In-depth proteome analysis of the rubber particle of Hevea brasiliensis (para rubber tree)

Plant Molecular Biology

Volumn 82, Issue 1-2, 2013, Pages 155-168

  Dai, Longjun ^a,b   Kang, Guijuan ^a,b   Li, Yu ^a,b   Nie, Zhiyi ^a,b   Duan, Cuifang ^a,b   Zeng, Rizhong ^a,b  

^a AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

^b INSTITUTE OF TROPICAL BIOSCIENCE AND BIOTECHNOLOGY   (China)

Author keywords

1 DE gel electrophoresis; Hevea brasiliensis; Mass spectrometry; MudPIT; Multiple reaction monitoring; Proteome; Rubber particle

Indexed keywords

PEPTIDE; PROTEOME; RUBBER; VEGETABLE PROTEIN;

ARTICLE; ELECTROSPRAY MASS SPECTROMETRY; FRACTIONATION; HEVEA; IMMUNOBLOTTING; IMMUNOLOGY; LIQUID CHROMATOGRAPHY; METABOLISM; METHODOLOGY; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PROTEOMICS; REPRODUCIBILITY; WESTERN BLOTTING;

BLOTTING, WESTERN; CHEMICAL FRACTIONATION; CHROMATOGRAPHY, LIQUID; HEVEA; IMMUNOBLOTTING; PEPTIDES; PLANT PROTEINS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; RUBBER; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; STRESS, PHYSIOLOGICAL;

EUKARYOTA; HEVEA BRASILIENSIS;

EID: 84877613126     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-013-0047-y     Document Type: Article

References (64)

1. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC et al (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 27: 633-641.
2. Anderson L, Hunter C (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5: 573-588.
3. Asawatreratanakul K, Zhang YW, Wititsuwannakul D, Wititsuwannakul R, Takahashi S, Rattanapittayaporn A, Koyama T (2003) Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferase from Hevea brasiliensis. Eur J Biochem 270: 4671-4680.
4. Baskin TI (2000) The cytoskeleton. In: Buchanan B, Gruissem W, Jones R (eds) Biochemistry and molecular biology of plants. American Society of Plant Physiology, Rockville, MD, pp 202-258.
5. Baumeister W, Walz J, Zuhl F, Seemuller E (1998) The proteasome: paradigm of a self-compartmentalizing protease. Cell 92: 367-380.
6. Berkowitz D, Jost R, Pollmann S, Masle J (2008) Characterization of TCTP, the translationally controlled tumor protein, from Arabidopsis thaliana. Plant Cell 20: 3430-3447.
7. Boevink P, Oparka K, Santa-Cruz S, Martin B, Betteridge A, Hawes C (1998) Stacks on tracks: the plant Golgi apparatus traffics on an actin/ER network. Plant J 15: 441-447.
8. Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV (2004) The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Plant Cell 16: 3285-3303.
9. Chen P, Li XW, Sun YL, Liu Z, Cao R, He QY, Wang MC, Xiong JX, Xie JY, Wang XC, Liang SP (2006) Proteomic analysis of rat hippocampal plasma membrane: characterization of potential neuronal-specific plasma membrane proteins. J Neurochem 98: 1126-1140.
10. Cho WK, Chen XY, Uddin NM, Rim Y, Moon J, Jung JH, Shi C, Chu H, Kim S, Kim SW, Park ZY, Kim JY (2009) Comprehensive proteome analysis of lettuce latex using multidimensional protein-identification technology. Phytochemistry 70: 570-578.
11. Chow KS, Wan KL, Isa MN, Bahari A, Tan SH, Harikrishna K, Yeang HY (2007) Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex. J Exp Bot 58: 2429-2440.
12. Chow KS, Mat-Isa MN, Bahari A, Ghazali AK, Alias H, Mohd-Zainudding Z, Hoh CC, Wan KL (2011) Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. J Exp Bot 63: 1863-1871.
13. Chrispeels MJ, Herman ET (2000) Endoplasmic reticulum-derived compartments function in storage and as mediators of vacuolar remodeling via a new type of organelle, precursor protease vesicles. Plant Physiol 123: 1227-1234.
14. Cornish K (2001) Similarities and differences in rubber biochemistry among plant species. Phytochemistry 57: 1123-1134.
15. Cornish K, Backhaus RA (1990) Rubber transferase activity in rubber particles of guayule. Phytochemistry 29: 3809-3813.
16. Cornish K, Siler DJ (1996) Characterization of cis-prenyl transferase activity localized in a buoyant fraction of rubber particles from Ficus elastica latex. Plant Physiol Biochem 34: 377-384.
17. Cornish K, Wood DF, Windle JJ (1999) Rubber particles from four different species, examined by transmission electron microscopy and electron-paramagnetic-resonance spin labeling, are found to consist of a homogenous rubber core enclosed by a contiguous monolayer biomembrane. Planta 210: 85-96.
18. Cox J, Mann M (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem 80: 273-299.
19. Das S, Bosley AD, Ye X, Chan KC, Chu I, Green JE, Issaq HJ, Veenstra TD, Andresson T (2010) Comparison of strong cation exchange and SDS-PAGE fractionation for analysis of multiprotein complexes. J Proteome Res 9: 6696-6704.
20. Dennis MS, Light DR (1989) Rubber elongation factor from Hevea brasiliensis. J Biol Chem 264: 18608-18617.
21. Duan CF, Nie ZY, Li Y, Zeng RZ (2006) Establishment of 2-DE system and primary analyses on the membrane proteins of rubber particles in Hevea brasiliensis by MALDI-TOF. Chin J Trop Crops 27(3): 22-29.
22. Duan CF, Rio M, Leclercq J, Bonnot F, Oliver G, Montoro P (2010) Gene expression pattern in response to wounding, methyl jasmonate and ethylene in the bark of Hevea brasiliesis. Tree Physiol 30: 1349-1359.
23. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214.
24. Goyvaerts E, Dennis M, Light D, Chua NH (1991) Cloning and sequencing of the cDNA encoding the rubber elongation factor of Hevea brasiliensis. Plant Physiol 97: 317-321.
25. Henry IM, Carpentier SC, Pampurova S, van Hoylandt A, Panis B, Swennen R, Remy S (2011) Structure and regulation of the Asr gene family in banana. Planta 234: 785-798.
26. Higaki T, Kutsuna N, Okubo E, Sano T, Hasezawa S (2006) Actin micofilaments regulate vacuolar structures and dynamics: dual observation of actin microfilaments and vacuolar membrane in living tobacco BY-2 cells. Plant Cell Physiol 47: 839-852.
27. Hillebrand A, Post JJ, Wurbs D, Wahler D, Lenders M, Krzyzanek V, Prufer D, Gronover CS (2012) Down-regulation of small rubber particle protein expression affects integrity of rubber particles and rubber content in Taraxacum brevicorniculatum. PLoS ONE 7: e41874. doi: 10. 1371/journal. pone. 0041874.
28. Isokpehi RD, Simmons SS, Cohly HH, Ekunwe SI, Begonia GB, Ayensu WK (2011) Identification of drought-responsive universal stress proteins in viridiplantae. Bioinform Biol Insights 5: 41-58.
29. Kalluri UC, Hurst GB, Lankford PK, Ranjan P, Pelletier DA (2009) Shotgun proteome profile of Populus developing xylem. Proteomics 9: 4871-4880.
30. Kang H, Kang MY, Han KH (2000) Identification of natural rubber and characterization of rubber biosynthetic activity in fig tree. Plant Physiol 123: 1133-1142.
31. Kim GT, Tsukaya H (2002) Regulation of the biosynthesis of plant hormones by cytochrome P450s. J Plant Res 115: 169-177.
32. Kim JS, Kim YK, Ryu HJ, Kwak YS, Lee JY, Kang HS (2003) Isolation of stress-related genes of rubber particles and latex in fig tree (Ficus carica) and their expressions by abiotic stress or plant hormone treatments. Plant Cell Physiol 44: 412-419.
33. Kim YM, Han YJ, Hwang OJ, Lee SS, Shin AY, Kim SY, Kim JI (2012) Overexpression of Arabidopsis translationally controlled tumor protein gene AtTCTP enhances drought tolerance with rapid ABA-induced stomatal closure. Mol Cells 33: 617-626.
