丧失顶端优势的樟子松突变体蛋白质组学研究及Rad23基因克隆
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摘要
在高等植物中,顶芽优先生长而抑制侧芽生长的现象称为顶端优势。本研究选用经嫁接自然芽变枝条而获得的丧失顶端优势的樟子松突变体和取自同一株母树上的正常枝条嫁接而获得正常对照植株为实验材料。形态学观察表明突变体外部形态表现为没有明显的主干、大量侧枝生长、节间短、矮化、叶片短小等顶端优势丧失的特征。细胞学石蜡切片观察表明突变体顶芽分生组织变异较大,细胞多而排列不规则,分生区与成熟区之间层次感不明显,大部分分生组织细胞着色较深,正在进行着异常的快速分裂与分化。进一步通过2DE-ESI-MS/MS联用技术比较了二者枯芽在休眠时期、萌发时期、萌发后10d、萌发后15d四个不同生长期蛋白质组的差异,共鉴定49个具有明显表达差异的蛋白质点。GO分析表明,差异蛋白参与了胁迫应答、蛋白质代谢、发育调控、DNA和RNA代谢、电子能量传递和物质运输等众多复杂的生物学过程。经文献检索和生物信息学分析,从差异蛋白中筛选出的ABA诱导蛋白、顺乌头酸水化酶和Rad23可能在三个层次上级联通过泛素／26S蛋白酶体降解途径、应答ABA、调控胞质Fe2+离子浓度、参与植物顶端优势的调控,进而将其中处于较高调控层次的Rad23基因克隆并对其一级序列进行了初步分析,同时对Rad23进行了蛋白体外表达纯化和多克隆抗体制备。本论文为进一步分析植物顶端优势的分子机理提供了重要线索和依据。
In higher plants, apical dominance is the phenomenon whereby the main central stem of the plant is dominant over other side stems. In the present study, the natural loss of apical dominance Pinus sylvestris var. mongolica mutant and the wild type which by grafting the mutant and normal branches respectively were used as materials, and the mutant displayed the phenotypes with no obvious morphological trunk, a large number of side stems, shorter internode and leaves, and dwarf. The cell biology examination indicated that the meristem was dramatically changed in mutant, being with irregular cell arrangement, no obvious layer between meristem and mature tissue, and rapidly divisional and differentiated cells. Then 49 different proteins were successfully identified by further proteomics analysis of the apical buds using 2DE-ESI-MS/MS at different processes of development (including the dormancy period, the germinating period,10 days after germination,15 days after germination). GO analysis showed that these proteins were involved in stress response, protein metabolism, developmental regulation, DNA and RNA metabolism, electron energy transfer, material transport, and many other complex biological processes. Moreover, according to document retrieval and bioinformatics, abscisic acid-and stress-induced protein, cytoplasmic aconitate hydratase and Rad23 screened from the different proteins were likely to participated in ABA responding, Fe ion controlling and ubiquitin/26S protesome pathway to regulate apical dominance at cascade levels, thus Rad23 gene was cloned and made preliminary sequence analysis, then Rad23 protein was expressed and purified in vitro to raise polyclone antibody. This work will provide important clues and basis for further studying plant apical dominance.
In higher plants, apical dominance is the phenomenon whereby the main central stem of the plant is dominant over other side stems. In the present study, the natural loss of apical dominance Pinus sylvestris var. mongolica mutant and the wild type which by grafting the mutant and normal branches respectively were used as materials, and the mutant displayed the phenotypes with no obvious morphological trunk, a large number of side stems, shorter internode and leaves, and dwarf. The cell biology examination indicated that the meristem was dramatically changed in mutant, being with irregular cell arrangement, no obvious layer between meristem and mature tissue, and rapidly divisional and differentiated cells. Then 49 different proteins were successfully identified by further proteomics analysis of the apical buds using 2DE-ESI-MS/MS at different processes of development (including the dormancy period, the germinating period,10 days after germination,15 days after germination). GO analysis showed that these proteins were involved in stress response, protein metabolism, developmental regulation, DNA and RNA metabolism, electron energy transfer, material transport, and many other complex biological processes. Moreover, according to document retrieval and bioinformatics, abscisic acid-and stress-induced protein, cytoplasmic aconitate hydratase and Rad23 screened from the different proteins were likely to participated in ABA responding, Fe ion controlling and ubiquitin/26S protesome pathway to regulate apical dominance at cascade levels, thus Rad23 gene was cloned and made preliminary sequence analysis, then Rad23 protein was expressed and purified in vitro to raise polyclone antibody. This work will provide important clues and basis for further studying plant apical dominance.
