PubMed  CAS  Google Scholar 

  39. Natarajan S, Xu C, Bae H et al (2007) Proteomic and genetic analysis of glycinin subunits of sixteen soybean genotypes. Plant Physiol Biochem 45:436–444

    Article  PubMed  CAS  Google Scholar 

  40. Dias LLC, Balbuena TS, Silveira V et al (2010) Two-dimensional gel electrophoretic protein profile analysis during seed development of Ocotea catharinensis: a recalcitrant seed species. Braz J Plant Physiol 22:23–33

    Article  Google Scholar 

  41. Pawłowski TA (2010) Proteomic approach to analyze dormancy breaking of tree seeds. Plant Mol Biol 73:15–25

    Article  PubMed  Google Scholar 

  42. Osborne TB (1908) Our present knowledge of plant proteins. Science 28:417–427

    Article  PubMed  CAS  Google Scholar 

  43. Shewry PR, Tatham AS (1990) The prolamin storage proteins of cereal seeds: structure and evolution. Biochem J 267:1–12

    PubMed  CAS  Google Scholar 

  44. Xu JH, Messing J (2009) Amplification of prolamin storage protein genes in different subfamies of the Poaceae. Theor Appl Genet 119:1397–1412

    Article  PubMed  CAS  Google Scholar 

  45. Shewry PR, Napier JA, Tatham AS (1995) Seed storage proteins: structures and biosynthesis. Plant Cell 7:945–956

    PubMed  CAS  Google Scholar 

  46. Herman EM, Larkins BA (1999) Protein storage bodies and vacuoles. Plant Cell 11:601–614

    PubMed  CAS  Google Scholar 

  47. Lending CR, Larkins BA (1989) Changes in the zein composition of protein bodies during maize endosperm development. Plant Cell 1:1011–1023

    PubMed  CAS  Google Scholar 

  48. zur Nieden U, Neumann D, Manteuffel R et al (1982) Electron microscopic immunocytochemical localization of storage proteins in Vicia faba seeds. Eur J Cell Biol 26:228–233

    PubMed  CAS  Google Scholar 

  49. Burr B, Burr FA (1976) Zein synthesis in maize endosperm by polyribosomes attached to protein bodies. Proc Natl Acad Sci USA 73:515–519

    Article  PubMed  CAS  Google Scholar 

  50. Krishnan HB, White JA (1995) Morphometric analysis of rice seed protein bodies (implication for a significant contribution of prolamin to the total protein content of rice endosperm). Plant Physiol 109:1491–1495

    PubMed  CAS  Google Scholar 

  51. Chrispeels MJ, Higgins TJ, Spencer D (1982) Assembly of storage protein oligomers in the endoplasmic reticulum and processing of the polypeptides in the protein bodies of developing pea cotyledons. J Cell Biol 93:306–313

    Article  PubMed  CAS  Google Scholar 

  52. Bollini R, Vitale A, Chrispeels MJ (1983) In vivo and in vitro processing of seed reserve protein in the endoplasmic reticulum: evidence for two glycosylation steps. J Cell Biol 96:999–1007

    Article  PubMed  CAS  Google Scholar 

  53. Kumamaru T, Uemura Y, Inoue Y et al (2010) Vacuolar processing enzyme plays an essential role in the crystalline structure of gluten in rice seed. Plant Cell Physiol 51:38–46

    Article  PubMed  CAS  Google Scholar 

  54. Vestal ML (2011) The future of biological mass spectrometry. J Am Soc Mass Spectrom 22:953–959

    Article  PubMed  CAS  Google Scholar 

  55. Miernyk JA, Johnston ML (2012) Digging deeper into the seed proteome: pre-fractionation of total proteins. In: Agrawal GK, Rakwal R (eds) Seed development: Omics technologies toward improvement of seed quality and crop yield. Springer, Berlin

    Google Scholar 

  56. Ferreira RB, Franco E, Teixeira AR (1999) Calcium- and magnesium-dependent aggregation of legume seed storage proteins. J Agric Food Chem 47:3009–3015

    Article  PubMed  CAS  Google Scholar 

  57. Krishnan HB, Oehrle NW, Natarajan SS (2009) A rapid and simple procedure for the depletion of abundant storage proteins from legume seeds to advance proteome analysis: a case study using Glycine max. Proteomics 9:3174–3188

