Gel-based comparative phosphoproteomic analysis on rice embryo during germination.

Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process.

[1]  Xiao-jing Wang,et al.  The Arabidopsis Ca(2+) -dependent protein kinase CPK12 negatively regulates abscisic acid signaling in seed germination and post-germination growth. , 2011, The New phytologist.

[2]  Jingyi Yang,et al.  Phosphorylation of the 12 S globulin cruciferin in wild-type and abi1-1 mutant Arabidopsis thaliana (thale cress) seeds. , 2007, The Biochemical journal.

[3]  L. An,et al.  Overexpression of profilin 3 affects cell elongation and F-actin organization in Arabidopsis thaliana , 2012, Plant Cell Reports.

[4]  Yuan Yao,et al.  Molecular analysis and expression patterns of the 14-3-3 gene family from Oryza sativa. , 2007, Journal of biochemistry and molecular biology.

[5]  T. Baskin,et al.  Inhibitors of Protein Kinases and Phosphatases Alter Root Morphology and Disorganize Cortical Microtubules , 1997, Plant physiology.

[6]  David Chevalier,et al.  14-3-3 and FHA domains mediate phosphoprotein interactions. , 2009, Annual review of plant biology.

[7]  W. Pratt,et al.  Hsp90-binding immunophilins in plants: the protein movers. , 2001, Trends in plant science.

[8]  Jialing Yao,et al.  Constructing the metabolic and regulatory pathways in germinating rice seeds through proteomic approach , 2011, Proteomics.

[9]  Mingui Zhao,et al.  Nitric Oxide Synthase-Dependent Nitric Oxide Production Is Associated with Salt Tolerance in Arabidopsis1[OA] , 2007, Plant Physiology.

[10]  Pingfang Yang,et al.  Proteomic analysis of rice (Oryza sativa) seeds during germination , 2007, Proteomics.

[11]  B. Svensson,et al.  Aspects of the barley seed proteome during development and germination. , 2004, Biochemical Society transactions.

[12]  Chuanping Yang,et al.  A shotgun phosphoproteomics analysis of embryos in germinated maize seeds , 2008, Planta.

[13]  M. Braun,et al.  Root hair formation: F-actin-dependent tip growth is initiated by local assembly of profilin-supported F-actin meshworks accumulated within expansin-enriched bulges. , 2000, Developmental biology.

[14]  M. Kashem,et al.  Possible involvement of phosphoinositide-Ca2+ signaling in the regulation of alpha-amylase expression and germination of rice seed (Oryza sativa L.). , 2000, Plant & cell physiology.

[15]  T. Pawłowski.  Proteome analysis of Norway maple (Acer platanoides L.) seeds dormancy breaking and germination: influence of abscisic and gibberellic acids , 2009, BMC Plant Biology.

[16]  Ganesh Kumar Agrawal,et al.  Plant phosphoproteomics: A long road ahead , 2006, Proteomics.

[17]  K. Shinozaki,et al.  Genetics and Phosphoproteomics Reveal a Protein Phosphorylation Network in the Abscisic Acid Signaling Pathway in Arabidopsis thaliana , 2013, Science Signaling.

[18]  Russell L. Jones,et al.  Sodium nitroprusside, cyanide, nitrite, and nitrate break Arabidopsis seed dormancy in a nitric oxide-dependent manner , 2006, Planta.

[19]  H. Hirt,et al.  Reactive oxygen species: metabolism, oxidative stress, and signal transduction. , 2004, Annual review of plant biology.

[20]  D. Breviario,et al.  The Plant Cytoskeleton: a Key Tool for Agro-Biotechnology , 2008 .

[21]  Kentaroh Watanabe,et al.  Characterization of a GDP-D-mannose 3'',5''-epimerase from rice. , 2006, Phytochemistry.

[22]  A. Altman,et al.  Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. , 2004, Trends in plant science.

[23]  Y. Karamanos,et al.  Regulation of De-N-Glycosylation Enzymes in Germinating Radish Seeds , 1996, Plant physiology.

[24]  Gerhard Leubner-Metzger,et al.  First off the mark: early seed germination. , 2011, Journal of experimental botany.

[25]  W. Jakoby,et al.  Glutathione S-transferase AA from rat liver. , 1976, Archives of biochemistry and biophysics.

[26]  Tom D. Bunney,et al.  14-3-3 protein is a regulator of the mitochondrial and chloroplast ATP synthase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Thomas A. DeFalco,et al.  Breaking the code: Ca2+ sensors in plant signalling. , 2009, The Biochemical journal.

[28]  H. Marschner,et al.  Magnesium deficiency and high light intensity enhance activities of superoxide dismutase, ascorbate peroxidase, and glutathione reductase in bean leaves. , 1992, Plant physiology.

[29]  S. Cutler,et al.  Abscisic acid: emergence of a core signaling network. , 2010, Annual review of plant biology.

[30]  Pingfang Yang,et al.  Analysis of Proteome Profile in Germinating Soybean Seed, and Its Comparison with Rice Showing the Styles of Reserves Mobilization in Different Crops , 2013, PloS one.

[31]  J. Bewley,et al.  Seed Germination and Dormancy. , 1997, The Plant cell.

[32]  M. Palmgren,et al.  The 14-3-3 protein interacts directly with the C-terminal region of the plant plasma membrane H(+)-ATPase. , 1997, The Plant cell.

[33]  X. Gu,et al.  Posttranslational regulation of pyruvate, orthophosphate dikinase in developing rice (Oryza sativa) seeds , 2006, Planta.

[34]  M. Nishiyama,et al.  Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity. , 1986, The Journal of biological chemistry.

