Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/22229
標題: Proteomic Analysis of Glutinous Rice and Improvement of Mass Spectrometric Approach for Identification of Phosphopeptides
糯性水稻蛋白質體分析與質譜鑑定磷酸化胜肽技術之改進
作者: 劉志偉
Liu, Chih-Wei
關鍵字: 糯稻
glutinous rice
澱粉生合成
質譜儀
電子轉移裂解
starch biosynthesis
Mass Spectrometry
electron-transfer dissociation
出版社: 分子生物學研究所
引用: Akihiro, T.; Mizuno, K.; Fujimura, T. Gene expression of ADP-glucose pyrophosphorylase and starch contents in rice cultured cells are cooperatively regulated by sucrose and ABA. Plant Cell Physiol. 2005, 46, 937-946. Asatsuma, S.; Sawada, C.; Itoh, K.; Okito, M.; Kitajima, A.; Mitsui, T. Involvement of alpha-amylase I-1 in starch degradation in rice chloroplasts. Plant Cell Physiol. 2005, 46, 858-869. Ball, S. G.; van de Wal, M. H. B. J.; Visser, R. G. F. Progress in understanding the biosynthesis of amylose. Trends Plant Sci. 1998, 3, 1360-1385. Ball, S.; Guan, H. P.; James, M.; Myers, A.; Keeling, P.; Mouille, G.; Buleon, A.; Colonna, P.; Preiss, J. From glycogen to amylopectin: a model for the biogenesis of the plant starch granule. Cell 1996, 86, 349-352. Ballicora, M. A.; Dubay, J. R.; Devillers, C. H.; Preiss, J. Resurrecting the ancestral enzymatic role of a modulatory subunit. J. Biol. Chem. 2005, 280, 10189-10195. Bancel, E.; Rogniaux, H.; Debiton, C.; Chambon, C.; Branlard, G. Extraction and proteome analysis of starch granule-associated proteins in mature wheat kernel (Triticum aestivum L.). J. Proteome Res. 2010, 9, 3299-3310. Beatty, M. K.; Rahman, A.; Cao, H.; Woodman, W.; Lee, M.; Myers, A. M.; James, M. G. Purification and molecular genetic characterization of ZPU1, a pullulanase-type starch-debranching enzyme from maize. Plant Physiol. 1999, 119, 255-266. Beckles, D. M.; Smith, A. M.; ap Rees, T. A cytosolic ADP-glucose pyrophosphorylase is a feature of graminaceous endosperms, but not of other starchstoring organs. Plant Physiol. 2001, 125, 818-827. Berkelman, T.; Stenstedt, T. in: Berkelman, T.; Stenstedt, T. (Eds.), Amersham Biosciences UK Limited, Buckinghamshire, England 1998. Bhave, M. R.; Lawrence, S.; Barton, C.; Hannah, L. C. Identification and molecular characterization of Shrunken-2 cDNA clones of maize. Plant Cell 1990, 2, 581-588. Blauth, S. L.; Kim, K. N.; Klucinec, J.; Shannon, J. C.; Thompson, D.; Guiltinan, M. Identification of Mutator insertional mutants of starch-branching enzyme 1 (sbe1) in Zea mays L. Plant Mol. Biol. 2002, 48, 287-297. Blauth, S. L; Yao, Y.; Klucinec, J. D.; Shannon, J. C.; Thompson, D. B.; Guilitinan, M. J. Identification of Mutator insertional mutants of starch-branching enzyme 2a in corn. Plant Physiol. 2001, 125, 1396-1405. Borovsky, D.; Smith, E. E.; Whelan, W. J. On the mechanism of amylase branching by potato Q-enzyme. Eur. J. Biochem. 1976, 62, 307-312. Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72, 248-254. Buleon, A.; Colonna, P.; Planchot, V.; Ball, S. Starch granules: structure and biosynthesis. Int. J. Biol. Macromol. 1998, 23, 85-112. Burton, R. A.; Jenner, H.; Carrangis, L.; Fahy, B. ; Fincher, G. B.; Hylton, C.; Laurie, D. A.; Parker, M.; Waite, D.; van Wegen, S.; Verhoeven, T.; Denyer, K. Starch granule initiation and growth are altered in barley mutants that lack isoamylase activity. Plant J. 2002, 31, 97-112. Burton, R. A.; Johnson, P. E.; Beckles, D. M.; Fincher, G. B.; Jenner, H. L.; Naldrett, M. J.; Denyer, K. Characterization of the genes encoding the cytosolic and plastidial forms of ADP-glucose pyrophosphorylase in wheat endosperm. Plant Physiol. 2002, 130, 1464-1475. Cao, H.; Imparl-Radosevich, J.; Guan, H.; Keeling, P. L.; James, M. G.; Myers, A. M. Identification of the soluble starch synthase activities of maize endosperm. Plant Physiol. 1999, 120, 205-216. Chen, C. L.; Li, C. C.; Sung, J. M. Carbohydrate metabolism enzymes in CO2-enriched developing rice grains of cultivars varying in grain size. Physiol. Plant 1994, 90, 79-85. Chen, H. M.; Chang, S. C.; Wu, C. C.; Cuo, T. S.; Wu, J. S.; Juang, R. H. Regulation of the catalytic behaviour of L-form starch phosphorylase from sweet potato roots by proteolysis. Physiol. Plant 2002, 114, 506-515. Chia, T.; Thorneycroft, D.; Chapple, A.; Messerli, G.; Chen, J.; Zeeman, S. C.; Smith, S. M.; Smith, A. M. A cytosolic glucosyltransferase is required for conversion of starch to sucrose in Arabidopsis leaves at night. Plant J. 2004, 37, 853-863. Choi, S. B.; Kim, K. H.; Kavakli, I. H.; Lee, S. K.; Okita, T. W. Transcriptional expression characteristics and subcellular localization of ADP-glucose pyrophosphorylase in the oil plant Perilla frutescens. Plant Cell Physiol. 