An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics research
详细信息 查看全文
- 作者：Wen-Ping Chen (1) (3) (5)
Xiao-Yuan Yang (2) (3) (6)
Geoffrey L Harms (4)
William M Gray (2) (3)
Adrian D Hegeman (1) (2) (3)
Jerry D Cohen (1) (3) - 刊名：Proteome Science
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：9
- 期：1
- 全文大小：974KB
- 参考文献：1. Schaefer J, Kier LD, Stejskal EO: Characterization of photorespiration in intact leaves using C-13 dioxide labeling. / Plant Physiol 1980, 65:254鈥?59. CrossRef
2. Loreto F, Pinelli P, Brancaleoni E, Ciccioli P: 13 C labeling reveals chloroplastic and extrachloroplastic pools of dimethylallyl pyrophosphate and their contribution to isoprene formation. / Plant Physiol 2004, 135:1903鈥?907. CrossRef
3. Cegelski L, Schaefer J: NMR determination of photorespiration in intact leaves using in vivo 13 CO 2 labeling. / J Magn Reson 2006, 178:1鈥?0. mr.2005.10.010">CrossRef
4. Calvin M: The photosynthetic carbon cycle. / J Chem Soc 1956, 1895鈥?915.
5. Osmond CB, Allaway WG, Sutton BG, Troughton JH, L眉ttge U, Winter K: Carbon Isotope Discrimination in Photosynthesis of CAM Plants. / Nature 1973, 246:41鈥?2. CrossRef
6. Schwender J, Goffman F, Ohlrogge JB, Shachar-Hill Y: Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds. / Nature 2004, 432:779鈥?82. CrossRef
7. Hutchinson CR, Hsia MT, Stephen CRA: Biosynthetic studies with carbon-13 dioxide of secondary plant metabolites. Nicotiana alkaloids. 1. Initial experiments. / J Am Chem Soc 1976, 98:6006鈥?011. CrossRef
8. Kurilich A, Britz S, Clevidence B, Novotny J: Isotopic labeling and LCAPCI-MS quantification for investigating absorption of carotenoids and phylloquinone from kale (
9. Leake JR, Ostle NJ, Ignacio Rangel-Castro J, Johnson D: Carbon fluxes from plants through soil organisms determined by field 13 CO 2 pulse-labelling in an upland grassland. / Applied Soil Ecology 2006, 33:152鈥?75. CrossRef
10. Kagawa A, Sugimoto A, Maximov TC: Seasonal course of translocation, storage and remobilization of 13 C pulse-labeled photoassimilate in naturally growing
11. Lee BR, Jin YL, Jung WJ, Avice JC, Morvan-Bertrand A, Ourry A, Park CW, Kim TH: Water-deficit accumulates sugars by starch degradation--not by de novosynthesis-- in white clover leaves (
12. Rittenberg D, Foster G: A new procedure for quantitative analysis by isotope dilution, with application to the determination of amino acids and fatty acids. / J Biol Chem 1940, 133:737鈥?44.
13. San Pietro A, Rittenberg D: A study of the rate of protein synthesis in humans: I. Measurement of the urea pool and urea space. / J Biol Chem 1953, 201:445鈥?55.