[35]  Sixue Chen,et al.  Proteomic insights into seed germination in response to environmental factors , 2013, Proteomics.

[36]  R. Tenhaken,et al.  Genome-wide analysis of the UDP-glucose dehydrogenase gene family in Arabidopsis, a key enzyme for matrix polysaccharides in cell walls. , 2007, Journal of experimental botany.

[37]  Huawu Jiang,et al.  Isolation and characterization of two fructokinase cDNA clones from rice. , 2003, Phytochemistry.

[38]  J. Vandekerckhove,et al.  Proteomic analysis of arabidopsis seed germination and priming. , 2001, Plant physiology.

[39]  E. Sánchez de Jiménez,et al.  Regulation of acidic ribosomal protein expression and phosphorylation in maize. , 2002, Biochemistry.

[40]  D. Toroser,et al.  Site‐specific regulatory interaction between spinach leaf sucrose‐phosphate synthase and 14‐3‐3 proteins , 1998, FEBS letters.

[41]  G. Fincher.  Molecular and Cellular Biology Associated with Endosperm Mobilization in Germinating Cereal Grains , 1989 .

[42]  R. Furbank,et al.  The role of the sucrose transporter, OsSUT1, in germination and early seedling growth and development of rice plants. , 2006, Journal of experimental botany.

[43]  C. Job,et al.  Patterns of Protein Oxidation in Arabidopsis Seeds and during Germination1[w] , 2005, Plant Physiology.

[44]  P. Khurana,et al.  The wheat chloroplastic small heat shock protein (sHSP26) is involved in seed maturation and germination and imparts tolerance to heat stress. , 2012, Plant, cell & environment.

[45]  C. Lloyd,et al.  Plant Tubulin Phosphorylation And Its Role In Cell Cycle Progression , 2008 .

[46]  T. Pawłowski.  Proteomics of European beech (Fagus sylvatica L.) seed dormancy breaking: Influence of abscisic and gibberellic acids , 2007, Proteomics.

[47]  N. Fedoroff,et al.  Mitogen-activated protein kinase signaling in postgermination arrest of development by abscisic acid , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  C. Job,et al.  Proteomics reveal tissue‐specific features of the cress (Lepidium sativum L.) endosperm cap proteome and its hormone‐induced changes during seed germination , 2010, Proteomics.

[49]  Douglas J. H. Olson,et al.  Proteome analysis of embryo and endosperm from germinating tomato seeds , 2005, Proteomics.

[50]  M. Matsuoka,et al.  GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice. , 2004, The Plant journal : for cell and molecular biology.

[51]  Yuji Kamiya,et al.  Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. , 2005, The Plant journal : for cell and molecular biology.

[52]  M. Holdsworth,et al.  Nicotinamidase activity is important for germination. , 2007, The Plant journal : for cell and molecular biology.

[53]  F. Botha,et al.  Respiratory metabolism and gene expression during seed germination , 1992, Plant Growth Regulation.

[54]  J. Vandekerckhove,et al.  The Effect of α-Amanitin on the Arabidopsis Seed Proteome Highlights the Distinct Roles of Stored and Neosynthesized mRNAs during Germination1 , 2004, Plant Physiology.

[55]  C. Silflow,et al.  Microtubule Components of the Plant Cell Cytoskeleton , 1994, Plant physiology.

[56]  J. Soll,et al.  14-3-3 Proteins Form a Guidance Complex with Chloroplast Precursor Proteins in Plants , 2000, Plant Cell.

[57]  J. Buchner,et al.  Hsp90: Chaperoning signal transduction , 2001, Journal of cellular physiology.

[58]  F. Carrari,et al.  Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport. , 2004, Current opinion in plant biology.

[59]  B. Usadel,et al.  The Interconversion of UDP-Arabinopyranose and UDP-Arabinofuranose Is Indispensable for Plant Development in Arabidopsis[C][W][OA] , 2011, Plant Cell.

[60]  M. Hajduch,et al.  Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. , 2012, Journal of proteome research.

[61]  C. Job,et al.  Proteomic Investigation of the Effect of Salicylic Acid on Arabidopsis Seed Germination and Establishment of Early Defense Mechanisms1[W][OA] , 2006, Plant Physiology.

[62]  S. Denery-Papini,et al.  Analysis of wheat storage proteins by exhaustive sequential extraction followed by RP‐HPLC and nitrogen determination , 1998 .

[63]  L. Copeland,et al.  Hexose kinases from the plant cytosolic fraction of soybean nodules. , 1985, Plant physiology.

[64]  J. Callis,et al.  Regulation of Protein Degradation. , 1995, The Plant cell.

[65]  S. Cutler,et al.  In vitro Reconstitution of an ABA Signaling Pathway , 2009, Nature.

[66]  R. Kalla,et al.  Gibberellin-regulated expression of a myb gene in barley aleurone cells: evidence for Myb transactivation of a high-pI alpha-amylase gene promoter. , 1995, The Plant cell.

[67]  L. Copeland,et al.  Germination of Wheat: A Functional Proteomics Analysis of the Embryo , 2009 .

[68]  Y. Kamiya,et al.  Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis thaliana seeds: a comparative study on dormant and non-dormant accessions. , 2009, Plant & cell physiology.

[69]  C. Job,et al.  Seed germination and vigor. , 2012, Annual review of plant biology.

[70]  K. Browning,et al.  The Phosphorylation State of the Wheat Translation Initiation Factors eIF4B, eIF4A, and eIF2 Is Differentially Regulated during Seed Development and Germination* , 1998, The Journal of Biological Chemistry.