引文
[1]Thimann, K., Skoog, F., On the inhibition of bud development and other functions of growth substance in Vicia faba. Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character 1934,114,317-339.
[2]Thimann, K., On the nature of inhibitions caused by auxin. American Journal of Botany 1937,24, 407-412.
[3]CLINE, M., Exogenous auxin effects on lateral bud outgrowth in decapitated shoots. Annals of Botany 1996,78,255-266.
[4]Snyder, W., Some responses of plants to 2,3,5-triiodobenzoic acid. Plant Physiology 1949,24, 195-206.
[5]Panigrahi, B., Audus, L., Apical dominance in Vicia faba. Annals of Botany 1966,30,457-473.
[6]Zenser, N., Ellsmore, A., Leasure, C., Callis, J., Auxin modulates the degradation rate of Aux/IAA proteins. Proceedings of the National Academy of Sciences of the United States of America 2001, 98,11795-11800.
[7]Snow, R., On the nature of correlative inhibition. New Phytologist 1937,36,283-300.
[8]Hillman, J., Math, V., Medlow, G., Apical dominance and the levels of indole acetic acid in Phaseolus lateral buds. Planta 1977,134,191-193.
[9]Palni, L., Burch, L., Horgan, R., The effect of auxin concentration on cytokinin stability and metabolism. Planta 1988,174,231-234.
[10]Eklof, S., Astot, C., Blackwell, J., Moritz, T., et al., Auxin-cytokinin interactions in wild-type and transgenic tobacco. Plant and Cell Physiology 1997,38,225-235.
[11]Li, C., Guevara, E., Herrera, J., Bangerth, F., Effect of apex excision and replacement by 1-naphthylacetic acid on cytokinin concentration and apical dominance in pea plants. Physiologia Plantarum 2006,94,465-469.
[12]Tanaka, M., Takei, K., Kojima, M., Sakakibara, H., et al., Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance. The Plant Journal 2006,45,1028-1036.
[13]Turnbull, C., Raymond, M., Dodd, I., Morris, S., Rapid increases in cytokinin concentration in lateral buds of chickpea (Cicer arietinum L.) during release of apical dominance. Planta 1997,202, 271-276.
[14]Booker, J., Sieberer, T., Wright, W., Williamson, L., et al., MAX1 encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoid-derived branch-inhibiting hormone. Developmental cell 2005,8,443-449.
[15]Sorefan, K., Booker, J., Haurogne, K., Goussot, M., et al., MAX4 and RMS1 are orthologous dioxygenase-like genes that regulate shoot branching in Arabidopsis and pea. Genes& development 2003,17,1469-1474.
[16]Snowden, K., Simkin, A., Janssen, B., Templeton, K., et al., The Decreased apical dominancel/Petunia hybrida CAROTENOID CLEAVAGE DIOXYGENASE8 gene affects branch production and plays a role in leaf senescence, root growth, and flower development. The Plant Cell 2005,17,746-759.
[17]Schwartz, S., Qin, X., Loewen, M., The biochemical characterization of two carotenoid cleavage enzymes from Arabidopsis indicates that a carotenoid-derived compound inhibits lateral branching. Journal of Biological Chemistry 2004,279,46940-46945.
[18]Gomez-Roldan, V., Fermas, S., Brewer, P., Puech-Pages, V., et al., Strigolactone inhibition of shoot branching. Nature 2008,455,189-194.
[19]Umehara, M., Hanada, A., Yoshida, S., Akiyama, K., et al., Inhibition of shoot branching by new terpenoid plant hormones. Nature 2008,455,195-200.
[20]Venter, J., Adams, M., Myers, E., Li, P., et al., The sequence of the human genome. science 2001, 291,1304-1351.
[21]Clark, B., Towards a total human protein map. Nature 1981,292,491.
[22]Pandey, A., Mann, M., Proteomics to study genes and genomes. Nature 2000,405,837-846.
[23]Swinbanks, D., Government backs proteome proposal. Nature 1995,378,653.
[24]Wasinger, V., Cordwell, S., Cerpa-Poljak, A., Yan, J., et al., Progress with gene-product mapping of the Mollicutes:Mycoplasma genitalium. Electrophoresis 2005,16,1090-1094.