2001, 42, 146-153. Commuri, P. D.; Keeling, P. L. Chain-length specificities of maize starch synthase I enzyme: studies of glucan affinity and catalytic properties. Plant J. 2001, 25, 475-486. Dauvillee, D.; Chochois, V.; Steup, M.; Haebel, S.; Eckermann, N.; Ritte, G.; Ral, J. P.; Colleoni, C.; Hicks, G.; Wattebled, F.; Deschamps, P.; d''Hulst, C.; Lienard, L.; Cournac, L.; Putaux, J. L.; Dupeyre, D.; Ball, S. G. Plastidial phosphorylase is required for normal starch synthesis in Chlamydomonas reinhardtii. Plant J. 2006, 48, 274-285. Delatte, T.; Umhang, M.; Trevisan, M.; Eicke, S.; Thorneycroft, D.; Smith, S. M.; Zeeman, S. C. Evidence for distinct mechanisms of starch granule breakdown in plants. J. Biol. Chem. 2006, 281, 12050-12059. Deng, X.; Hahne, T.; Schroder, S.; Redweik, S.; Nebija, D.; Schmidt, H.; Janssen, O.; Lachmann, B.; Watzig, H. The challenge to quantify proteins with charge trains due to isoforms or conformers. Electrophoresis 2012, 33, 263-269. Denyer, K.; Dunlap, F.; Thorbjornsen, T.; Keeling, P.; Smith, A. M. The major form of ADP-glucose pyrophosphorylase in maize endosperm is extra-plastidial. Plant Physiol. 1996, 112, 779-785. Dian, W.; Jiang, H.; Chen, Q.; Liu, F.; Wu, P. Cloning and characterization of the granule-bound starch synthase II gene in rice: gene expression is regulated by the nitrogen level, sugar and circadian rhythm. Planta 2003, 218, 261-268. Dian, W.; Jiang, H.; Wu, P. Evolution and expression analysis of starch synthase III and IV in rice. J. Exp. Bot. 2005, 56, 623-632. Dinges, J. R.; Colleoni, C.; James, M. G.; Myers, A. M. Mutational analysis of the pullulanase-type debranching enzyme of maize indicates multiple functions in starch metabolism. Plant Cell 2003, 15, 666-680. Doehlert, D. C.; Lambert, R. J. Metabolic characteristics associated with starch, protein and oil deposition in developing maize kernels. Crop Sci.1991, 31, 151-157. Ewart, M. H.; Siminovitch, D.; Briggs, D. R. Studies on the Chemistry of the Living Bark of the Black Locust in Relation to its Frost Hardiness. VIII. Possible Enzymatic Processes Involved in Starch-Sucrose Interconversions. Plant Physiol. 1954, 29, 407-413. Fu, Y.; Ballicora, M. A.; Leykam, J. F.; Preiss, J. Mechanism of reductive activation of potato tuber ADP-glucose pyrophosphorylase. J. Biol. Chem. 1998, 273, 25045-25052. Fujita, N.; Hasegawa, H.; Taira, T. The isolation and characterization of a waxy mutant of diploid wheat (Triticum monococcum L.). Plant Sci. 2001, 160, 595-602. Fujita, N.; Kubo, A.; Francisco Jr., P. B.; Nakakita, M.; Harada, K.; Minaka, N.; Nakamura, Y. Purification, characterization, and cDNA structure of isoamylase from developing endosperm of rice. Planta 1999, 208, 283-293. Fujita, N.; Kubo, A.; Suh, D. S.; Wong, K. S.; Jane, J. L.; Ozawa, K.; Takaiwa, F.; Inaba, Y.; Nakamura, Y. Antisense inhibition of isoamylase alters the structure of amylopectin and the physicochemical properties of starch in rice endosperm. Plant Cell Physiol. 2003, 44, 607-618. Fujita, N.; Toyosawa, Y.; Utsumi, Y.; Higuchi, T.; Hanashiro, I.; Ikegami, A.; Akuzawa, S.; Yoshida, M.; Mori, A.; Inomata, K.; Inomata, R.; Miyao, A.; Hirochika, H.; Satoh, H.; Nakamura, Y. Characterization of pullulanase (PUL)-deficient mutants of rice (Oryza sativa L.) and the function of PUL on starch biosynthesis in the developing rice endosperm. J. Exp. Bot. 2009, 60, 1009-1023. Fujita, N.; Yoshida, M.; Asakura, N.; Ohdan, T.; Miyao, A.; Hirochika, H.; Nakamura, N. Function and characterization of starch synthase I using mutants in rice. Plant Physiol. 2006, 140, 1070-1084. Fujita, N.; Yoshida, M.; Kondo, T.; Saito, K.; Utsumi, Y.; Tokunaga, T.; Nishi, A.; Satoh, H.; Park, J. H.; Jane, J. L.; Miyao, A.; Hirochika, H.; Nakamura, Y. Characterization of SSIIIa-deficient mutants of rice: the function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm. Plant Physiol. 2007, 144, 2009-2023. Gao, M.; Wanat, J.; Stinard, P. S.; James, M. G.; Myers, A. M. Characterization of dull1, a maize gene coding for a novel starch synthase. Plant Cell 1998, 10, 399-412. Geigenberger, P. Regulation of Starch Biosynthesis in Response to a Fluctuating Environment. Plant Physiol. 