Please use this identifier to cite or link to this item:
標題: Label-Free Quantitative Peptidomics Analysis of Mutants in Oryza sativa
作者: 蘇建元
Jian-Yuan Su
關鍵字: 質譜術;胜肽質體學;非標定定量;mass spectrometry;peptidomics;label-free quantitation
引用: Baggerman G, Verleyen P, Clynen E, Huybrechts J, De Loof A, Schoofs L. Peptidomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2004, 803 : 3-16. Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. J Proteomics. 2014, 96 : 253-262. Biela I, Tidten-Luksch N, Immekus F, Glinca S, Nguyen TX, Gerber HD, Heine A, Klebe G, Reuter K. Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor. PLoS One. 2013, 8 : e64240. Bialek K, Cohen JD. Isolation and Partial Characterization of the Major Amide-Linked Conjugate of Indole-3-Acetic Acid from Phaseolus vulgaris L. Plant Physiol. 1986, 80 : 99-104. Butenko MA, Patterson SE, Grini PE, Stenvik GE, Amundsen SS, Mandal A, Aalen RB. Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants. Plant Cell. 2003, 15 : 2296-2307. Bladergroen MR, van der Burgt YE. Solid-phase extraction strategies to surmount body fluid sample complexity in high-throughput mass spectrometry-based proteomics. J Anal Methods Chem. 2015, doi : 10.1155. Bassham J, Benson A, Calvin M. The path of carbon in photosynthesis. J Biol Chem. 1950, 185 : 781-787. Chen YL, Lee CY, Cheng KT, Chang WH, Huang RN, Nam HG, Chen YR. Quantitative peptidomics study reveals that a wound-induced peptide from PR-1 regulates immune signaling in tomato. Plant Cell. 2014, 10 : 4135-4148. Cologna CT, Cardoso Jdos S, Jourdan E, Degueldre M, Upert G, Gilles N, Uetanabaro AP, Costa Neto EM, Thonart P, de Pauw E, Quinton L. Peptidomic comparison and characterization of the major components of the venom of the giant ant Dinoponera quadriceps collected in four different areas of Brazil. J Proteomics. 2013, 94 : 413-422. Castro LM, Cavalcanti DM, Araujo CB, Rioli V, Icimoto MY, Gozzo FC, Juliano M, Juliano L, Oliveira V, Ferro ES. Peptidomic analysis of the neurolysin-knockout mouse brain. J Proteomics. 2014, 111 : 238-248. Chu H, Qian Q, Liang W, Yin C, Tan H, Yao X, Yuan Z, Yang J, Huang H, Luo D, Ma H, Zhang D. The floral organ number4 gene encoding a putative ortholog of Arabidopsis CLAVATA3 regulates apical meristem size in rice. Plant Physiol. 2006, 142 : 1039-1052. Casamitjana-Martínez E, Hofhuis HF, Xu J, Liu CM, Heidstra R, Scheres B. Root-specific CLE19 overexpression and the sol1/2 suppressors implicate a CLV-like pathway in the control of Arabidopsis root meristem maintenance. Curr Biol. 2003, 13 : 1435-1441. Chelius D, Bondarenko PV. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res. 2002, 1 :317-323. Cosette A, Eliane DG, Jenny R, Kjell S. Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance. Int J Plant Genomics. 2012, doi : 10.1155. David NP, John RG, Richard DU, Michael JW, Emma C, Andrew JKW, Anthony DW. An Assessment of Peptide Enrichment Methods Employing mTRAQ Quantification Approaches. Anal. Chem.2012, 84 : 5604−5610. de Souza Cândido E, e Silva Cardoso MH, Sousa DA, Viana JC, de Oliveira-Júnior NG, Miranda V, Franco OL. The use of versatile plant antimicrobial peptides in agribusiness and human health. Peptides. 