[25]Park, O., Proteomic studies in plants. Journal of biochemistry and molecular biology 2004,37, 133-138.
[26]Thiellement, H., Plant proteomics:methods and protocols, Humana Pr Inc 2007.
[27]Supek, F., Peharec, P., Krsnik-Rasol, M., muc, T., Enhanced analytical power of SDS-PAGE using machine learning algorithms. Proteomics 2007,8,28-31.
[28]Braun, R., Kinkl, N., Beer, M., Ueffing, M., Two-dimensional electrophoresis of membrane proteins. Analytical and Bioanalytical Chemistry 2007,389,1033-1045.
[29]van den Broeck, H., America, A., Smulders, M., Gilissen, L., van der Meer, I., Staining efficiency of specific proteins depends on the staining method:Wheat gluten proteins. Proteomics 2008,8, 1880-1884.
[30]Witzel, K., Surabhi, G., Jyothsnakumari, G., Sudhakar, C., et al., Quantitative proteome analysis of barley seeds using ruthenium (Ⅱ)-tris-(bathophenanthroline-disulphonate) staining. J. Proteome Res 2007,6,1325-1333.
[31]Jacobsen, S., Grove, H., Jensen, K., S rensen, H., et al., Multivariate analysis of 2-DE protein patterns-Practical approaches. Electrophoresis 2007,28,1289-1299.
[32]Berth, M., Moser, F., Kolbe, M., Bernhardt, J., The state of the art in the analysis of two-dimensional gel electrophoresis images. Applied microbiology and biotechnology 2007,76,1223-1243.
[33]Maurer, M., Software analysis of two-dimensional electrophoretic gels in proteomic experiments. Current Bioinformatics 2006,1,255-262.
[34]Demianova, Z., Shimmo, M., P ys, E., Franssila, S., Baumann, M., Toward an integrated microchip sized 2-D polyacrylamide slab gel electrophoresis device for proteomic analysis. Electrophoresis 2006,28,422-428.
[35]Bohler, S., Bagard, M., Oufir, M., Planchon, S., et al., A DIGE analysis of developing poplar leaves subjected to ozone reveals major changes in carbon metabolism. Proteomics 2007,7,1584-1599.
[36]Deng, Z., Zhang, X., Tang, W., Oses-Prieto, J., et al., A proteomics study of brassinosteroid response in Arabidopsis. Molecular & Cellular Proteomics 2007,6,2058-2071.
[37]van Noorden, G., Kerim, T., Goffard, N., Wiblin, R., et al., Overlap of proteome changes in Medicago truncatula in response to auxin and Sinorhizobium meliloti. Plant Physiology 2007,144, 1115-1131.
[38]Gomez, S., Nishio, J., Faull, K., Whitelegge, J., The chloroplast grana proteome difined by intact mass measurements from LC-MS. Molecular & Cellular Proteomics 2002,1,46-59.
[39]D'Amici, G., Timperio, A., Zolla, L., Coupling of native liquid phase isoelectrofocusing and blue native polyacrylamide gel electrophoresis:a potent tool for native membrane multiprotein complex separation. J. Proteome Res 2008,7,1326-1340.
[40]Xi, J., Wang, X., Li, S., Zhou, X., et al., Polyethylene glycol fractionation improved detection of low-abundant proteins by two-dimensional electrophoresis analysis of plant proteome. Phytochemistry 2006,67,2341-2348.
[41]Cellar, N., Kuppannan, K., Langhorst, M., Ni, W., et al., Cross species applicability of abundant protein depletion columns for ribulose-1,5-bisphosphate carboxylase/oxygenase. Journal of Chromatography B 2008,861,29-39.
[42]Li, G., Nallamilli, B., Tan, F., Peng, Z., Removal of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endosperm. Electrophoresis 2008,29,604-617.
[43]Nowaczyk, M., Hebeler, R., Schlodder, E., Meyer, H., et al., Psb27, a cyanobacterial lipoprotein, is involved in the repair cycle of photosystem Ⅱ. The Plant Cell Online 2006,18,3121-3131.
[44]Palmblad, M., Mills, D., Bindschedler, L., Heat-shock response in Arabidopsis thaliana explored by multiplexed quantitative proteomics using differential metabolic labeling. J. Proteome Res 2008,7,780-785.