2011, 155, 1566-1577. Geigenberger, P.; Kolbe, A.; Tiessen, A. Redox regulation of carbon storage and partitioning in response to light and sugars. J. Exp. Bot. 2005, 56, 1469-1479. Gorg, A.; Obermaier, C.; Boguth, G.; Weiss, W. Recent developments in two-dimensional gel electrophoresis with immobilized pH gradients: Wide pH gradients up to pH 12, longer separation distances and simplified procedures. Electrophoresis 1999, 20, 712-717. Greene, T. W.; Hannah, L. C. Maize endosperm ADP-glucose pyrophosphorylase SHRUNKEN2 and BRITTLE2 subunit interactions. Plant Cell 1998, 10, 1295-1306. Grimaud, F.; Rogniaux, H.; James, M. G.; Myers, A. M.; Planchot, V. Proteome and phosphoproteome analysis of starch granule-associated proteins from normal maize and mutants affected in starch biosynthesis. J. Exp. Bot. 2008, 59, 3395-3406. Guan, H.; Keeling, P. L. Starch biosynthesis: understanding the functions and interactions of multiple isozymes of starch synthase and branching enzyme. Trends Glycosci. Glycotechnol. 1998, 10, 307-319. Guan, H.; Li, P.; Imparl-Radosevich, J.; Preiss, J.; Keeling, P. Comparing the properties of Escherichia coli branching enzyme and maize branching enzyme. Arch. Biochem. Biophys. 1997, 342, 92-98. Han, Y.; Sun, F. J.; Rosales-Mendoza, S.; Korban, S. S. Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants. Gene 2007, 401, 123-130. Hanashiro, I.; Abe, J.; Hizukuri, S. A periodic distribution of the chain length of amylopectin as revealed by high-performance anion-exchange chromatography. Carbohydr. Res. 1996, 283, 151-159. Hanashiro, I.; Itoh, K.; Kuratomi, Y.; Yamazaki, M.; Igarashi, T.; Matsugasako, J.; Takeda, Y. Granule-bound starch synthase I is responsible for biosynthesis of extra-long unit chains of amylopectin in rice. Plant Cell Physiol. 2008, 49, 925-933. Hannah, L. C.; James, M. The complexities of starch biosynthesis in cereal endosperms. Curr. Opin. Biotechnol. 2008, 19, 160-165. Hannah, L. C.; Shaw, J. R.; Giroux, M. J.; Reyss, A.; Prioul, J. L.; Bae, J. M.; Lee, J. Y. Maize genes encoding the small subunit of ADP-glucose pyrophosphorylase. Plant Physiol. 2001, 127, 173-183. Hennen-Bierwagen, T. A.; Liu, F.; Marsh, R. S.; Kim, S.; Gan, Q.; Tetlow, I. J.; Emes, M. J.; James, M. G.; Myers, A. M. Starch biosynthetic enzymes from developing maize endosperm associate in multisubunit complexes. Plant Physiol. 2008, 146, 1892-1908. Hirano, H. Y.; Eiguchi, M.; Sano, Y. A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol. Biol. Evol. 1998, 15, 978-987. Hirose, T.; Ohdan, T.; Nakamura, Y.; Terao, T. Expression profiling of genes related to starch synthesis in rice leaf sheaths during the heading period. Physiol. Plant 2006, 128, 425-435. Hirose, T.; Terao, T. A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta 2004, 220, 9-16. Hwang, S. K.; Nishi, A.; Satoh, H.; Okita, T. W. Rice endosperm-specific plastidial alpha-glucan phosphorylase is important for synthesis of short-chain malto-oligosaccharides. Arch. Biochem. Biophys. 2010, 495, 82-92. Itoh, K.; Ozaki, H.; Okada, K.; Hori, H.; Takeda, Y.; Mitsui, T. Introduction of Wx transgene into rice wx mutants leads to both high- and low-amylose rice. Plant Cell Physiol. 2003, 44, 473-480. James, M. G.; Denyer, K.; Myers, A. M. Starch synthesis in the cereal endosperm. Curr. Opin. Plant Biol. 2003, 6, 215-222. James, M. G.; Robertson, D. S.; Myers, A. M. Characterization of the maize gene sugary1, a determinant of starch composition in kernels. Plant Cell 1995, 7, 417-429. Jane, J.; Chen, Y. Y.; Lee, L. F.; Mc Pherson, A. E.; Wong, K. S.; Radosavljevic, M.; Kasemsuwan, T. Effects of amylopectin branch chain length and amylase content on the gelatinization and pasting properties of starch. Cereal Chem. 1999, 76, 629-637. Jeng, T. L.; Tseng, T. H.; Wang, C. S.; Chen, C. L.; Sung, J. M. Starch biosynthesizing enzymes in developing grains of rice cultivar Tainung 67 and its sodium azide-induced rice mutant. Field Crop. Res. 2003, 84, 261-269. Jeng, T. L.; Wang, C. S.; Tseng, T. H.; Sung, J. M. Expression of granule-bound starch synthase in developing rice grain. J. Sci. Food Agric. 2007, 87, 2456-2463. Jenkins, P. J.; Cameron, R. E.; Donald, A. M. A universal feature in the structure of starch granules from different botanical sources. Starch 1993, 45, 417-420. Jenner, C. F.; Siwek, K.; Hawker, J. S. The synthesis of (14C) starch from (14C) sucrose in isolated wheat grains is dependent upon the activity of soluble starch synthase. J. Plant Physiol.1993, 20, 329-335. Jiang, H.; Dian, W.; Liu, F.; Wu, P. Molecular cloning and expression analysis of three genes encoding starch synthase II in rice. Planta 2004, 218, 1062-1070. Johnson, P. E.; Patron, N. J.; Bottrill, A. R.; Dinges, J. R.; Fahy, B. F.; Parker, M. L.; Waite, D. N.; Denyer, K. A low-starch barley mutant, riso16, lacking the cytosolic small subunit of ADP-glucose pyrophosphorylase, reveals the importance of the cytosolic isoform and the identity of the plastidial small subunit. Plant Physiol. 