2014, 55 : 65-78. Duval A, Malécot CO, Pelhate M, Piek T. Poneratoxin, a new toxin from an ant venom, reveals an interconversion between two gating modes of the Na channels in frog skeletal muscle fibres. Pflugers Arch. 1992, 420 : 239-247. Esteban-Fernández D, Cañas B, Pizarro I, Palaciosa MA, Gómez-Gómez MM. SEC-ICP-MS and ESI-MS as tools to study the interaction between cisplatin and cytosolic biomolecules. J. Anal. At. Spectrom. 2007, 22 : 1113-1121. Farrokhi N, Whitelegge JP, Brusslan JA. Plant peptides and peptidomics. Plant Biotechnol J. 2008, 6 : 105-134. Fricker LD, Lim J, Pan H, Che FY. Peptidomics: identification and quantification of endogenous peptides in neuroendocrine tissues. Mass Spectrom Rev. 2006, 25 : 327-344. Ford KL, Cassin A, Bacic A. Quantitative proteomic analysis of wheat cultivars with differing drought stress tolerance. Front Plant Sci. 2011, doi : 10.3389. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999, 17 : 994-999. Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012, doi : 10.1074. Held JM, Schilling B, D'Souza AK, Srinivasan T, Behring JB, Sorensen DJ, Benz CC, Gibson BW. Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions. Int J Proteomics. 2013, doi: 10.1155/2013/791985. Huffaker A, Pearce G, Ryan CA. An endogenous peptide signal in Arabidopsis activates components of the innate immune response. Proc Natl Acad Sci U S A. 2006, 103 : 10098-10103. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005, 436 : 793-800. Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics. 2005, 4 :1265-1272. Jones KA, Kim PD, Patel BB, Kelsen SG, Braverman A, Swinton DJ, Gafken PR, Jones LA, Lane WS, Neveu JM, Leung HC, Shaffer SA, Leszyk JD, Stanley BA, Fox TE, Stanley A, Hall MJ, Hampel H, South CD, de la Chapelle A, Burt RW, Jones DA, Kopelovich L, Yeung AT. Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers. J Proteome Res. 2013, 12 : 4351-4365. Jagannathan B, Golbeck JH. Understanding of the binding interface between PsaC and the PsaA/PsaB heterodimer in photosystem I. Biochemistry. 2009, 48 : 5405-5416. Keast JF and Grant BR. Chlorophyll a-B Ratios in Some Siphonous Green-Algae in Relation to Species and Environment. Journal of Phycology. 1976, 12 : 197-209. Kurata N, Miyoshi K, Nonomura K, Yamazaki Y, Ito Y. Rice mutants and genes related to organ development, morphogenesis and physiological traits. Plant Cell Physiol. 2005, 46 : 48-62. Katz E, Fon M, Eigenheer RA, Phinney BS, Fass JN, Lin D, Sadka A, Blumwald E. A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development. Proteome Sci. 2010, doi : 10.1186. Kuhn-Nentwig L. Antimicrobial and cytolytic peptides of venomous arthropods. Cell Mol Life Sci. 2003, 60 : 2651-2668. Kehry MR, Doak TG, Dahlquist FW. Stimulus-induced changes in methylesterase activity during chemotaxis in Escherichia coli. J Biol Chem. 1984, 259 : 11828-11835. Lee JE, Atkins N Jr, Hatcher NG, Zamdborg L, Gillette MU, Sweedler JV, Kelleher NL. Endogenous peptide discovery of the rat circadian clock: a focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry. Mol Cell Proteomics. 