Plasma membrane proteomics

Plant Proteomics

Volumn , Issue , 2007, Pages 186-206

  Alexandersson, Erik ^a   Gustavsson, Niklas ^a   Bernfur, Katja ^a   Kjellbom, Per ^a   Larsson, Christer ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 56449129174     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-540-72617-3_13     Document Type: Chapter

References (66)

1. Alexandersson E, Saalbach G, Larsson C, Kjellbom P (2004) Arabidopsis plasma membrane proteomics identifies components of transport, signal transduction and membrane trafficking. Plant Cell Physiol 45:1543-1556.
2. Bayer EM, Bottrill AR, Walshaw J, Vigouroux M, Naldrett MJ, Thomas CL, Maule AJ (2006) Arabidopsis cell wall proteome defined using multidimensional protein identification technology. Proteomics 6:301-311.
3. Bordier C (1981) Phase separation of integral membrane proteins in Triton X-114 solution. J Biol Chem 256:1604-1607.
4. Borner GH, Sherrier DJ, Stevens TJ, Arkin IT, Dupree P (2002) Prediction of glycosylphosphatidylinositol- Anchored proteins in Arabidopsis. A genomic analysis. Plant Physiol 129:486-499.
5. Borner GH, Sherrier DJ, Weimar T, Michaelson LV, Hawkins ND, Macaskill A, Napier JA, Beale MH, Lilley KS, Dupree P (2005) Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol 137:104-116.
6. Brouillard F, Bensalem N, Hinzpeter A, Tondelier D, Trudel S, Gruber AD, Ollero M, Edelman A (2005) Blue native/SDS-PAGE analysis reveals reduced expression of the mClCA3 protein in cystic fibrosis knock-out mice. Mol Cell Proteomics 4:1762-1775.
7. Burre J, Beckhaus T, Schagger H, Corvey C, Hofmann S, Karas M, Zimmermann H, Volknandt W (2006) Analysis of the synaptic vesicle proteome using three gel-based protein separation techniques. Proteomics 6:6250-6262.
8. Cheng D, Hoogenraad CC, Rush J, Ramm E, Schlager MA, Duong DM, Xu P, Wijayawardana SR, Hanfelt J, Nakagawa T, Sheng M, Peng J (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics 5:1158-1170.
9. Delom F, Szponarski W, Sommerer N, Boyer JC, Bruneau JM, Rossignol M, Gibrat R (2006) The plasma membrane proteome of Saccharomyces cerevisiae and its response to the antifungal calcofluor. Proteomics 6:3029-3039.
10. Distler AM, Kerner J, Peterman SM, Hoppel CL (2006) A targeted proteomic approach for the analysis of rat liver mitochondrial outer membrane proteins with extensive sequence coverage. Anal Biochem 356:18-29.
11. Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS (2004) Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 3:1128-1134.
12. Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P, Lilley KS (2006) Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci USA 103:6518-6523.
13. Elortza F, Nühse TS, Foster LJ, Stensballe A, Peck SC, Jensen ON (2003) Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins. Mol Cell Proteomics 2:1261-1270.
14. Elortza F, Mohammed S, Bunkenborg J, Foster LJ, Nühse TS, Brodbeck U, Peck SC, Jensen ON (2006) Modification-specific proteomics of plasma membrane proteins: Identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J Proteome Res 5:935-943.
15. Ephritikhine G, Ferro M, Rolland N (2004) Plant membrane proteomics. Plant Physiol Biochem 42:943-962.
16. 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. J Proteome Res 2:413-425.
17. Fujiki Y, Hubbard AL, Fowler S, Lazarow PB (1982) Isolation of intracellular membranes by means of sodium carbonate treatment: Application to endoplasmic reticulum. J Cell Biol 93:97-102.
18. Han J, Schey KL (2004) Proteolysis and mass spectrometric analysis of an integral membrane: Aquaporin 0. J Proteome Res 3:807-812.
19. Hartinger J, Stenius K, Hogemann D, Jahn R (1996) 16-BAC/SDS-PAGE: A two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. Anal Biochem 240:126-133.
