Proteomic analysis of highly purified peroxisomes from etiolated soybean cotyledons

Plant and Cell Physiology

Volumn 49, Issue 4, 2008, Pages 526-539

  Arai, Yuko ^a   Hayashi, Makoto ^a   Nishimura, Mikio ^a  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

Author keywords

Expressed sequence tag; Glyoxysome; Matrix assisted laser desorption ionization time of flight mass spectrometry; Peroxisome; Proteomics; Soybean

Indexed keywords

GLYCINE MAX;

PEPTIDE; PROTEOME; SIGNAL PEPTIDE; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CELL FRACTIONATION; CHEMISTRY; CONSENSUS SEQUENCE; COTYLEDON; DENSITY GRADIENT CENTRIFUGATION; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PEPTIDE MAPPING; PEROXISOME; PHYLOGENY; PROTEIN TRANSPORT; PROTEOMICS; SEQUENCE ALIGNMENT; SOYBEAN; TWO DIMENSIONAL GEL ELECTROPHORESIS;

AMINO ACID SEQUENCE; CENTRIFUGATION, DENSITY GRADIENT; CONSENSUS SEQUENCE; COTYLEDON; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PEPTIDES; PEROXISOMES; PHYLOGENY; PLANT PROTEINS; PROTEIN SORTING SIGNALS; PROTEIN TRANSPORT; PROTEOME; PROTEOMICS; SEQUENCE ALIGNMENT; SOYBEANS; SUBCELLULAR FRACTIONS;

EID: 44349182030     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcn027     Document Type: Article

References (54)