    Article  PubMed  CAS  Google Scholar 

  58. Miernyk JA, Johnston ML (2006) Chemical cross-linking immobilized-Concanavan A for use in proteomic analyses. Prep Biochem Biotechnol 36:203–213

    Article  PubMed  CAS  Google Scholar 

  59. Field JM, Shewry PR, Miflin BJ (1983) Aggregation states of alcohol-soluble storage proteins of barley, rye, wheat and maize. J Sci Food Agric 34:362–369

    Article  PubMed  CAS  Google Scholar 

  60. Righetti PG, Castagna A, Herbert B et al (2003) Prefractionation techniques in proteome analysis. Proteomics 3:1397–1407

    Article  PubMed  CAS  Google Scholar 

  61. Vincent D, Balesdent M-H, Gibon J et al (2009) Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE. Electrophoresis 32:4118–4136

    Article  Google Scholar 

  62. Richardson MR, Liu S, Ringham HN et al (2008) Sample complexity reduction for two-dimensional electrophoresis using solution isoelectric focusing prefractionation. Electrophoresis 29:2637–2644

    Article  PubMed  CAS  Google Scholar 

  63. Natarajan SS, Savithiry S, Krishnan HB et al (2009) An efficient extraction method to enhance analysis of low abundant proteins from soybean seed. Anal Biochem 394:259–268

    Article  PubMed  CAS  Google Scholar 

  64. Hirabayashi J (2004) Lectin-based structural glycomics: glycoproteomics and glycan profiling. Glycoconj J 21:35–40

    Article  PubMed  Google Scholar 

  65. Van Damme EJ (2011) Lectins as tools to select for glycosylated proteins. Methods Mol Biol 753:289–297

    Article  PubMed  Google Scholar 

  66. Maruyama N, Katsube T, Wada Y et al (1998) The roles of the N-linked glycans and extension regions of soybean beta-conglycinin in folding, assembly and structural features. Eur J Biochem 258:854–862

    Article  PubMed  CAS  Google Scholar 

  67. Boschetti E, Monsarrat B, Righetti PG (2007) The “Invisible Proteome”: how to capture the low abundance proteins via combinatorial ligand libraries. Curr Proteomics 4:198–208

    Article  CAS  Google Scholar 

  68. Boschetti E, Righetti PG (2009) The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 9:1492–1510

    Article  PubMed  CAS  Google Scholar 

  69. Boschetti E, Bindschedler LV, Tang C et al (2009) Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price. J Chromatogr A 1216:1215–1222

    Article  PubMed  CAS  Google Scholar 

  70. Boschetti E, Righetti PG (2008) The ProteoMiner in the proteomic arena: a non-depleting tool for discovering low-abundance species. J Proteomics 71:255–264

    Article  PubMed  CAS  Google Scholar 

  71. Fasoli E, D'Amato A, Kravchuk AV et al (2011) Popeye strikes again: the deep proteome of spinach leaves. J Proteomics 74:127–136

    Article  PubMed  CAS  Google Scholar 

  72. Chait BT (2011) Mass spectrometry in the postgenomic era. Annu Rev Biochem 80:239–246

    Article  PubMed  CAS  Google Scholar 

  73. Bandeira N, Nesvizhskii A, McIntosh M (2011) Advancing next-generation proteomics through computational research. J Proteome Res 10:2895

    Article  PubMed  CAS  Google Scholar 

  74. Gibbs PE, Strongin KB, McPherson A (1989) Evolution of legume seed storage proteins—a domain common to legumins and vicilins is duplicated in vicins. Mol Biol Evol 6:614–623

    PubMed  CAS  Google Scholar 

  75. Esen A (1990) An immunodominant site of gamma-zein1 is in the region of tandem hexapeptide repeats. J Protein Chem 9:453–460

    Article  PubMed  CAS  Google Scholar 

  76. Feeney KA, Wellner N, Gilbert SM et al (2003) Molecular structures and interactions of repetitive peptides based on wheat glutenin subunits depend on chain length. Biopolymers 72:123–131

    Article  PubMed  CAS  Google Scholar 

  77. Stevenson SE, Chu Y, Ozias-Akins P et al (2009) Validation of gel-free, label-free quantitative proteomics approaches: applications for seed allergen profiling. J Proteomics 72:555–566