2010, 9 : 285-297. Lee JE, Zamdborg L, Southey BR, Atkins N Jr, Mitchell JW, Li M, Gillette MU, Kelleher NL, Sweedler JV. Quantitative Peptidomics for Discovery of Circadian-Related Peptides from the Rat Suprachiasmatic Nucleus. J Proteome Res. 2013, 12 : 585-593. Moreno-Gordaliza E, Cañas B, Palacios MA, Gómez-Gómez MM. Top-down mass spectrometric approach for the full characterization of insulin-cisplatin adducts. Anal Chem. 2009, 81 : 3507-3516. Marmiroli N, Maestri E. Plant peptides in defense and signaling. Peptides. 2014, 56 : 30-44. Matsubayashi Y, Sakagami Y. Phytosulfokine, sulfated peptides that induce the proliferation of single mesophyll cells of Asparagus officinalis L. Proc Natl Acad Sci U S A. 1996, 93 : 7623-7627. Matsubayashi Y, Sakagami Y. Peptide hormones in plants. Annu Rev Plant Biol. 2006, 57 : 649-674. Mishima M, Takayama S, Sasaki K, Jee JG, Kojima C, Isogai A, Shirakawa M. Structure of the male determinant factor for Brassica self-incompatibility. J Biol Chem. 2003, 278 : 36389-36395. Mergaert P, Nikovics K, Kelemen Z, Maunoury N, Vaubert D, Kondorosi A, Kondorosi E. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol. 2003, 132 : 161-173. Miles GP, Samuel MA, Ranish JA, Donohoe SM, Sperrazzo GM, Ellis BE. Quantitative proteomics identifies oxidant-induced, AtMPK6-dependent changes in Arabidopsis thaliana protein profiles. Plant Signal Behav. 2009, 4 : 497-505. Michalski A, Cox J, Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res. 2011, 10 : 1785-1793. Mitchell P. The protonmotive Q cycle: a general formulation. FEBS Lett. 1975, 59 : 137-139. Narita NN, Moore S, Horiguchi G, Kubo M, Demura T, Fukuda H, Goodrich J, Tsukaya H. Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters leaf shape in Arabidopsis thaliana. Plant J. 2004, 38 : 699-713. Narváez-Vásquez J, Pearce G, Ryan CA. The plant cell wall matrix harbors a precursor of defense signaling peptides. Proc Natl Acad Sci U S A. 2005, 102 : 12974-12977. Nicholls DG and Ferguson SL. Bioenergetics. 2002, Amsterdam: Academic Press. Ooi LS, Tian L, Su M, Ho WS, Sun SS, Chung HY, Wong HN, Ooi VE. Isolation, characterization, molecular cloning and modeling of a new lipid transfer protein with antiviral and antiproliferative activities from Narcissus tazetta. Peptides. 2008, 12 : 2101-2109. Pearce G, Moura DS, Stratmann J, Ryan CA. Production of multiple plant hormones from a single polyprotein precursor. Nature. 2001a, 411 : 817-820. Pearce G, Moura DS, Stratmann J, Ryan CA Jr. RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development. Proc Natl Acad Sci U S A. 2001b, 98 : 12843-12847. Pearce G, Bhattacharya R, Chen YC, Barona G, Yamaguchi Y, Ryan CA. Isolation and characterization of hydroxyproline-rich glycopeptide signals in black nightshade leaves. Plant Physiol. 2009, 150 : 1422-1433. Pearce G, Strydom D, Johnson S, Ryan CA. A polypeptide from tomato leaves induces wound-inducible proteinase inhibitor proteins. Science. 