[45]Hebeler, R., Oeljeklaus, S., Reidegeld, K., Eisenacher, M., et al., Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N labeling and difference gel electrophoresis. Molecular & Cellular Proteomics 2008,7,108-120.
[46]Hartman, N., Sicilia, F., Lilley, K., Dupree, P., Proteomic complex detection using sedimentation. Anal. Chem 2007,79,2078-2083.
[47]Dunkley, T., Hester, S., Shadforth, I., Runions, J., et al., Mapping the Arabidopsis organelle proteome. Proceedings of the National Academy of Sciences of the United States of America 2006, 103,6518-6523.
[48]Nuhse, T., Bottrill, A., Jones, A., Peck, S., Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses. The Plant Journal 2007,51,931-940.
[49]Larrainzar, E., Wienkoop, S., Weckwerth, W., Ladrera, R., et al., Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress. Plant Physiology 2007,144,1495-1507.
[50]Zybailov, B., Rutschow, H., Friso, G, Rudella, A., et al., Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One 2008,3, e1994.
[51]Lee, J., Garrett, W., Cooper, B., Shotgun proteomic analysis of Arabidopsis thaliana leaves. Journal of Separation Science 2007,30,2225-2230.
[52]Mann, M., Jensen, O., Proteomic analysis of post-translational modifications. Nature biotechnology 2003,21,255-261.
[53]Kia-Ki, H., Martinage, A., Post-translational chemical modification (s) of proteins. International Journal of Biochemistry 1992,24,19-28.
[54]Appel, R., Bairoch, A., Post-translational modifications:A challenge for proteomics and bioinformatics. Proteomics 2004,4,1525-1526.
[55]Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A., et al., Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Molecular Systems Biology 2008,4,193.
[56]Tan, F., Li, G., Chitteti, B., Peng, Z., Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa). Proteomics 2007,7,4511-4527.
[57]Heazlewood, J., Durek, P., Hummel, J., Selbig, J., et al., PhosPhAt:a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Research 2007,1-7.
[58]Lemaire, S., Michelet, L., Zaffagnini, M., Massot, V., Issakidis-Bourguet, E., Thioredoxins in chloroplasts. Current Genetics 2007,51,343-365.
[59]Winger, A., Taylor, N., Heazlewood, J., Day, D., Millar, A., Identification of intra-and intermolecular disulphide bonding in the plant mitochondrial proteome by diagonal gel electrophoresis. Proteomics 2007,7,4158-4170.
[60]Alkhalfioui, F., Renard, M., Vensel, W., Wong, J., et al., Thioredoxin-linked proteins are reduced during germination of Medicago truncatula seeds. Plant Physiology 2007,144,1559-1579.
[61]Lefebvre, B., Furt, F., Hartmann, M., Michaelson, L., et al., Characterization of lipid rafts from Medicago truncatula root plasma membranes:a proteomic study reveals the presence of a raft-associated redox system. Plant Physiology 2007,144,402-418.
[62]Washburn, M., Wolters, D., Yates, J., Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature biotechnology 2001,19,242-247.
[63]Minic, Z., Jamet, E., Negroni, L., Arsene der Garabedian, P., et al., A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases. Journal of experimental botany 2007.
[64]Friedberg, E., Eukaryotic DNA repair:glimpses through the yeast Saccharomyces cerevisiae. BioEssays 2005,13,295-302.
[65]Prakash, S., Sung, P., Prakash, L., DNA repair genes and proteins of Saccharomyces cerevisiae. Annual review of genetics 1993,27,33-70.
[66]Batty, D., Wood, R., Damage recognition in nucleotide excision repair of DNA. Gene 2000,241, 193-204.
[67]de Laat, W., Incision Coordination in Nucleotide Excision Repair 1995.
[68]Lambertson, D., Chen, L., Madura, K., Pleiotropic defects caused by loss of the proteasome-interacting factors Rad23 and Rpn10 of Saccharomyces cerevisiae. Genetics 1999,153,69-79.
[69]Elsasser, S., Chandler-Militello, D., Muller, B., Hanna, J., Finley, D., Rad23 and Rpn10 serve as alternative ubiquitin receptors for the proteasome. Journal of Biological Chemistry 2004,279, 26817-26822.