    Article  PubMed  CAS  Google Scholar 

  78. Huang Y, Houston NL, Tovar-Mendez A et al (2010) A quantitative mass spectrometry-based approach for identifying protein kinase-clients and quantifying kinase activity. Anal Biochem 402:69–76

    Article  PubMed  CAS  Google Scholar 

  79. Lundgren DH, Hwang S-I, Wu L et al (2010) Role of spectral counting in quantitative proteomics. Expert Rev Proteomics 7:39–53

    Article  PubMed  CAS  Google Scholar 

  80. Farley AR, Link AJ (2009) Identification and quantification of protein posttranslational modifications. Methods Enzymol 463:725–763

    Article  PubMed  CAS  Google Scholar 

  81. Siuti N, Kelleher NL (2007) Decoding protein modifications using top-down mass spectrometry. Nat Methods 4:817–821

    Article  PubMed  CAS  Google Scholar 

  82. Agrawal GK, Thelen JJ (2009) A high-resolution two dimensional gel- and Pro-Q DPS-based proteomics workflow for phosphoprotein identification and quantitative profiling. Meth Mol Biol 527:3–19

    Article  CAS  Google Scholar 

  83. Lewandowska-Gnatowska E, Johnston M, Antoine W et al (2011) Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding. Phytochemistry 72:1285–1292

    Article  PubMed  CAS  Google Scholar 

  84. Nesvizhskii AI (2012) Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 12:1639–1655

    Article  PubMed  CAS  Google Scholar 

  85. Gache V, Waridel P, Winter C et al (2010) Xenopus meiotic microtubule-associated interactome. PLoS One 5:e9248

    Article  PubMed  Google Scholar 

  86. Sharon M (2010) How far can we go with structural mass spectrometry of protein complexes? J Am Soc Mass Spectrom 21:487–500

    Article  PubMed  CAS  Google Scholar 

  87. Heeren RM, Ron MA, Smith DF et al (2009) Imaging mass spectrometry: hype or hope? J Am Soc Mass Spectrom 20:1006–1014

    Article  PubMed  CAS  Google Scholar 

  88. Stauber J, MacAleese L, Franck J et al (2010) On-tissue protein identification and imaging by MALDI-ion mobility mass spectrometry. J Am Soc Mass Spectrom 21:338–347

    Article  PubMed  CAS  Google Scholar 

  89. Lee YJ, Perdian DC, Song Z et al (2012) Use of mass spectrometry for imaging metabolites in plants. Plant J 70:81–95

    Article  PubMed  CAS  Google Scholar 

  90. Sparvero LJ, Amoscato AA, Dixon CE et al (2012) Mapping of phospholipids by MALDI imaging (MALDI-MSI): realities and expectations. Chem Phys Lipids 165:545–562

    Article  PubMed  CAS  Google Scholar 

  91. Schober Y, Guenther S, Spengler B et al (2012) High-resolution matrix-assisted laser desorption/ionization imaging of tryptic peptides from tissue. Rapid Commun Mass Spectrom 26:1141–1146

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The graphics were created by M.L. Johnston. Professor J.J. Thelen provided the antibodies used in Fig. 2d.

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Authors and Affiliations

  1. USDA, Agricultural Research Service, Plant Genetics Research Unit, Department of Biochemistry, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA

    Ján A. Miernyk

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  1. Ján A. Miernyk
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Editors and Affiliations

  1. Dept of Biochem & Molecular Bio, University of Cordoba, Cordoba, Spain

    Jesus V. Jorrin-Novo

  2. University of Tsukuba National Institute of Crop Science, Tsukuba, Japan

    Setsuko Komatsu

  3. Molecular Systems Biology, University of Vienna, Vienna, Austria

    Wolfram Weckwerth

  4. Dept. Molecular Systems Biology, University of Vienna, Vienna, Austria

    Stefanie Wienkoop

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Miernyk, J.A. (2014). Seed Proteomics. In: Jorrin-Novo, J., Komatsu, S., Weckwerth, W., Wienkoop, S. (eds) Plant Proteomics. Methods in Molecular Biology, vol 1072. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-631-3_26

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  • DOI: https://doi.org/10.1007/978-1-62703-631-3_26

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-630-6

  • Online ISBN: 978-1-62703-631-3

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