20. 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 Physiol 139:598-609.
21. Huang F, Fulda S, Hagemann M, Norling B (2006) Proteomic screening of salt-stress-induced changes in plasma membranes of Synechocystis sp. strain PCC 6803. Proteomics 6:910-920.
22. Hynek R, Svensson B, Jensen ON, Barkholt V, Finnie C (2006) Enrichment and identification of integral membrane proteins from barley aleurone layers by reversed-phase chromatography, SDS-PAGE, and LC-MS/MS. J Proteome Res 5:3105-3113.
23. Johansson F, Olbe M, Sommarin M, Larsson C (1995) Brij 58, a polyoxyethylene acyl ether, creates membrane vesicles of uniform sidedness. A new tool to obtain inside-out (cytoplasmic side- out) plasma membrane vesicles. Plant J 7:165-173.
24. Kawamura Y, Uemura M (2003) Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associated with cold acclimation. Plant J 36:141-154.
25. Kjell J, Rasmusson AG, Larsson H, Widell S (2004) Protein complexes of the plant plasma membrane resolved by Blue Native PAGE. Physiol Plant 121:546-555.
26. Kjellbom P, Larsson C (1984) Preparation and polypeptide composition of chlorophyll-free plasma membranes from leaves of light-grown spinach and barley. Physiol Plant 62:501-509.
27. Komatsu S (2005) Rice proteome database: A step toward functional analysis of the rice genome. Plant Mol Biol 59:179-190.
28. Larsson C, Sommarin M, Widell S (1994) Isolation of highly purified plant plasma membranes and separation of inside-out and right-side-out vesicles. Methods Enzymol 228:451-469.
29. Lee S, Lee EJ, Yang EJ, Lee JE, Park AR, Song WH, Park OK (2004) Proteomic identification of annexins, calcium-dependent membrane binding proteins that mediate osmotic stress and abscisic acid signal transduction in Arabidopsis. Plant Cell 16:1378-1391.
30. Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J, Barbier-Brygoo H, Ephritikhine G (2004) Identification of new intrinsic proteins in arabidopsis plasma membrane proteome. Mol Cell Proteomics 3:675-691.
31. Millar AH, Heazlewood JL (2003) Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis. Plant Physiol 131:443-453.
32. Mongrand S, Morel J, Laroche J, Claverol S, Carde JP, Hartmann MA, Bonneu M, Simon-Plas F, Lessire R, Bessoule JJ (2004) Lipid rafts in higher plant cells: purification and characterization of Triton X-100-insoluble microdomains from tobacco plasma membrane. J Biol Chem 279:36277-36286.
33. Morel J, Claverol S, Mongrand S, Furt F, Fromentin J, Bessoule JJ, Blein JP, Simon-Plas F (2006) Proteomics of plant detergent-resistant membranes. Mol Cell Proteomics 5:1396-1411.
34. Morré DJ (1990) Plasma membrane cytochemistry. In: Larsson C, Møller IM (eds) The plant plasma membrane Springer, Berlin, pp 76-92.
35. Murphy AS, Bandyopadhyay A, Holstein SE, Peer WA (2005) Endocytotic cycling of PM proteins. Annu Rev Plant Biol 56:221-251.
36. Navarre C, Degand H, Bennett KL, Crawford JS, Mortz E, Boutry M (2002) Subproteomics: Identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae. Proteomics 2:1706-1714.
37. Nelson CJ, Hegeman AD, Harms AC, Sussman MR (2006) A quantitative analysis of arabidopsis plasma membrane using trypsin-catalyzed 18O labeling. Mol Cell Proteomics 5:1382-1395.
38. Nielsen PA, Olsen JV, Podtelejnikov AV, Andersen JR, Mann M, Wisniewski JR (2005) Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics 4:402-408.
39. Nühse TS, Stensballe A, Jensen ON, Peck SC (2003) Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics 2:1234-1243.
40. Nühse TS, Stensballe A, Jensen ON, Peck SC (2004) Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell 16:2394-2405.
41. Olsen JV, Andersen JR, Nielsen PA, Nielsen ML, Figeys D, Mann M, Wisniewski JR (2004) HysTag - A novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain. Mol Cell Proteomics 3:82-92.