[70]Guzder, S., Sung, P., Prakash, L., Prakash, S., Affinity of yeast nucleotide excision repair factor 2, consisting of the Rad4 and Rad23 proteins, for ultraviolet damaged DNA. Journal of Biological Chemistry 1998,273,31541-31546.
[71]Jansen, L., Verhage, R., Brouwer, J., Preferential binding of yeast Rad4 Rad23 complex to damaged DNA. Journal of Biological Chemistry 1998,273,33111-33114.
[72]Mu, D., Hsu, D., Sancar, A., Reaction mechanism of human DNA repair excision nuclease. Journal of Biological Chemistry 1996,271,8285-8294.
[73]Prakash, S., Prakash, L., Nucleotide excision repair in yeast. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2000,451,13-24.
[74]Farmer, L., Book, A., Lee, K., Lin, Y., et al., The RAD23 Family Provides an Essential Connection between the 26S Proteasome and Ubiquitylated Proteins in Arabidopsis. The Plant Cell 2010,22,124-142.
[75]Schultz, T., Quatrano, R., Characterization and expression of a rice RAD23 gene. Plant molecular biology 1997,34,557-562.
[76]Rensing, S., Lang, D., Zimmer, A., Terry, A., et al., The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. science 2008,319,64-69.
[77]Xie, Q., Guo, H., Dallman, G., Fang, S., et al., SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature 2002,419,167-170.
[78]Del Pozo, J., Dharmasiri, S., Hellmann, H., Walker, L., et al., AXR1-ECR1-dependent conjugation of RUB1 to the Arabidopsis cullin AtCUL1 is required for auxin response. The Plant Cell 2002,14,421-433.
[79]Gray, W., Kepinski, S., Rouse, D., Leyser, O., Estelle, M., Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature 2001,414,271-276.
[80]Auldridge, M., McCarty, D., Klee, H., Plant carotenoid cleavage oxygenases and their apocarotenoid products. Current opinion in plant biology 2006,9,315-321.
[81]Bulteau, A., Ikeda-Saito, M., Szweda, L., Redox-dependent modulation of aconitase activity in intact mitochondria. Biochemistry 2003,42,14846-14855.
[82]Matasova, L., Popova, T., Aconitate hydratase of mammals under oxidative stress. Biochemistry (Moscow) 2008,73,957-964.
[83]Chen, L., Madura, K., Rad23 promotes the targeting of proteolytic substrates to the proteasome. Molecular and Cellular Biology 2002,22,4902-4913.
[2]Thimann, K., On the nature of inhibitions caused by auxin. American Journal of Botany 1937,24, 407-412.
[3]CLINE, M., Exogenous auxin effects on lateral bud outgrowth in decapitated shoots. Annals of Botany 1996,78,255-266.
[4]Snyder, W., Some responses of plants to 2,3,5-triiodobenzoic acid. Plant Physiology 1949,24, 195-206.
[5]Panigrahi, B., Audus, L., Apical dominance in Vicia faba. Annals of Botany 1966,30,457-473.
[6]Zenser, N., Ellsmore, A., Leasure, C., Callis, J., Auxin modulates the degradation rate of Aux/IAA proteins. Proceedings of the National Academy of Sciences of the United States of America 2001, 98,11795-11800.
[7]Snow, R., On the nature of correlative inhibition. New Phytologist 1937,36,283-300.
[8]Hillman, J., Math, V., Medlow, G., Apical dominance and the levels of indole acetic acid in Phaseolus lateral buds. Planta 1977,134,191-193.
[9]Palni, L., Burch, L., Horgan, R., The effect of auxin concentration on cytokinin stability and metabolism. Planta 1988,174,231-234.
[10]Eklof, S., Astot, C., Blackwell, J., Moritz, T., et al., Auxin-cytokinin interactions in wild-type and transgenic tobacco. Plant and Cell Physiology 1997,38,225-235.
[11]Li, C., Guevara, E., Herrera, J., Bangerth, F., Effect of apex excision and replacement by 1-naphthylacetic acid on cytokinin concentration and apical dominance in pea plants. Physiologia Plantarum 2006,94,465-469.
[12]Tanaka, M., Takei, K., Kojima, M., Sakakibara, H., et al., Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance. The Plant Journal 2006,45,1028-1036.
[13]Turnbull, C., Raymond, M., Dodd, I., Morris, S., Rapid increases in cytokinin concentration in lateral buds of chickpea (Cicer arietinum L.) during release of apical dominance. Planta 1997,202, 271-276.