2003, 131, 684-696. Kleinert, P.; Kuster, T.; Arnold, D.; Jaeken, J.; Heizmann, C. W.; Troxler, H. Effect of glycosylation on the protein pattern in 2-D-gel electrophoresis. Proteomics 2007, 7, 15-22. Kubo, A.; Fujita, N.; Harada, K.; Matsuda, T.; Satoh, H.; Nakamura, Y. The starch debranching enzymes isoamylase and pullulanase are both involved in amylopectin biosynthesis in rice endosperm. Plant Physiol. 1999, 121, 399-410. Kubo, A.; Rahman, S.; Utsumi, Y.; Li, Z.; Mukai, Y.; Yamamoto, M.; Ugaki, M.; Harada, K.; Satoh, H.; Konik-Rose, C.; Morell, M.; Nakamura, Y. Complementation of sugary-1 phenotype in rice endosperm with the wheat isoamylase1 gene supports a direct role for isoamylase1 in amylopectin biosynthesis. Plant Physiol. 2005, 137, 43-56. Kudo, M. Genetical and thremmatological studies of characters, physiological or ecological, in the hybrids between ecological rice groups. Bull. Natl. Inst. Agric. Sci. Ser. 1968, 19, 1-84. Lee, S. K.; Hwang, S. K.; Han, M.; Eom, J. S.; Kang, H. G.; Han, Y.; Choi, S. B.; Cho, M. H.; Bhoo, S. H.; An, G.; Hahn, T. R.; Okita, T. W.; Jeon, J. S. Identification of the ADP-glucose pyrophosphorylase isoforms essential for starch synthesis in the leaf and seed endosperm of rice (Oryza sativa L.). Plant Mol. Biol. 2007, 65, 531-546. Li, Q. F.; Zhang, G. Y.; Dong, Z. W.; Yu, H. X.; Gu, M. H.; Sun, S. S.; Liu, Q. Q. Characterization of expression of the OsPUL gene encoding a pullulanase-type debranching enzyme during seed development and germination in rice. Plant Physiol. 2009, 47, 351-358. Li, Z.; Mouille, G.; Kosar-Hashemi, B.; Rahman, S.; Clarke, B.; Gale, K. R.; Appels, R.; Morell, M. K. The structure and expression of the wheat starch synthase III gene. Motifs in the expressed gene define the lineage of the starch synthase III gene family. Plant Physiol. 2000, 123, 613-624. Liang, J.; Zhang, J.; Cao, X. Grain sink strength may be related to the poor grain filling of Indica-Japonica rice (Oryza sativa) hybrids. Physiol. Plant 2001, 112, 470-477. Lloyd, J. R.; Kossmann, J.; Ritte, G. Leaf starch degradation comes out of the shadows. Trends Plant Sci. 2005, 10, 130-137. Lu, Y.; Sharkey, T. D. The importance of maltose in transitory starch breakdown. Plant Cell Environ. 2006, 29, 353-366. Lu, Y.; Sharkey, T. D. The role of amylomaltase in maltose metabolism in the cytosol of photosynthetic cells. Planta 2004, 218, 466-473. Morell, M. K.; Kosar-Hashemi, B.; Cmiel, M.; Samuel, M. S.; Chandler, P.; Rahman, S.; Buleon, A.; Batey, I. L.; Li, Z. Barley sex6 mutants lack starch synthase IIa activity and contain a starch with novel properties. Plant J. 2003, 34, 173-185. Morell, M. K.; Myers, A. M. Towards the rational design of cereal starches. Curr. Opin. Plant Biol. 2005, 8, 204-210. Myers, A. M.; Morell, M. K.; James, M. G.; Ball, S. G. Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol. 2000, 122, 989-997. Myers, A. M.; Morell, M. K.; James, M. G.; Ball, S. G. Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol. 2000, 122, 989-997. Nagai, Y. S.; Sakulsingharoj, C.; Edwards, G. E.; Satoh, H.; Greene, T. W.; Blakeslee, B.; Okita, T. W. Control of starch synthesis in cereals: metabolite analysis of transgenic rice expressing an up-regulated cytoplasmic ADPglucose pyrophosphorylase in developing seeds. Plant Cell Physiol. 2009, 50, 635-643. Nakamura, T.; Yamamori, M.; Hirano, H.; Hidaka, S.; Nagamine, T. Production of waxy (amylose-free) wheats. Mol. Gen. Genet. 1995, 248, 253-259. Nakamura, Y. Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: rice endosperm as a model tissue. Plant Cell Physiol. 2002, 43, 718-725. Nakamura, Y.; Francisco Jr., P. B.; Hosaka, Y.; Sato, A.; Sawada, T.; Kubo, A.; Fujita, N. Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol. Biol. 2005, 58, 213-227. Nakamura, Y.; Kubo, A.; Shimamune, T.; Matsuda, T.; Harada, K.; Satoh, H. Correlation between activities of starch debranching enzyme and a-polyglucan structure in endosperms of sugary-1 mutants of rice. Plant J. 1997, 12, 143-153. Nakamura, Y.; Sakurai, A.; Inaba, Y.; Kimura, K.; Iwasawa, N.; Nagamine, T. The fine structure of amylopectin in endosperm from Asian cultivated rice can be largely classified into two classes. Starch 2002, 54, 117-131. Nakamura, Y.; Umemoto, T.; Ogata, N.; Kuboki, Y.; Yano, M.; Sasaki, T. Starch debranching enzyme (R-enzyme or pullulanase) from developing rice endosperm: purification, cDNA and chromosomal localization of the gene. Planta 1996, 199, 209-218. Nelson, O.; Pan, D. Starch synthesis in maize endosperms. Ann. Rev. Plant Physiol. Mol. Biol.1995, 46, 475-497. Niittyla, T.; Comparot-Moss, S.; Lue, W. L.; Messerli, G.; Trevisan, M.; Seymour, M. D. J.; Gatehouse, J. A.; Villadsen, D.; Smith, S. M.; Chen, J.; Zeeman, S. C.; Smith, A. M. Similar protein phosphatases control starch metabolism in plants and glycogen metabolism in mammals. J. Biol. Chem. 2006, 281, 11815-11818. Nishi, A.; Nakamura, Y.; Tanaka, N.; Satoh, H. Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. Plant Physiol. 2001, 127, 459-472. Ohdan, T.; Francisco Jr., P. B.; Sawada, T.; Hirose, T.; Terao, T.; Satoh, H.; Nakamura, Y. Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J. Exp. Bot. 2005, 56, 3229-3244. Okita, T. W.; Nakata, P. A.; Anderson, J. M.; Sowokinos, J.; Morell, M.; Preiss, J. The subunit structure of potato tuber ADP glucose pyrophosphorylase. Plant Physiol. 1990, 93, 785-790. Okita, T.W. Is there an alternative pathway for starch synthesis? Plant Physiol. 1992, 100, 560-564. Palma, J. M.; Sandalio, L. M.; Corpas, F. J.; Romero-Puertas, M. C.; McCarthy, I.; del Rio, L. A. Plant peoteases, protein degradation, and oxidative stress: role of peroxisomes. Plant Physiol. Biochem. 2002, 40, 521-530. Paton, L. N.; Gerrard, J. A.; Bryson, W. G. Investigations into charge heterogeneity of wool intermediate filament proteins. J. Proteomics 2008, 71, 513-529. Patron, N. J.; Greber, B.; Fahy, B. F.; Laurie, D. A.; Parker, M. L.; Denyer, K. The lys5 mutations of barley reveal the nature and importance of plastidial ADP-Glc transporters for starch synthesis in cereal endosperm. Plant Physiol. 2004, 135, 2088-2097. Patron, N. J.; Smith, A. M.; Fahy, B. F.; Hylton, C. M.; Naldrett, M. J.; Rossnagel, B. G.; Denyer, K. The altered pattern of amylose accumulation in the endosperm of low-amylose barley cultivars is attributable to a single mutant allele of granule-bound starch synthase I with a deletion in the 5'-non-coding region. Plant Physiol. 2002, 130, 190-198. Perdivara, I.; Deterding, L. J.; Przybylski, M.; Tomer, K. B. Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: chemical artifact or post-translational modification? J. Am. Soc. Mass. Spectrom. 2010, 21, 1114-1117. Prioul, J. L.; Jeannette, E.; Reyss, A.; Gregory, N.; Giroux, M.; Hannah, L. C.; Causse, M. Expression of ADP-glucose pyrophosphorylase in maize (Zea mays L.) grain and source leaf during grain filling. Plant Physiol. 1994, 104, 179-187. Rabilloud, T.; Carpentier, G.; Tarroux, P. Improvement and simplification of low-background silver staining of proteins by using sodium dithionite. Electrophoresis 1988, 9, 288-291. Regina, A.; Kosar-Hashemi, B.; Li, Z.; Pedler, A.; Mukai, Y.; Yamamoto, M.; Gale, K.; Sharp, P. J.; Morell, M. K.; Rahman, S. Starch branching enzyme IIb in wheat is expressed at low levels in the endosperm compared to other cereals and encoded at a non-syntenic locus. Planta 2005, 222, 899-909. Rocher, J. P.; Lecharny, P. A.; Regss, A.; Joussaime, M. Genetic variability in carbon fixation, sucrose-p-synthase and ADP glucose pyrophosphorylase in maize plants of differing growth rate. Plant Physiol. 1989, 89, 416-420. Rockwell, K. R.; Huber, B. T. Biologically distinct conformations of Bcl-x can be resolved using 2D isoelectric focusing. Mol. Immunol. 2009, 46, 1605-1612. Roldan, I.; Wattebled, F.; Mercedes Lucas, M.; Delvalle, D.; Planchot, V.; Jimenez, S.; Perez, R.; Ball, S.; D'Hulst, C.; Merida, A.; The phenotype of soluble starch synthase IV defective mutants of Arabidopsis thaliana suggests a novel function of elongation enzymes in the control of starch granule formation. Plant J. 2007, 49, 492-504. Ryoo, N.; Yu, C.; Park, C. S.; Baik, M. Y.; Park, I. M.; Cho, M. H.; Bhoo, S. H.; An, G.; Hahn, T. R.; Jeon, J. S. Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). Plant Cell Rep. 2007, 26, 1083-1095. Sakulsingharoja, C.; Choi, S. B.; Hwang, S. K.; Edwards, G. E.; Bork, J.; Meyer, C. R.; Preiss, J.; Okita, T. W: Engineering starch biosynthesis for increasing rice seed weight: the role of the cytoplasmic ADP-glucose pyrophosphorylase. Plant Sci. 2004, 167, 1323-1333. Sano, Y. Differential regulation of waxy gene expression in rice endosperm. Theor. Appl. Genet. 1984, 64, 467-473. Sano, Y.; Katsumata, M.; Okuno, K.; Genetic studies of speciation in cultivated rice. 5. Inter- and intraspecific differentiation in the waxy gene expression of rice. Euphytica 1986, 35, 1-9. Satoh, H.; Nishi, A.; Yamashita, K.; Takemoto, Y.; Tanaka, Y.; Hosaka, Y.; Sakurai, A.; Fujita, N.; Nakamura, Y. Starch-branching enzyme I-deficient mutation specifically affects the structure and properties of starch in rice endosperm. Plant Physiol. 