34. Ko JH, Chow KS, Han KH (2003) Transcriptome analysis reveals novel features of the molecular events occurring in the laticifers of Hevea brasiliensis (para rubber tree). Plant Mol Biol 53: 479-492.
35. Konrad Z, Bar-Zvi D (2008) Synergism between the chaperone-like activity of the stress regulated ASR1 protein and the osmolyte glycine-betaine. Planta 227: 1213-1219.
36. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH et al (2002) Subcellular localization of the yeast proteome. Genes Dev 16: 707-719.
37. Kush A (1994) Isoprenoid biosynthesis: the Hevea factory. Plant Physiol Biochem 32: 761-767.
38. Lange V, Picotti P, Domon B, Aebersold R (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4: 222. doi: 10. 1038/msb. 2008. 61.
39. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomics with massively parallel short read sequencing. Genome Res 20: 265-272.
40. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26: 966-968.
41. Marat AL, McPherson PS (2010) The connecdenn family, Rab35 guanine nucleotide exchange factors interfacing with the clathrin machinery. J Biol Chem 285: 10627-10637.
42. Miserey-Lenkei S, Chalancon G, Bardinm S, Formstecher E, Goud B, Echard A (2010) Rab and actomyosin-dependent fission of transport vesicles at the Golgi complex. Nat Cell Biol 12: 645-654.
43. Mizutani M, Ohta D (2010) Diversification of P450 genes during land plant evolution. Annu Rev Plant Biol 61: 291-315.
44. Mizutani M, Sato F (2011) Unusual P450 reactions in plant secondary metabolism. Arch Biochem Biophys 507: 194-203.
45. Negrutskii BS, El'skaya AV (1998) Eukaryotic translation elongation factor 1 alpha: structure, expression, functions, and possible role in aminoacyl-tRNA channeling. Prog Nucleic Acid Res Mol Biol 60: 47-78.
46. Oh SK, Kang H, Shin DH, Yang J, Chow KS, Yeang HY, Wagner B, Breitender H, Han KH (1999) Isolation, characterization, and functional analysis of a novel cDNA clone encoding a small rubber particle protein from Hevea brasiliensis. J Biol Chem 274: 17132-17138.
47. Pan Z, Durst F, Werck-Reichhart D, Gardner HW, Camara B, Cornish K, Backhaus RA (1995) The major protein of guayule rubber particles is a cytochrome P450. Characterization based on cDNA cloning and spectroscopic analysis of the solubilized enzyme and its reaction products. J Biol Chem 270: 8487-8494.
48. Pfeffer SR (2001) Rab GTPases: specifying and deciphering organelle identity and function. Trends Cell Biol 11: 487-491.
49. Post J, van Deenen N, Fricke J, Kowalski N, Wurbs D, Schaller H, Eisenreich W, Huber C, Twyman RM, Prüfer D, Gronover CS (2012) Laticifer-specific cis-prenyltransferase silencing affects the rubber, triterpene, and inulin content of Taraxacum brevicorniculatum. Plant Physiol 158: 1406-1417.
50. Pucadyil TJ, Schmid SL (2009) Conserved function of membrane active GTPases in coated vesicle formation. Science 325: 1217-1220.
51. Qin YX, Shi F, Tang CR (2011) Molecular characterization and expression analysis of cDNAs encoding four Rab and two Arf GTPases in the latex of Hevea brasiliensis. Plant Physiol Biochem 49: 729-737.
52. Richter S, Voss U, Jurgens G (2009) Post-Golgi traffic in plants. Traffic 10: 819-828.
53. Schmidt T, Lenders M, Hillebrand A, van Deenen N, Munt O, Reichelt R, Eisenreich W, Fisher R, Prufer D, Gronover CS (2010) Characterization of rubber particles and rubber chain elongation in Taraxacum koksaghyz. BMC Biochem 11: 11. doi: 10. 1186/1471-2091-11-11.
54. Scott DJ, da Costa BM, Espy SC, Keasling JD, Cornish K (2003) Activation and inhibition of rubber transferases by metal cofactors and pyrophosphate substrates. Phytochemistry 64: 123-134.
55. Siler DJ, Goodrich-Tanrikulu M, Cornish K, Stafford AE, Mckeon TA (1997) Composition of rubber particles of Hevea brasiliensis, Parthenium argentatum, Ficus elastica and Euphorbia lactiflua indicates unconventional surface structure. Plant Physiol Biochem 35: 881-889.
56. Singh AP, Wi SG, Chung GC, Kim YS, Kang H (2003) The micromorphology and protein characterization of rubber particles in Ficus carica, Ficus benghalensis and Hevea brasiliensis. J Exp Bot 54: 985-992.
57. Sirpio S, Khrouchtchova A, Allahverdiyeva Y, Hansson M, Fristedt R, Veber AV, Scheller HV, Jensen PE, Haldrup A, Aro EM (2008) AtCYP38 ensures early biogenesis, correct assembly and sustenance of photosystem II. Plant J 55: 639-651.
58. Song JP, Sun RJ, Li DZ, Tan FJ, Li X, Jiang PP, Huang XJ, Lin L, Deng ZN, Zhang Y (2012) An improvement of shotgun proteomics analysis by adding next-generation sequencing transcriptome data in orange. PLoS ONE 7: e39494. doi: 10. 1371/journal. pone. 0039494.
59. van Beilen JB, Poirier Y (2007) Establishment of new crops for the production of natural rubber. Trends Biotech 25: 522-529.
60. Wahler D, Colby T, Kowalski NA, Harzen A, Wotzka SY, Hillbrand A, Fisher R, Helsper J, Schmidt J, Gronover CS, Prufer D (2012) Proteomic analysis of latex from the rubber-producing plant Taraxacum brevicorniculatum. Proteomics 12: 901-905.
61. Wang XH, Shi MJ, Lu XL, Ma RF, Wu CG, Guo AP, Peng M, Tian WM (2010) A method for protein extraction from different subcellular fractions of laticifer latex in Hevea brasiliensis compatible with 2DE and MS. Proteome Sci 8: 35-44.
62. Wu CC, MacCoss MJ (2002) Shotgun proteomics: tools for the analysis of complex biological systems. Curr Opin Mol Therapeutics 4: 242-250.
63. Xiang QL, Xia KC, Dai LJ, Kang GJ, Li Y, Nie ZY, Duan CF, Zeng RZ (2012) Proteome analysis of the large and the small rubber particles of Hevea brasiliensis using 2D-DIGE. Plant Physiol Biochem 60: 207-213.
64. Xu J, Zhang B, Jiang C, Ming F (2011) RceIF5A, encoding an eukaryotic translation initiation factor 5A in Rosa chinensis, can enhance thermotolerance, oxidative and osmotic stress resistance of Arabidopsis thaliana. Plant Mol Biol 75: 167-178.