14. Epstein E, Cohen JD, Bandurski RS: Concentration and metabolic turnover of indoles in germinating kernels of
15. Baldi B, Maher B, Slovin J, Cohen JD: Stable isotope labeling in vivo of D and L tryptophan pools in
16. Hedden P: Modern methods for the quantitative analysis of plant hormones. / Annu Rev Plant Physiol Plant Mol Biol 1993, 44:107鈥?29. CrossRef
17. Barkawi LS, Tam YY, Tillman JA, Pederson B, Calio J, Al-Amier H, Emerick M, Normanly J, Cohen JD: A high-throughput method for the quantitative analysis of indole-3-acetic acid and other auxins from plant tissue. / Anal Biochem 2008, 372:177鈥?88. CrossRef
18. R枚misch-Margl W, Schramek N, Radykewicz T, Ettenhuber C, Eylert E, Huber C, R枚misch-Margl L, Schwarz C, Dobner M, Demmel N, Winzenh枚rlein B, Bacher A, Eisenreich W: 13 CO 2 as a universal metabolic tracer in isotopologue perturbation experiments. / Phytochemistry 2007, 68:2273鈥?289. m.2007.03.034">CrossRef
19. Huege J, Sulpice R, Gibon Y, Lisec J, Koehl K, Kopka J: GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13 CO 2 labeling. / Phytochemistry 2007, 68:2258鈥?272. m.2007.03.026">CrossRef
20. Roessner-Tunali U, Liu JL, Leisse A, Balbo I, Perez-Melis A, Willmitzer L, Fernie AR: Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in C-13 labelled isotopes. / Plant J 2004, 39:668鈥?79. CrossRef
21. Ettenhuber C, Radykewicz T, Kofer W, Koop HU, Bacher A, Eisenreich W: Metabolic flux analysis in complex isotopomer space. Recycling of glucose in tobacco plants. / Phytochemistry 2005, 66:323鈥?35. m.2004.12.014">CrossRef
22. Kruger NJ, Huddleston JE, Le Lay P, Brown ND, Ratcliffe RG: Network flux analysis: impact of 13 C-substrates on metabolism in
23. Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR: Stable Isotope Assisted Assignment of Elemental Compositions for Metabolomics. / Anal Chem 2007,79(18):6912鈥?921. CrossRef
24. Birkemeyer C, Wagner C, Erban A, Kopka J: Metabolome analysis: the potential of
25. Giavalisco P, Hummel J, Lisec J, Inostroza AC, Catchpole G, Willmitzer L: High-resolution direct infusion-based mass spectrometry in combination with whole 13 C metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. / Anal Chem 2008, 80:9417鈥?425. CrossRef
26. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR: Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. / Plant Cell 2001, 13:11鈥?9. CrossRef
27. Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L: Metabolite profiling for plant functional genomics. / Nat Biotechnol 2000, 18:1157鈥?161. CrossRef
28. Desbrosses GG, Kopka J, Udvardi MK:
29. Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR: Gas chromatography mass spectrometry-based metabolite profiling in plants. / Nat Protocols 2006, 1:387鈥?96. CrossRef
30. van Winden W, Verheijen P, Heijnen S: Possible pitfalls of flux calculations based on 13 C-labeling. / Metab Eng 2001, 3:151鈥?62. mben.2000.0174">CrossRef
31. Loreto F, Ciccioli P, Cecinato A, Brancaleoni E, Frattoni M, Fabozzi C, Tricoli D: Evidence of the Photosynthetic Origin of Monoterpenes Emitted by
32. Schaefer J, Beard CF: C-13 nuclear magnetic resonance analysis of metabolism in soybeans labelled by 13 CO 2 . / Plant Physol 1975, 55:1048鈥?053. CrossRef
33. Ostle N, Ineson P, Benham D, Sleep D: Carbon assimilation and turnover in grassland vegetation using an
34. Chen W-P, Yang X-Y, Hegeman AD, Gray WM, Cohen JD: Micro-scale preparation of derivatized amino acids with methyl chloroformate for gas chromatography-mass spectrometry analysis. / J Chromatogr B 2010, 878:2199鈥?208. mb.2010.06.027">CrossRef
35. Cerling TE, Ayliffe LK, Dearing MD, Ehleringer JR, Passey BH, Podlesak DW, Torregrossa AM, West AG: Determining biological tissue turnover using stable isotopes: the reaction progress variable. / Oecologia 2007, 151:175鈥?89. CrossRef