[14]Booker, J., Sieberer, T., Wright, W., Williamson, L., et al., MAX1 encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoid-derived branch-inhibiting hormone. Developmental cell 2005,8,443-449.
[15]Sorefan, K., Booker, J., Haurogne, K., Goussot, M., et al., MAX4 and RMS1 are orthologous dioxygenase-like genes that regulate shoot branching in Arabidopsis and pea. Genes& development 2003,17,1469-1474.
[16]Snowden, K., Simkin, A., Janssen, B., Templeton, K., et al., The Decreased apical dominancel/Petunia hybrida CAROTENOID CLEAVAGE DIOXYGENASE8 gene affects branch production and plays a role in leaf senescence, root growth, and flower development. The Plant Cell 2005,17,746-759.
[17]Schwartz, S., Qin, X., Loewen, M., The biochemical characterization of two carotenoid cleavage enzymes from Arabidopsis indicates that a carotenoid-derived compound inhibits lateral branching. Journal of Biological Chemistry 2004,279,46940-46945.
[18]Gomez-Roldan, V., Fermas, S., Brewer, P., Puech-Pages, V., et al., Strigolactone inhibition of shoot branching. Nature 2008,455,189-194.
[19]Umehara, M., Hanada, A., Yoshida, S., Akiyama, K., et al., Inhibition of shoot branching by new terpenoid plant hormones. Nature 2008,455,195-200.
[20]Venter, J., Adams, M., Myers, E., Li, P., et al., The sequence of the human genome. science 2001, 291,1304-1351.
[21]Clark, B., Towards a total human protein map. Nature 1981,292,491.
[22]Pandey, A., Mann, M., Proteomics to study genes and genomes. Nature 2000,405,837-846.
[23]Swinbanks, D., Government backs proteome proposal. Nature 1995,378,653.
[24]Wasinger, V., Cordwell, S., Cerpa-Poljak, A., Yan, J., et al., Progress with gene-product mapping of the Mollicutes:Mycoplasma genitalium. Electrophoresis 2005,16,1090-1094.
[25]Park, O., Proteomic studies in plants. Journal of biochemistry and molecular biology 2004,37, 133-138.
[26]Thiellement, H., Plant proteomics:methods and protocols, Humana Pr Inc 2007.
[27]Supek, F., Peharec, P., Krsnik-Rasol, M., muc, T., Enhanced analytical power of SDS-PAGE using machine learning algorithms. Proteomics 2007,8,28-31.
[28]Braun, R., Kinkl, N., Beer, M., Ueffing, M., Two-dimensional electrophoresis of membrane proteins. Analytical and Bioanalytical Chemistry 2007,389,1033-1045.
[29]van den Broeck, H., America, A., Smulders, M., Gilissen, L., van der Meer, I., Staining efficiency of specific proteins depends on the staining method:Wheat gluten proteins. Proteomics 2008,8, 1880-1884.
[30]Witzel, K., Surabhi, G., Jyothsnakumari, G., Sudhakar, C., et al., Quantitative proteome analysis of barley seeds using ruthenium (Ⅱ)-tris-(bathophenanthroline-disulphonate) staining. J. Proteome Res 2007,6,1325-1333.
[31]Jacobsen, S., Grove, H., Jensen, K., S rensen, H., et al., Multivariate analysis of 2-DE protein patterns-Practical approaches. Electrophoresis 2007,28,1289-1299.
[32]Berth, M., Moser, F., Kolbe, M., Bernhardt, J., The state of the art in the analysis of two-dimensional gel electrophoresis images. Applied microbiology and biotechnology 2007,76,1223-1243.
[33]Maurer, M., Software analysis of two-dimensional electrophoretic gels in proteomic experiments. Current Bioinformatics 2006,1,255-262.
[34]Demianova, Z., Shimmo, M., P ys, E., Franssila, S., Baumann, M., Toward an integrated microchip sized 2-D polyacrylamide slab gel electrophoresis device for proteomic analysis. Electrophoresis 2006,28,422-428.
[35]Bohler, S., Bagard, M., Oufir, M., Planchon, S., et al., A DIGE analysis of developing poplar leaves subjected to ozone reveals major changes in carbon metabolism. Proteomics 2007,7,1584-1599.