1991, 23 : 895-897. Pearce G, Johnson S, Ryan CA. Structure-activity of deleted and substituted systemin, an 18-amino acid polypeptide inducer of plant defensive genes. J Biol Chem. 1993, 268 : 212-216. Pearce G, Ryan CA. Systemic signaling in tomato plants for defense against herbivores. Isolation and characterization of three novel defense-signaling glycopeptide hormones coded in a single precursor gene. J Biol Chem. 2003, 278 : 30044-30050. Pearce G, Yamaguchi Y, Barona G, Ryan CA. A subtilisin-like protein from soybean contains an embedded, cryptic signal that activates defense-related genes. Proc Natl Acad Sci U S A. 2010, 107 : 14921-14925. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999, 20 : 3551-3567. Pluzhnikov K, Nosyreva E, Shevchenko L, Kokoz Y, Schmalz D, Hucho F, Grishin E. Analysis of ectatomin action on cell membranes. Eur J Biochem. 1999, 262 : 501-506. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 2004, 3 : 1154-1169. Röhrig H, Schmidt J, Miklashevichs E, Schell J, John M. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc Natl Acad Sci U S A. 2002, 99 : 1915-1920. Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol. 2014, 32 : 219-223. Ryan CA. Proteinase inhibitors in plants: genes for improving the defenses against insects and pathogens. Annu. Rev. Phytopathol. 1990, 28 : 425-429. Reinbothe S1, Reinbothe C. Regulation of Chlorophyll Biosynthesis in Angiosperms. Plant Physiol. 1996, 111: 1-7. Ranson SL, Thomas M. Crassulacean acid metabolism. Annual Rev Plant. 1960, 11 : 81-110. Sharma S, Singh R, Rana S. Bioactive Peptides: A Review. Int. J. Bio automation. 2011, 15 : 223-250. Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc. 2015, 10 : 426-441. Schoofs L, Baggerman G. Peptidomics in Drosophila melanogaster. Brief Funct Genomic Proteomic. 2003, 2 : 114-120. Schmelz EA, Carroll MJ, LeClere S, Phipps SM, Meredith J, Chourey PS, Alborn HT, Teal PE. Fragments of ATP synthase mediate plant perception of insect attack. Proc Natl Acad Sci U S A. 2006, 103 : 8894-8899. Shen Y, Tolić N, Masselon C, Pasa-Tolić L, Camp DG 2nd, Hixson KK, Zhao R, Anderson GA, Smith RD. Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Anal Chem. 2004, 76 : 144-154. Sauter M. Phytosulfokine peptide signalling. J Exp Bot. 2015, doi : 10.1093. Stratmann JW. Long distance run in the wound response--jasmonic acid is pulling ahead. Trends Plant Sci. 2003, 8 : 247-250. Slack CR, Hatch MD. Comparative studies on the activity of carboxylases and other enzymes in relation to the new pathway of photosynthetic carbon dioxide fixation in tropical grasses. Biochem J. 1967, 103 : 660-665. Sasaki T. The rice genome project in Japan. Proc Natl Acad Sci USA. 1998, 95: 2027-2028. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408 : 796-815. Topping JF, Lindsey K. Promoter trap markers differentiate structural and positional components of polar development in Arabidopsis. Plant Cell. 1997, 9 : 1713-1725. Takayama S1, Shiba H, Iwano M, Shimosato H, Che FS, Kai N, Watanabe M, Suzuki G, Hinata K, Isogai A. The pollen determinant of self-incompatibility in Brassica campestris. Proc Natl Acad Sci U S A. 2000, 97 : 1920-1925. Tachibana Y, Vayssieres L, Durrant JR. Artificial photosynthesis for solar water-splitting. Nature Photonics. 2012, 6 : 511-518. Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods. 2004, 1 : 39-45. Wu H, Johnson MC, Lu CH, Fritsche KL, Thomas AL, Lai Y, Cai Z, Greenlief CM. Peptidomics study of anthocyanin-rich juice of elderberry. Talanta. 