A versatile method for deciphering plant membrane proteomes

Journal of Experimental Botany

Volumn 57, Issue 7, 2006, Pages 1579-1589

  Rolland, Norbert ^a   Ferro, Myriam ^b   Ephritikhine, Geneviève ^a   Marmagne, Anne ^a   Ramus, Claire ^b   Brugière, Sabine ^b   Salvi, Daniel ^a   Seigneurin Berny, Daphné ^a   Bourguignon, Jacques ^a   Barbier Brygoo, Hélène ^a   Joyard, Jacques ^a   Garin, Jérome ^b  

^a CNRS   (France)

^b CEA GRENOBLE   (France)

Author keywords

Arabidopsis; Membrane proteins; Plant; Proteomics; Subcellular localization

Indexed keywords

CELLS; CHLOROPHYLL; GENES; PROTEINS;

ARABIDOPSIS; MEMBRANE PROTEINS; PLANT; PROTEOMICS; SUBCELLULAR LOCALIZATION;

BIOLOGICAL MEMBRANES;

ALKALI; ARABIDOPSIS PROTEIN; INORGANIC SALT; MEMBRANE PROTEIN;

ARABIDOPSIS; ARTICLE; BIOLOGY; CELL FRACTIONATION; INTRACELLULAR MEMBRANE; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; PROTEOMICS; ULTRASTRUCTURE; VALIDATION STUDY;

ALKALIES; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL FRACTIONATION; COMPUTATIONAL BIOLOGY; INTRACELLULAR MEMBRANES; MEMBRANE PROTEINS; PROTEOMICS; SALTS;

ARABIDOPSIS; SPINACIA OLERACEA;

EID: 33646269041     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erj162     Document Type: Article

References (50)