2003, 133, 1111-1121. Satoh, H.; Shibahara, K.; Tokunaga, T.; Nishi, A.; Tasaki, M.; Hwang, S. K.; Okita, T. W.; Kaneko, N.; Fujita, N.; Yoshida, M.; Hosaka, Y.; Sato, A.; Utsumi, Y.; Ohdan, T.; Nakamura, Y. Mutation of the plastidial alpha-glucan phosphorylase gene in rice affects the synthesis and structure of starch in the endosperm. Plant Cell 2008, 20, 1833-1849. Sawada, T.; Francisco Jr., P. B.; Aihara, S.; Utsumi, Y.; Yoshida, M.; Oyama, Y.; Tsuzuki, M.; Satoh, H.; Nakamura, Y. Chlorella starch branching enzyme II (BEII) can complement the function of BEIIb in rice endosperm. Plant Cell Physiol. 2009, 50, 1062-1074. Scheible, W. R.; Gonzalez-Fontes, A.; Lauerer, M.; Muller-Rober, B.; Caboche, M.; Stitt, M. Nitrate acts as a signal to induce organic acid metabolism and repress starch metabolism in tobacco. Plant Cell 1997, 9, 783-798. Shannon, J. C.; Pien, F. M.; Cao, H.; Liu, K. C. Brittle-1, an adenylate translocator, facilitates transfer of extraplastidial synthesized ADP-glucose into amyloplasts of maize endosperms. Plant Physiol. 1998, 117, 1235-1252. Shimomura, S.; Nagai, M.; Fukui, T. Comparative glucan specificities of two types of spinach leaf phosphorylase. J. Biochem. 1982, 91, 703-717. Sikka, V. K.; Choi, S. B.; Kavakli, H.; Sakulsingharoj, C.; Gupta, S.; Ito, H.; Okita, T. W. Subcellular compartmentation and allosteric regulation of the rice endosperm ADP glucose pyrophosphorylase. Plant Sci. 2001, 161, 461-468. Slattery, C. J.; Kavakli, I. H.; Okita, T. W. Engineering starch for increased quantity and quality. Trends Plant Sci. 2000, 5, 1360-1385. Smidansky, E. D.; Clancy, M.; Meyer, F. D.; Lanning, S. P.; Blake, N. K.; Talbert, L. E.; Giroux, M. J.; Enhanced ADP-glucose pyrophosphorylase activity in wheat endosperm increases seed yield. Proc. Natl. Acad. Sci. U S A 2002, 99, 1724-1729. Smidansky, E. D.; Martin, J. M.; Hannah, L. C.; Fischer, A. M.; Giroux, M. J. Seed yield and plant biomass increases in rice are conferred by deregulation of endosperm ADP-glucose pyrophosphorylase. Planta 2003, 216, 656-664. Smith, A. M.; Denyer, K.; Martin, C. The synthesis of the starch granule. Ann. Rev. Plant Physiol. Mol. Biol. 1997, 48, 67--87. Sokolov, L. N.; De'jardin, A.; Kleczkowski, L. A. Sugars and light/dark exposure trigger differential regulation of ADP-glucose pyrophosphorylase genes in Arabidopsis thaliana (thale cress). Biochem. J. 1998, 336, 681-687. Sonnewald, U.; Basner, A.; Greve, B.; Steup, M. A second L-type isozyme of potato glucan phosphorylase: cloning, antisense inhibition and expression analysis. Plant Mol. Biol. 1995, 27, 567-576. Stark, D. M.; Timmerman, K. P.; Barry, G.; Preiss, J.; Kishore, G. M. Regulation of the amount of starch in plant tissues by ADPglucose pyrophosphorylase. Science 1992, 258, 287-292. Stinard, P. S.; Robertson, D. S.; Schnable, P. S. Genetic isolation, cloning, and analysis of a Mutator - induced, dominant antimorph of the Maize amylase extender1 locus. Plant Cell 1993, 5, 1555-1566. Streb, S.; Delatte, T.; Umhang, M.; Eicke, S.; Schorderet, M.; Reinhardt, D.; Zeeman, S. C. Starch granule biosynthesis in Arabidopsis is abolished by removal of all debrancing enzymes but restored by the subsequent removal of an endoamylase. Plant Cell 2008, 20, 3448-3466. Szydlowski, N.; Ragel, P.; Raynaud, S.; Lucas, M. M.; Roldan, I. Montero, M.; Munoz, F. J.; Ovecka, M.; Bahaji, A.; Planchot, V.; Pozueta-Romero, J.; D'Hulst, C.; Merida, A. Starch granule initiation in Arabidopsis requires the presence of either class IV or class III starch synthases. Plant Cell 2009, 21, 2443-2457. Tanaka, N.; Fujita, N.; Nishi, A.; Satoh, H.; Hosaka, Y.; Ugaki, M.; Kawasaki, S.; Nakamura, Y. The structure of starch can be manipulated by changing the expression levels of starch branching enzyme IIb in rice endosperm. Plant Biotechnol. J. 2004, 2, 507-516. Tester, R. F.; Karkalas, J.; Qi, X. Starch structure and digestibility enzymeestructure relationship. Worlds Poult. Sci. J. 2004, 60, 186-195. Tetlow, I. J.; Morell, M. K.; Emes, M. J. Recent developments in understanding the regulation of starch metabolism in higher plants. J. Exp. Bot. 2004, 55, 2131-2145. Tetlow, I. J.; Wait, R.; Lu, Z.; Akkasaeng, R.; Bowsher, C. G.; Esposito, S.; Kosar-Hashemi, B.; Morell, M. K.; Emes, M. J. Protein phosphorylation in amyloplasts regulates starch branching enzyme activity and protein-protein interactions. Plant Cell 2004, 16, 694-708. Thompson, D. B. On the non-random nature of amylopectin branching. Carbohydr. Polym. 