36. Park S, Cohen JD, Slovin JP: Strawberry fruit protein with a novel indole-acyl modification. / Planta 2006, 224:1015鈥?022. CrossRef
37. Beynon RJ, Pratt JM: Metabolic labeling of proteins for proteomics. / Mol Cell Proteomics 2005, 4:857鈥?72. mcp.R400010-MCP200">CrossRef
38. Yang XY, Chen WP, Rendahl AK, Hegeman AD, Gray WM, Cohen JD: Measuring the turnover rates of
39. Gibeaut DM, Hulett J, Cramer GR, Seemann JR: Maximal biomass of
40. Bradford MM: A rapid and sensitive for the quantitation of microgram quantitites of protein utilizing the principle of protein-dye binding. / Anal Biochem 1976, 72:248鈥?54. CrossRef
41. Candiano G, Bruschi M, Musante L, Santucci L, Ghiggeri GM, Carnemolla B, Orecchia P, Zardi L, Righetti PG: Blue silver: A very sensitive colloidal Coomassie G-250 staining for proteome analysis. / Electrophoresis 2004, 25:1327鈥?333. CrossRef
42. Shevchenko A, Wilm M, Vorm O, Mann M: Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. / Anal Chem 1996, 68:850鈥?58. CrossRef
43. Griffin TJ, Xie H, Bandhakavi S, Popko J, Mohan A, Carlis JV, Higgins L: iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. / J Proteome Res 2007, 6:4200鈥?209. CrossRef
44. MacCoss MJ, Wu CC, Matthews DE, Yates JR: Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. / Anal Chem 2005, 77:7646鈥?653. CrossRef
45. Kubinyi H: Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem. / Analytica Chimica Acta 1991, 247:107鈥?11. CrossRef
46. Lee WN, Byerley LO, Bergner EA, Edmond J: Mass isotopomer analysis: theoretical and practical considerations. / Biol Mass Spectrom 1991, 20:451鈥?58. ms.1200200804">CrossRef
47. Hellerstein MK, Neese RA: Mass isotopomer distribution analysis at eight years: theoretical, analytic, and experimental considerations. / Am J Physiol 1999, 276:1146鈥?170. - 作者单位：Wen-Ping Chen (1) (3) (5)
Xiao-Yuan Yang (2) (3) (6)
Geoffrey L Harms (4)
William M Gray (2) (3)
Adrian D Hegeman (1) (2) (3)
Jerry D Cohen (1) (3)
1. Department of Horticultural Science, University of Minnesota, Saint Paul, USA
3. Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, USA
5. Yeastern Biotech Co., Ltd, 6F, 23, Lane 169, Kang Ning St., Shijr, Taipei, Taiwan
2. Department of Plant Biology, University of Minnesota, Saint Paul, USA
6. Room S1-411, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West BeiChen road, ChaoYang district, Beijing, PR China
4. Saint Paul Apparatus Shop, University of Minnesota, Saint Paul, USA
文摘
Background Labeling whole Arabidopsis (Arabidopsis thaliana) plants to high enrichment with 13C for proteomics and metabolomics applications would facilitate experimental approaches not possible by conventional methods. Such a system would use the plant's native capacity for carbon fixation to ubiquitously incorporate 13C from 13CO2 gas. Because of the high cost of 13CO2 it is critical that the design conserve the labeled gas. Results A fully enclosed automated plant growth enclosure has been designed and assembled where the system simultaneously monitors humidity, temperature, pressure and 13CO2 concentration with continuous adjustment of humidity, pressure and 13CO2 levels controlled by a computer running LabView software. The enclosure is mounted on a movable cart for mobility among growth environments. Arabidopsis was grown in the enclosure for up to 8 weeks and obtained on average >95 atom% enrichment for small metabolites, such as amino acids and >91 atom% for large metabolites, including proteins and peptides. Conclusion The capability of this labeling system for isotope dilution experiments was demonstrated by evaluation of amino acid turnover using GC-MS as well as protein turnover using LC-MS/MS. Because this 'open source' Arabidopsis 13C-labeling growth environment was built using readily available materials and software, it can be adapted easily to accommodate many different experimental designs.