[36]Deng, Z., Zhang, X., Tang, W., Oses-Prieto, J., et al., A proteomics study of brassinosteroid response in Arabidopsis. Molecular & Cellular Proteomics 2007,6,2058-2071.
[37]van Noorden, G., Kerim, T., Goffard, N., Wiblin, R., et al., Overlap of proteome changes in Medicago truncatula in response to auxin and Sinorhizobium meliloti. Plant Physiology 2007,144, 1115-1131.
[38]Gomez, S., Nishio, J., Faull, K., Whitelegge, J., The chloroplast grana proteome difined by intact mass measurements from LC-MS. Molecular & Cellular Proteomics 2002,1,46-59.
[39]D'Amici, G., Timperio, A., Zolla, L., Coupling of native liquid phase isoelectrofocusing and blue native polyacrylamide gel electrophoresis:a potent tool for native membrane multiprotein complex separation. J. Proteome Res 2008,7,1326-1340.
[40]Xi, J., Wang, X., Li, S., Zhou, X., et al., Polyethylene glycol fractionation improved detection of low-abundant proteins by two-dimensional electrophoresis analysis of plant proteome. Phytochemistry 2006,67,2341-2348.
[41]Cellar, N., Kuppannan, K., Langhorst, M., Ni, W., et al., Cross species applicability of abundant protein depletion columns for ribulose-1,5-bisphosphate carboxylase/oxygenase. Journal of Chromatography B 2008,861,29-39.
[42]Li, G., Nallamilli, B., Tan, F., Peng, Z., Removal of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endosperm. Electrophoresis 2008,29,604-617.
[43]Nowaczyk, M., Hebeler, R., Schlodder, E., Meyer, H., et al., Psb27, a cyanobacterial lipoprotein, is involved in the repair cycle of photosystem Ⅱ. The Plant Cell Online 2006,18,3121-3131.
[44]Palmblad, M., Mills, D., Bindschedler, L., Heat-shock response in Arabidopsis thaliana explored by multiplexed quantitative proteomics using differential metabolic labeling. J. Proteome Res 2008,7,780-785.
[45]Hebeler, R., Oeljeklaus, S., Reidegeld, K., Eisenacher, M., et al., Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N labeling and difference gel electrophoresis. Molecular & Cellular Proteomics 2008,7,108-120.
[46]Hartman, N., Sicilia, F., Lilley, K., Dupree, P., Proteomic complex detection using sedimentation. Anal. Chem 2007,79,2078-2083.
[47]Dunkley, T., Hester, S., Shadforth, I., Runions, J., et al., Mapping the Arabidopsis organelle proteome. Proceedings of the National Academy of Sciences of the United States of America 2006, 103,6518-6523.
[48]Nuhse, T., Bottrill, A., Jones, A., Peck, S., Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses. The Plant Journal 2007,51,931-940.
[49]Larrainzar, E., Wienkoop, S., Weckwerth, W., Ladrera, R., et al., Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress. Plant Physiology 2007,144,1495-1507.
[50]Zybailov, B., Rutschow, H., Friso, G, Rudella, A., et al., Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One 2008,3, e1994.
[51]Lee, J., Garrett, W., Cooper, B., Shotgun proteomic analysis of Arabidopsis thaliana leaves. Journal of Separation Science 2007,30,2225-2230.
[52]Mann, M., Jensen, O., Proteomic analysis of post-translational modifications. Nature biotechnology 2003,21,255-261.
[53]Kia-Ki, H., Martinage, A., Post-translational chemical modification (s) of proteins. International Journal of Biochemistry 1992,24,19-28.
[54]Appel, R., Bairoch, A., Post-translational modifications:A challenge for proteomics and bioinformatics. Proteomics 2004,4,1525-1526.
[55]Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A., et al., Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Molecular Systems Biology 2008,4,193.
[56]Tan, F., Li, G., Chitteti, B., Peng, Z., Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa). Proteomics 2007,7,4511-4527.
[57]Heazlewood, J., Durek, P., Hummel, J., Selbig, J., et al., PhosPhAt:a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Research 2007,1-7.
[58]Lemaire, S., Michelet, L., Zaffagnini, M., Massot, V., Issakidis-Bourguet, E., Thioredoxins in chloroplasts. Current Genetics 2007,51,343-365.
[59]Winger, A., Taylor, N., Heazlewood, J., Day, D., Millar, A., Identification of intra-and intermolecular disulphide bonding in the plant mitochondrial proteome by diagonal gel electrophoresis. Proteomics 2007,7,4158-4170.