2015, 131 : 640-644. Wittenberg G, Sheffler W, Darchi D, Baker D, Noy D. Accelerated electron transport from photosystem I to redox partners by covalently linked ferredoxin. Phys Chem Chem Phys. 2013, 15 : 19608-19614. Wang X, Gowik U, Tang H, Bowers JE, Westhoff P, Paterson AH. Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol. 2009, doi : 10.1186. Wang Y, Chen J, Chen L, Zheng P, Xu HB, Lu J, Zhong J, Lei Y, Zhou C, Ma Q, Li Y, Xie P. Urinary peptidomics identifies potential biomarkers for major depressive disorder. Psychiatry Res. 2014, 217 : 25-33. Wen J, Lease KA, Walker JC. DVL, a novel class of small polypeptides: overexpression alters Arabidopsis development. Plant J. 2004, 37 : 668-677. Yamaguchi Y, Huffaker A. Endogenous peptide elicitors in higher plants. Curr Opin Plant Biol. 2011, 14 : 351-357. Yang F, Song Y, Yang H, Liu Z, Zhu G, Yang Y. An auxin-responsive endogenous peptide regulates root development in Arabidopsis. J Integr Plant Biol. 2014, 56 : 635-647. Yang H, Matsubayashi Y, Nakamura K, Sakagami Y. Oryza sativa PSK gene encodes a precursor of phytosulfokine-alpha, a sulfated peptide growth factor found in plants. Proc Natl Acad Sci U S A. 1999, 96 : 13560-13565. Yamazaki T, Takaoka M, Katoh E, Hanada K, Sakita M, Sakata K, Nishiuchi Y, Hirano H. A possible physiological function and the tertiary structure of a 4-kDa peptide in legumes. Eur J Biochem. 2003, 27 : 1269-1276. Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem. 2001, 73 : 2836-2842. Zhang K, McKinlay C, Hocart CH, Djordjevic MA. The Medicago truncatula small protein proteome and peptidome. J Proteome Res. 2006, 5 : 3355-3367. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2005, 5 :2339-2347. Zhu W, Smith JW, Huang CM. Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol. 2010, doi : 10.1155.
水稻為全球主要糧食作物之一,自基因體解序以來,水稻已累積豐富遺傳資料庫,目前台灣農民常栽種之水稻品種已超過四十種,且有許多文獻利用質譜術搭配蛋白體學分析方法進行品種間差異性研究,然而以新興之胜肽質體學 (peptidomics) 角度探討之資訊仍然不足。植物體內含有許多未被發現之活性胜肽,其功能類似動物體內之荷爾蒙,可調控植物之生長或免疫機制,由於活性胜肽胺基酸序列較短,容易降解且含量稀少不易偵測,因此發展一個高靈敏度及高精確度之方法為現今重要之研究議題。本實驗以台農 67 號 (TNG67) 與其經疊氮化納誘變之突變株 SA0405、SA0407 和 SA0408 水稻葉片為樣本。突變株和 TNG67 在外表性狀與生理狀況有明顯不同,突變株較為矮小且葉片顏色偏淡,但都能有完整生長、抽穗並且成熟。本實驗以胜肽質體學技術搭配超高效能液相層析儀 (ultra performance liquid chromatography, UPLC) 串聯三重四極桿時間飛行式串聯質譜儀 (TripleTOF mass spectrometry) 探討最高分蘗期、抽穗期與成熟期 TNG67 與突變株之差異,利用統計軟體找出其表現差異之胜肽片段。將數據搜尋蛋白質資料庫後,於最高分蘗期和抽穗期中與光系統相關蛋白質 ferredoxin-1 和 oxygen-evolving enhancer protein 3 之降解胜肽於突變株中表現量增加,可能影響突變株之光合成效率。於 de novo sequencing 結果中,photosystem I P700 chlorophyll a apoprotein A1 之 N 端胺基酸、photosystem I reaction center subunit IV 之 C 端胺基酸和 photosystem I reaction center subunit II-2 C 端胺基酸序列,推測可能為水稻葉片活性胜肽候選者。於抽穗期突變株中鑑定到 phosphoglycerate kinase 之 C 端胺基酸序列可能與能量生合成有密切相關。實驗成功建立水稻葉片胜肽質體萃取平台,未來希望對鑑定到之胜肽進行植物生理功能分析,進一步了解活性胜肽於植物體內調控機制。
Rights: 同意授權瀏覽/列印電子全文服務,2018-08-21起公開。
Appears in Collections:分子生物學研究所

Files in This Item:
File Description SizeFormat Existing users please Login
nchu-104-7102055002-1.pdf10.1 MBAdobe PDFThis file is only available in the university internal network    Request a copy
Show full item record

Google ScholarTM


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.