2000, 43, 223-239. Thorbjornsen, T.; Villand, P.; Denyer, K.; Olsen, O. A.; Smith, A. M. Distinct isoforms of ADP glucose pyrophosphorylase occur inside and outside the amyloplasts in barley endosperm. Plant J. 1996, 10, 243-250. Tickle, P.; Burrell M. M.; Coates, S. A.; Emes, M. J.; Tetlow, I. J.; Bowsher, C. G. Characterization of plastidial starch phosphorylase in Triticum aestivum L. endosperm. J. Plant Physiol. 2009, 166, 1465-1478. Tiessen, A.; Hendriks, J. H. M.; Stitt, M.; Branscheid, A.; Gibon, Y.; Farre', E. M.; Geigenberger, P. Starch synthesis in potato tubers is regulated by post-translational redox modification of ADP-glucose pyrophosphorylase: a novel regulatory mechanism linking starch synthesis to the sucrose supply. Plant Cell 2002, 14, 2191-2213. Tiessen, A.; Prescha, K.; Branscheid, A.; Palacios, N.; McKibbin, R.; Halford, N. G.; Geigenberger, P. Evidence that SNF1-related kinase and hexokinase are involved in separate sugar-signalling pathways modulating post-translational redox activation of ADP-glucose pyrophosphorylase in potato tubers. Plant J. 2003, 35, 490-500. Tsai, C. Y. The function of waxy locus in starch synthesis in maize endosperm. Biochem. Genet. 1974, 11, 83-96. Umemoto, T.; Aoki, N.; Lin, H.; Nakamura, Y.; Inouchi, N.; Sato, Y.; Yano, M.; Hirabayashi, H.; Maruyama, S. Natural variation in rice starch synthase IIa affects enzyme and starch properties. Funct. Plant Biol. 2004, 31, 671-684. Umemoto, T.; Nakamura, Y.; Satoh, H.; Terashima, K.; Differences in amylopectin structure between two rice varieties in relation to the effects of temperature during grain-filling. Starch - Starke 1999, 51, 58-62. Umemoto, T.; Yano, M.; Satoh, H.; Shomura, A.; Nakamura, Y. Mapping of a gene responsible for the difference in amylopectin structure between japonica-atype and indica-type rice varieties. Theor. Appl. Genet. 2002, 104, 1-8. Van Camp, W. Yield enhancement genes: seeds for growth. Curr. Opin. Biotechnol. 2005, 16, 147-153. Vrinten, P. L.; Nakamura, T. Wheat granule-bound starch synthase I and II are encoded by separate genes that are expressed in different tissues. Plant Physiol. 2000, 122, 255-264. Wang, C. S.; Tseng, T. H.; Lin, C. Y. Rice biotech research at the Taiwan Agricultural Research Institute. APBN. 2002, 6, 950-956. Wang, Z. Y.; Zheng, F. Q.; Shen, G. Z.; Goa, J. P.; Snustad, D. P.; Li, M. G.; Zhang, J. L.; Hong, M. M. The amylase content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J.1995, 7, 613-622. Wang, Z.; Chen, X.; Wang, J.; Liu, T.; Liu, Y.; Zhao, L.; Wang, G. Increasing maize seed weight by enhancing the cytoplasmic ADPglucose pyrophosphorylase activity in transgenic plants. Plant Cell Tiss. Organ. Cult. 2007, 88, 83-92. Wei, M. L.; Sung, J. M. Carbohydrate metabolism enzymes in developing grains of rice cultured in solution with calcium supplement. Crop Sci. 1993, 33, 174-177. Yamamori, M.; Fujita, S.; Hayakawa, K.; Matsuki, J.; Yasui, T. Genetic elimination of a starch granule protein, SGP-1, of wheat generates an altered starch with apparent high amylose. Theor. Appl. Genet. 2000, 101, 21-29. Yamanouchi, H.; Nakamura, Y. Organ specificity of isoforms of starch branching enzyme (Q-enzyme) in rice. Plant Cell Physiol. 1992, 33, 985-991. Yoo, S. H.; Jane, J. Structural and physical characteristics of waxy and other wheat starches. Carbohydr. Polym. 2002, 49, 297-305. Young, G. H.; Chen, H. M.; Lin, C. T.; Tseng, K. C.; Wu, J. S.; Juang, R. H. Site-specific phosphorylation of L-form starch phosphorylase by the protein kinase activity from sweet potato roots. Planta 2006, 223, 468-478. Yu, T. S.; Zeeman, S. C.; Thorneycroft, D.; Fulton, D. C.; Dunstan, H.; Lue, W. L.; Hegemann, B.; Tung, S. Y.; Umemoto, T.; Chapple, A.; Tsai, D. L.; Wang, S. M.; Smith, A. M.; Chen, J.; Smith, S. M. alpha-Amylase is not required for breakdown of transitory starch in Arabidopsis leaves. J. Biol. Chem. 2005, 280, 9773-9779. Yun, S. H.; Matheson, N. K. Structure of the amylopectins of waxy, normal, amylose-extender, and wx:ae genotypes and of the phytoglycogen of maize. Carbohydr. Res. 1993, 243, 307-321. Zeeman, S. C.; Smith, S. M.; Smith, A. M. The diurnal metabolism of leaf starch. Biochem. J. 2007, 401, 13-28. Zeeman, S. C.; Thorneycroft, D.; Schupp, N.; Chapple, A.; Weck, M.; Dunstan, H.; Haldimann, P.; Bechtold, N.; Smith, A. M.; Smith, S. M. Plastidial alpha-glucan phosphorylase is not required for starch degradation in Arabidopsis leaves but has a role in the tolerance of abiotic stress. Plant Physiol. 2004, 135, 849-858. Zhang, X.; Colleoni, C.; Ratushna, V.; Sirghie-Colleoni, M.; James, M. G.; Myers, A. M. Molecular characterization demonstrates that the Zea mays gene sugary2 codes for the starch synthase isoform SSIIa. Plant Mol.