1. Alexandersson E, Saalbach G, Larsson C, Kjellbom P. 2004. Arabidopsis plasma membrane proteomics identifies components of transport, signal transduction and membrane trafficking. Plant and Cell Physiology 45, 1543-1556.
2. Barbier-Brygoo H, Gaymard F, Rolland N, Joyard J. 2001. Strategies to identify transport systems in plants, Trends in Plant Science 6, 577-585.
3. Block MA, Dorne AJ, Joyard J, Douce R. 1983. Preparation and characterization of membrane fractions enriched in outer and inner envelope membranes from spinach chloroplasts. I. Electrophoresis and immunochemical analyses. The Journal of Biological Chemistry 258, 13273-13280.
4. Bolter B, Soll J, Hill K, Hemmler R, Wagner R. 1999. A rectifying ATP-regulated solute channel in the chloroplastic outer envelope from pea. The EMBO Journal 18, 5505-5516.
5. Brugière S, Kowalski S, Ferro M, et al. 2004. The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions. Phytochemistry 65, 1693-1707.
6. Buettner R, Papoutsoglou G, Scemes E, Spray DC, Dermietzel R. 2000. Evidence for secretory pathway localization of a voltage-dependent anion channel isoform. Proceedings of the National Academy of Sciences, USA 97, 3201-3206.
7. Chew O, Whelan J. 2004. Just read the message: a model for sorting of proteins between mitochondria and chloroplasts. Trends in Plant Science 9, 318-319.
8. Chevallet M, Santoni V, Poinas A, Rouquie D, Fuchs A, Kieffer S, Rossignol M, Lunardi J, Garin J, Rabilloud T. 1998. New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 19, 1901-1909.
9. Cline K, Andrews J, Mersey B, Newcomb EH, Keegstra K. 1981. Separation and characterization of inner and outer envelope membranes of pea chloroplasts. Proceedings of the National Academy of Sciences, USA 78, 3595-3599.
10. Daram P, Brunner S, Rausch C, Steiner C, Amrhein N, Bucher M. 1999. Pht2;1 encodes a low-affinity phosphate transporter from Arabidopsis. The Plant Cell 11, 2153-2166.
11. Douce R, Joyard J. 1982. Purification of the chloroplast envelope. In: Edelman M, Hallick R, Chua NH, eds. Methods in chloroplast molecular biology. North-Holland, Amsterdam: Elsevier, 139-256.
12. Douce R, Joyard J. 1990. Biochemistry and function of the plastid envelope. Annual Review of Cell Biology 6, 173-216.
13. Durand P, Medigue C, Morgat A, Vandenbrouck Y, Viari A, Rechenmann F. 2003. Integration of data and methods for genome analysis. Current Opinion in Drug Discovery and Development 6, 346-352.
14. Ephritikhine G, Ferro M, Rolland N. 2004. Plant membrane proteomics. Plant Physiology and Biochemistry 42, 943-962.
15. Eubel H, Heinemeyer J, Sunderhaus S, Braun HP. 2004. Respiratory chain complexes in plant mitochondria. Plant Physiology and Biochemistry 42, 937-942.
16. Ferro M, Salvi D, Brugière S, Miras S, Kowalski S, Louwagie M, Garin J, Joyard J, Rolland N. 2003. Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana. Molecular and Cellular Proteomics 2, 325-345.
17. Ferro M, Salvi D, Rivière-Rolland H, Vermat T, Seigneurin-Berny D, Grunwald D, Garin J, Joyard J, Rolland N. 2002. Integral membrane proteins of the chloroplast envelope: identification and subcellular localization of new transporters. Proceedings of the National Academy of Sciences, USA 99, 11487-11492.
18. Ferro M, Seigneurin-Berny D, Rolland N, Chapel A, Salvi D, Garin J, Joyard J. 2000. Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins. Electrophoresis 21, 3517-3526.
19. Friso G, Giacomelli L, Ytterberg AJ, Peltier JB, Rudella A, Sun Q, van Wijk KJ. 2004. In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. The Plant Cell 16, 478-499.
20. Froehlich JE, Wilkerson CG, Ray WK, McAndrew RS, Osteryoung KW, Gage DA, Phinney BS. 2003. Proteomic study of the Arabidopsis thaliana chloroplastic envelope membrane utilizing alternatives to traditional two-dimensional electrophoresis. Journal of Proteome Research 2, 413-425.
21. Heazlewood JL, Toniti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH. 2004. Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. The Plant Cell 16, 241-256.
22. Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH. 2005. Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiology 139, 598-609.
23. Gutiérrez RA, Green PJ, Keegstra K, Ohlrogge JB. 2004. Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? Genome Biology 5, R53.
24. Koo AJ, Ohlrogge JB. 2002. The predicted candidates of Arabidopsis plastid inner envelope membrane proteins and their expression profiles. Plant Physiology 130, 823-836.
25. Kruft V, Eubel H, Jansch L, Werhahn W, Braun HP. 2001. Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiology 127, 1694-1710.
26. Luche S, Santoni V, Rabilloud T. 2003. Evaluation of non-ionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics 3, 249-253.
27. Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Garin J, Joyard J, Barbier-Brygoo H, Ephritikhine G. 2004. Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome. Molecular and Cellular Proteomics 3, 675-691.
28. Marmagne A, Salvi D, Rolland N, Ephritikhine G, Joyard J, Barbier-Brygoo H. 2006. Purification and fractionation of Arabidopsis membranes for proteomic analyses. In: Salinas J, Sanchez-Serrano JJ, eds. Arabidopsis protocols, 2nd edn. Humana Press (in press).
29. Miège C, Maréchal E, Shimojima M, Awai K, Block MA, Ohta H, Takamiya K, Douce R, Joyard J. 1999. Biochemical and topological properties of type A MGDG synthase, a spinach chloroplast envelope enzyme catalysing the synthesis of both prokaryotic and eukaryotic MGDG. European Journal of Biochemistry 265, 990-1001.
30. Millar AH, Heazlewood JL. 2003. Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis. Plant Physiology 131, 443-453.
31. Millar AH, Sweetlove LJ, Giege P, Leaver CJ. 2001. Analysis of the Arabidopsis mitochondrial proteome. Plant Physiology 127, 1711-1727.
32. Peltier JB, Ytterberg AJ, Sun Q, Van Wijk KJ. 2004. New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast and versatile fractionation strate. The Journal of Biological Chemistry 279, 49367-49393.
33. Rabilloud T. 2003. Membrane proteins ride shotgun. Nature Biotechnology 21, 508-510.
34. Rabilloud T, Adessi C, Giraudel A, Lunardi J. 1997. Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 18, 307-316.
35. Rolland N, Ferro M, Seigneurin-Berny D, Garin J, Douce R, Joyard J. 2003. Proteomics of chloroplast envelope membranes. Photosynthesis Research 78, 205-230.
36. Santoni V, Doumas P, Rouquié D, Mansion M, Rabilloud T, Rossignol M. 1999. Large scale characterization of plant plasma membrane proteins. Biochimie 81, 655-661.
37. Santoni V, Molloy M, Rabilloud T. 2000. Membrane proteins and proteomics: un amour impossible? Electrophoresis 21, 1054-1070.
38. Santoni V, Rouquié D, Doumas P, et al. 1998. Use of a proteome strategy for tagging proteins present at the plasma membrane, The Plant Journal 16, 633-641.
39. Santoni V, Vinh J, Pflieger D, Sommerer N, Maurel C. 2003. A proteomic study reveals novel insights into the diversity of aquaporin forms expressed in the plasma membrane of plant roots. The Biochemical Journal 373, 289-296.
40. Schwacke R, Flügge UI, Kunze R. 2004. Plant membrane proteome databases. Plant Physiology and Biochemistry 42, 1023-1034.
41. Schwacke R, Schneider A, Van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flügge UI, Kunze R. 2003. ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiology 131, 16-26.
42. Seigneurin-Berny D, Rolland N, Garin J, Joyard J. 1999. Technical advance: differential extraction of hydrophobic proteins from chloroplast envelope membranes: a subcellular-specific proteomic approach to identify rare intrinsic membrane proteins. The Plant Journal 19, 217-228.
43. Sun Q, Emanuelsson O, van Wijk KJ. 2004. Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties. Plant Physiology 135, 723-734.
44. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
45. Van Wijk KJ. 2004. Plastid proteomics. Plant Physiology and Biochemistry 42, 963-977.
46. Vandenbrouck Y, Garin J, Jaquinod M, Bruley C. 2005. Protéomique: analyse des données issues des spectromètres de masse. BioFutur 252, 27-31.
47. Versaw WK, Harrison MJ. 2002. A chloroplast phosphate transporter, PHT2;1, influences allocation of phosphate within the plant and phosphate-starvation responses. The Plant Cell 14, 1751-1766.
48. Wandrey M, Trevaskis B, Brewin N, Udvardi MK. 2004. Molecular and cell biology of a family of voltage-dependent anion channel porins in Lotus japonicus. Plant Physiology 134, 1-12.
49. Ward JM. 2001. Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics 17, 560-563.
50. Whitelegge JP. 2003. Thylakoid membrane proteomics. Photosynthesis Research 78, 265-277.