[60]Alkhalfioui, F., Renard, M., Vensel, W., Wong, J., et al., Thioredoxin-linked proteins are reduced during germination of Medicago truncatula seeds. Plant Physiology 2007,144,1559-1579.
[61]Lefebvre, B., Furt, F., Hartmann, M., Michaelson, L., et al., Characterization of lipid rafts from Medicago truncatula root plasma membranes:a proteomic study reveals the presence of a raft-associated redox system. Plant Physiology 2007,144,402-418.
[62]Washburn, M., Wolters, D., Yates, J., Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature biotechnology 2001,19,242-247.
[63]Minic, Z., Jamet, E., Negroni, L., Arsene der Garabedian, P., et al., A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases. Journal of experimental botany 2007.
[64]Friedberg, E., Eukaryotic DNA repair:glimpses through the yeast Saccharomyces cerevisiae. BioEssays 2005,13,295-302.
[65]Prakash, S., Sung, P., Prakash, L., DNA repair genes and proteins of Saccharomyces cerevisiae. Annual review of genetics 1993,27,33-70.
[66]Batty, D., Wood, R., Damage recognition in nucleotide excision repair of DNA. Gene 2000,241, 193-204.
[67]de Laat, W., Incision Coordination in Nucleotide Excision Repair 1995.
[68]Lambertson, D., Chen, L., Madura, K., Pleiotropic defects caused by loss of the proteasome-interacting factors Rad23 and Rpn10 of Saccharomyces cerevisiae. Genetics 1999,153,69-79.
[69]Elsasser, S., Chandler-Militello, D., Muller, B., Hanna, J., Finley, D., Rad23 and Rpn10 serve as alternative ubiquitin receptors for the proteasome. Journal of Biological Chemistry 2004,279, 26817-26822.
[70]Guzder, S., Sung, P., Prakash, L., Prakash, S., Affinity of yeast nucleotide excision repair factor 2, consisting of the Rad4 and Rad23 proteins, for ultraviolet damaged DNA. Journal of Biological Chemistry 1998,273,31541-31546.
[71]Jansen, L., Verhage, R., Brouwer, J., Preferential binding of yeast Rad4 Rad23 complex to damaged DNA. Journal of Biological Chemistry 1998,273,33111-33114.
[72]Mu, D., Hsu, D., Sancar, A., Reaction mechanism of human DNA repair excision nuclease. Journal of Biological Chemistry 1996,271,8285-8294.
[73]Prakash, S., Prakash, L., Nucleotide excision repair in yeast. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2000,451,13-24.
[74]Farmer, L., Book, A., Lee, K., Lin, Y., et al., The RAD23 Family Provides an Essential Connection between the 26S Proteasome and Ubiquitylated Proteins in Arabidopsis. The Plant Cell 2010,22,124-142.
[75]Schultz, T., Quatrano, R., Characterization and expression of a rice RAD23 gene. Plant molecular biology 1997,34,557-562.
[76]Rensing, S., Lang, D., Zimmer, A., Terry, A., et al., The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. science 2008,319,64-69.
[77]Xie, Q., Guo, H., Dallman, G., Fang, S., et al., SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature 2002,419,167-170.
[78]Del Pozo, J., Dharmasiri, S., Hellmann, H., Walker, L., et al., AXR1-ECR1-dependent conjugation of RUB1 to the Arabidopsis cullin AtCUL1 is required for auxin response. The Plant Cell 2002,14,421-433.
[79]Gray, W., Kepinski, S., Rouse, D., Leyser, O., Estelle, M., Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature 2001,414,271-276.
[80]Auldridge, M., McCarty, D., Klee, H., Plant carotenoid cleavage oxygenases and their apocarotenoid products. Current opinion in plant biology 2006,9,315-321.
[81]Bulteau, A., Ikeda-Saito, M., Szweda, L., Redox-dependent modulation of aconitase activity in intact mitochondria. Biochemistry 2003,42,14846-14855.
[82]Matasova, L., Popova, T., Aconitate hydratase of mammals under oxidative stress. Biochemistry (Moscow) 2008,73,957-964.
[83]Chen, L., Madura, K., Rad23 promotes the targeting of proteolytic substrates to the proteasome. Molecular and Cellular Biology 2002,22,4902-4913.