摘要: Rice (Oryza sativa) is one of the most important cereals in the world. The grains of the rice are the important source of starch, and starch biosynthesis is the major metabolic pathway in the developing grains. Starch consists of the amylose and amylopectin. The starch reserves of the rice grains generally contain more than 75% amylopectin; however, the abundance of amylose can affect the properties of starch in the grains. The amylase contents in the grains are usually used to evaluate the quality of rice. Therefore, the mechanisms of starch biosynthesis (especially amylase) are widely discussed and studied recently. In this study, we use the Tainung 67 (TNG67) and its sodium azide-induced mutant SA0419 as the investigated materials. The low amylose content in SA0419 grains (8%) is apparently different from TNG67 grains (20%). Moreover, the superior efficiency of starch biosynthesis and shorter developing period are observed in SA419. We want to resolve the regulated mechanisms of starch biosynthesis in rice endosperm from protein expression level and to provide the useful information for further agriculture breeding and gene study. Endosperm proteome of the grains of 14 days after anthesis (DAA) were extracted and separated by 2D-PAGE (pI 4-7). MS-based protein identification strategy was used to analyze the total proteome and differential-expression proteome of TNG67 and SA0419. The qualitative database of endosperm soluble proteome in TNG67 grains was established, and 620 out of 726 protein spots were successful identified. Endosperm proteome major involved in carbohydrate metabolic process, and the final products of α-D-glucose-1P were produced and as the substrates for starch biosynthesis. Moreover, total 121 protein spots were determined as the differential-expression proteome between TNG67 and SA0419 after software analysis. The higher abundance of enzymes in SA0419 were used to produce the more α-D-glucose-1P, and high level of starch biosynthesis enzyme (2.7.7.27) were generated to produce the ADP-glucose and to accelerate the accumulations of starch. Furthermore, lack of granule-bound starch synthase (GBSS) in SA0419 is the major key factor to cause the low amylose content. Overall, the starch biosynthesis model in the rice endosperm was presented in this study. The increased in gluconeogenesis pathway and reduction of the other metabolism pathway in SA0419 elevated the substrate contents for starch biosynthesis. The enzymes of 2.7.7.27, 2.4.1.1 and debranching enzyme (PUL) was highly expressed to accelerate the accumulation of starch and shorten the developing periods. In the past decade, tandem mass spectrometry (MS/MS) has played a major role in the bottom-up approach of protein identification and post-translational modifications (PTMs) analysis. Collision-induced dissociation (CID) is the most widely used peptide fragmentation technique in protein identification; however, it has the limitations for PTMs analysis. The emerging ion activation method, electron-transfer dissociation (ETD), has been shown to be useful for investigating PTMs and identifying large peptides and small proteins. There are specific problems in double-charged phosphopeptides identification by CID and ETD methods, and lack of the unsuitable searching algorithms. Thus, in this study, we demonstrated that the ET/CID fragmentation is powerful for sequencing of doubly-charged phosphopeptides without spectra-processing and successfully improves the applications of ETD technique in phosphorylation analysis.
水稻是世界上最重要的穀類作物之一。水稻的澱粉儲存器官-穀粒(種子),是重要的澱粉來源,榖粒之充實內容物以澱粉為主。澱粉可分為直鏈性澱粉(amylose)與支鏈性澱粉(amylopectin),amylopectin是澱粉的主要成分,通常佔有75%以上。然而,amylose的含量可決定澱粉的特性,高含量amylose會造成飯粒之柔軟度、黏著度、色澤、光澤等食味品性質之下降,amylose含量亦常被用來作為米質之評估指標,所以,對於澱粉(特別是直鏈性澱粉)之合成因子廣受研究與探討。本研究以水稻台農67號(TNG67)及其糯性突變株SA0419作為研究材料,SA0419穀粒內的amylose含量只有8%;相對於TNG67穀粒所含20% amylose,具有明顯差異;另一方面,SA0419發育期的穀粒澱粉充實速率相對於TNG67較快速,且成熟期提早一星期。於此,欲從蛋白質表現層次解析、了解水稻胚乳澱粉生合成與調控的機制,以利後續的水稻育種與基因研究。 萃取抽穗後第14天的穀粒胚乳蛋白質體,透過二維凝膠電泳分離蛋白質點,對TNG67與SA0419的蛋白質體與差異表現蛋白質體進行全面的定性,建構TNG67穀粒胚乳可溶性蛋白質體全定性資料庫,共定性726個蛋白質點,其中620個蛋白質點可成功鑑定其身分,此結果可幫助後人在研究其他水稻突變體胚乳差異表現蛋白質體,能快速得知其身分,作為參考資料庫使用。胚乳蛋白質體所參與的胚乳生理反應,主要是參與醣類相關代謝路徑,再細分這些牽涉路徑發現,酵素主要往α-D-glucose-1P的生成反應,可作為澱粉生合成的受質,供給澱粉生合成酵素使用。透過比對軟體判定SA0419的表現蛋白質體,共121個蛋白質點被判定為具有差異表現量,發現SA0419表現更多的酵素可幫助累積α-D-glucose-1P;且SA0419具有更高的澱粉生合成酵素表現量(2.7.7.27)幫助合成ADP-glucose,加速澱粉累積。另外,SA0419缺少GBSS表現,是影響SA0419直鏈性澱粉含量偏低的主因。最後透過人工重新判定所有參與醣類生合成酵素的表現量,提出水稻穀粒胚乳澱粉生合成路徑模型,分析SA0419具有比TNG67較快的澱粉充實速率、較短充實期的特性,是由於SA0419提升gluconeogenesis的生合成反應,並減低其他代謝路徑的表現,使得供給澱粉生合成的受質相對提升含量,再加上2.7.7.27、2.4.1.1與debranching enzyme(PUL)較強烈的表現,使澱粉累積加快,縮短充實期,並且不影響SA0419的總澱粉含量。 近年來,以質譜為基礎的蛋白質體學發展快速,其中,蛋白質身分鑑定與後轉譯修飾分析為質譜在蛋白質體學領域的主要研究內容,目前常用的碰撞引致裂解(collision-induced dissociation,CID),是最常應用於蛋白質身分鑑定分析,但對於後轉譯修飾分析上,仍存在許多缺點;電子轉移裂解(electron-transfer dissociation,ETD)雖是新興的片段化方法,較適合用於大片段的胜肽與後轉譯修飾研究,然而,碰撞引致裂解與電子轉移裂解對於正二價磷酸化鑑定分析仍有其各自缺陷,且有電腦比對演繹法軟體無法完全適應的問題,常造成正二價磷酸化胜肽鑑定上的困難,在本實驗,我們提出的ET/CID裂解策略,可以很容易鑑定到正二價磷酸化胜肽的身分,且不需任何圖譜處理,成功改善正二價磷酸化鑑定的效率,提升電子轉移裂解對於正二價磷酸化分析的應用性。
URI: http://hdl.handle.net/11455/22229
其他識別: U0005-1904201222361100
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-1904201222361100
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