42. Palmgren MG, Askerlund P, Fredrikson K, Widell S, Sommarin M, Larsson C (1990) Sealed inside-out and right-side-out plasma membrane vesicles-optimal conditions for formation and separation. Plant Physiol 92:871-880.
43. 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 strategy. J Biol Chem 279:49367-49383.
44. Prime TA, Sherrier JD, Mahon P, Packman LC, Dupree P (2000) A proteomic analysis of organelles from Arabidopsis thaliana. Electrophoresis 21:3488-3499.
45. Rais I, Karas M, Schagger H (2004) Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomics 4:2567-2571.
46. Roland JC (1978) General preparation and staining of thin sections. In: Hall JL (ed) Electron microscopy and cytochemistry of plant cells. Elsevier, Amsterdam, pp 1-62.
47. Rolland N, Ferro M, Ephritikhine G, Marmagne A, Ramus C, Brugiere S, Salvi D, Seigneurin- Berny D, Bourguignon J, Barbier-Brygoo H, Joyard J, Garin J (2006) A versatile method for deciphering plant membrane proteomes. J Exp Bot 57:1579-1589.
48. Šamaj J, Read ND, Volkmann D, Menzel D, Baluška F (2005) The endocytic network in plants. Trends Cell Biol 15:425-433.
49. Sandelius AS, Morré DJ (1990) Plasma membrane isolation. In: Larsson C, Møller IM (eds) The plant plasma membrane. Springer, Berlin, pp 44-75.
50. Sandelius AS, Penel C, Auderset G, Brightman A, Millard M, Morré DJ (1986) Isolation of highly purified fractions of plasma membrane and tonoplast from the same homogenate of soybean hypocotyls by free-flow electrophoresis. Plant Physiol 81:177-185.
51. Santoni V, Doumas P, Rouquie D, Mansion M, Rabilloud T, Rossignol M (1999) Large scale characterization of plant plasma membrane proteins. Biochimie 81:655-661.
52. Santoni V, Kieffer S, Desclaux D, Masson F, Rabilloud T (2000) Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties. Electrophoresis 21:3329-3344.
53. 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. Biochem J 373:289-296.
54. Schägger H, von Jagow G (1991) Blue Native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199:223-231.
55. Schindler J, Nothwang HG (2006) Aqueous polymer two-phase systems: Effective tools for plasma membrane proteomics. Proteomics 6:5409-5417.
56. Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flugge UI, Kunze R (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol 131:16-26.
57. 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. Plant J 19:217-228.
58. Shiu SH, Bleecker AB (2001) Plant receptor-like kinase gene family: Diversity, function, and signaling. Sci STKE 2001:RE22.
59. Szponarski W, Sommerer N, Boyer JC, Rossignol M, Gibrat R (2004) Large-scale characterization of integral proteins from Arabidopsis vacuolar membrane by two-dimensional liquid chromatography. Proteomics 4:397-406.
60. Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, Kawamura Y, Mitsui T, Mikami S, Tozawa Y, Yoshinaga T, Komatsu S (2004) Proteomics of the rice cell: Systematic identification of the protein populations in subcellular compartments. Mol Genet Genomics 271:566-576.
61. Van Montfort BA, Doeven MK, Canas B, Veenhoff LM, Poolman B, Robillard GT (2002) Combined in-gel tryptic digestion and CNBr cleavage for the generation of peptide maps of an integral membrane protein with MALDI-TOF mass spectrometry. Biochim Biophys Acta 1555:111-115.
62. Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242-247.
63. Wu CC, MacCoss MJ, Howell KE, Yates JR 3rd (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21:532-538.
64. Yoshinaka K, Kumanogoh H, Nakamura S, Maekawa S (2004) Identification of V-ATPase as a major component in the raft fraction prepared from the synaptic plasma membrane and the synaptic vesicle of rat brain. Neurosci Lett 363:168-172.
65. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621-2632.
66. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5:2339-2347.