1. Baker, A., Graham, I.A., Holdsworth, M., Smith, S.M. and Theodoulou, F.L. (2006) Chewing the fat: beta-oxidation in signalling and development. Trends Plant Sci. 11: 124-132.
2. Beeching, J.R. and Northcote, D.H. (1987) Nucleic acid (cDNA) and amino acid sequences of isocitrate lyase from castor bean. Plant Mol. Biol. 8: 471-475.
3. Berkemeyer, M., Scheibe, R. and Ocheretina, O. (1998) A novel, non-redox-regulated NAD-dependent malate dehydrogenase from chloroplasts of Arabidopsis thaliana L. J. Biol. Chem. 273: 27927-27933.
4. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 3497-3500.
5. Clausen, C., Ilkavets, I., Thomson, R., Philippar, K., Vojta, A., Möhlmann, T., Neuhaus, E., Fulgosi, H. and Soll, J. (2004) Intracellular localization of VDAC proteins in plants. Planta 220: 30-37.
6. Corpas, F.J., Sandalio, L.M., Brown, M.J., del Rio, L.A. and Trelease, R.N. (2000) Identification of porin-like polypeptide(s) in the boundary membrane of oilseed glyoxysomes. Plant Cell Physiol. 41: 1218-1228.
7. D'Arcy-Lameta, A., Ferrari-Iliou, R., Contour-Ansel, D., Pham-Thi, A. and Zuily-Fodil, Y. (2006) Isolation and characterization of four ascorbate peroxidase cDNAs responsive to water deficit in cowpea leaves. Ann. Bot. 97: 133-140.
8. Eastmond, P.J. and Graham, I.A. (2000) The multifunctional protein AtMFP2 is co-ordinately expressed with other genes of fatty acid beta-oxidation during seed germination in Arabidopsis thaliana (L.) Heynh. Biochem Soc. Trans. 28: 95-99.
9. Fukao, Y., Hayashi, M., Hara-Nishimura, I. and Nishimura, M. (2003) Novel glyoxysomal protein kinase, GPK1, identified by proteomic analysis of glyoxysomes in etiolated cotyledons of Arabidopsis thaliana. Plant Cell Physiol. 44: 1002-1012.
10. Fukao, Y., Hayashi, M. and Nishimura, M. (2002) Proteomic analysis of leaf peroxisomal proteins in greening cotyledons of Arabidopsis thaliana. Plant Cell Physiol. 43: 689-696.
11. Gebhardt, J.S., Wadsworth, G.J. and Matthews, B.F. (1998) Characterization of a single soybean cDNA encoding cytosolic and glyoxysomal isozymes of aspartate aminotransferase. Plant Mol. Biol. 37: 99-108.
12. Gharahdaghi, F., Weinberg, C.R., Meagher, D.A., Imai, B.S. and Mische, S.M. (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20: 601-605.
13. Guex, N., Henry, H., Flach, J., Richter, H. and Widmer, F. (1995) Glyoxysomal malate dehydrogenase and malate synthase from soybean cotyledons (Glycine max L.): enzyme association, antibody production and cDNA cloning. Planta 197: 369-375.
14. Hatano, K., Shimada, T., Hiraiwa, N., Nishimura, M. and Hara-Nishimura, I. (1997) A rapid increase in the level of binding protein (BiP) is accompanied by synthesis and degradation of storage proteins in pumpkin cotyledons. Plant Cell Physiol. 38: 344-351.
15. Hayashi, H., De Bellis, L., Ciurli, A., Kondo, M., Hayashi, M. and Nishimura, M. (1999) A novel acyl-CoA oxidase that can oxidize short-chain acyl-CoA in plant peroxisomes. J. Biol. Chem. 274: 12715-12721.
16. Hayashi, M., Aoki, M., Kondo, M. and Nishimura, M. (1997) Changes in targeting efficiencies of proteins to plant microbodies caused by amino acid substitutions in the carboxy-terminal tripeptide. Plant Cell Physiol. 38: 759-768.
17. Hayashi, M. and Nishimura, M. (2006) Arabidopsis thaliana - a model organism to study plant peroxisomes. Biochim. Biophys. Acta 1763: 1382-1391.
18. Heins, L., Mentzel, H., Schmid, A., Benz, R. and Schmitz, U.K. (1994) Biochemical, molecular, and functional characterization of porin isoforms from potato mitochondria. J. Biol. Chem. 269: 26402-26410.
19. Kamada, T., Nito, K., Hayashi, H., Mano, S., Hayashi, M. and Nishimura, M. (2003) Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana. Plant Cell Physiol. 44: 1275-1289.
20. Kamigaki, A., Mano, S., Terauchi, K., Nishi, Y., Tachibe-Kinoshita, Y., Nito, K., Kondo, M., Hayashi, M., Nishimura, M. and Esaka, M. (2003) Identification of peroxisomal targeting signal of pumpkin catalase and the binding analysis with PTS1 receptor. Plant J. 33: 161-175.
21. Kato, A., Hayashi, M., Mori, H. and Nishimura, M. (1995) Molecular characterization of a glyoxysomal citrate synthase that is synthesized as a precursor of higher molecular mass in pumpkin. Plant Mol. Biol. 27: 377-390.
22. Kato, A., Hayashi, M., Takeuchi, Y. and Nishimura, M. (1996) cDNA cloning and expression of a gene for 3-ketoacyl-CoA thiolase in pumpkin cotyledons. Plant Mol. Biol. 31: 843-852.
23. Koumoto, Y., Tsugeki, R., Shimada, T., Mori, H., Kondo, M., Hara-Nishimura, I. and Nishimura, M. (1996) Isolation and characterization of a cDNA encoding mitochondrial chaperonin 10 from Arabidopsis thaliana by functional complementation of an Escherichia coli groES mutant. Plant J. 10: 1119-1125.
24. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 5259: 680-685.
25. Lee, Y., Sultana, R., Pertea, G., Cho, J., Karamycheva, S., et al. (2002) Cross-referencing eukaryotic genomes. Genome Res. 12: 493-502.
26. Legaria, J., Rajsbaum, R., Munoz-Clares, R.A., Villegas-Sepúlveda, N., Simpson, J. and Iturriaga, G. (1998) Molecular characterization of two genes encoding betaine aldehyde dehydrogenase from amaranth. Expression in leaves under short-term exposure to osmotic stress or abscisic acid. Gene 218: 69-76.
27. Liepman, A.H. and Olsen, L.J. (2003) Alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of Arabidopsis. Plant Physiol. 131: 215-227.
28. Ma, C.L., Haslbeck, M., Babujee, L., Jahn, O. and Reumann, S. (2006) Identification and characterization of a stress-inducible and a constitutive small heat-shock protein targeted to the matrix of plant peroxisomes. Plant Physiol. 141: 47-60.
29. Mano, S., Hayashi, M., Kondo, M. and Nishimura, M. (1997) Hydroxypyruvate reductase with a carboxy-terminal targeting signal to microbodies is expressed in Arabidopsis. Plant Cell Physiol. 38: 449-455.
30. Nakagawa, T., Suzuki, T., Murata, S., Nakamura, S., Hino, T., et al. (2007) Improved Gateway binary vectors: high-performance vectors for creation of fusion constructs in transgenic analysis of plants. Biosci. Biotechnol. Biochem. 71: 2095-2100.
31. Nguyen, T., Zelechowska, M., Foster, H., Bergmann, H. and Verma, D.P. (1985) Primary structure of the soybean noduli-35 gene encoding uricase II localized in the peroxisomes of uninfected cells of nodules. Proc. Natl Acad. Sci. USA 82: 5040-5044.
32. Nishimura, M. and Akazawa, T. (1974) Structure and function of chloroplast proteins. XXIV. Spinach leaf ribulosebisphosphate carboxylase. Carboxylase and oxygenase reaction examined by immunochemical methods. Biochemistry 13: 2277-2281.
33. Ni, W., Turley, R.B. and Trelease, R.N. (1990) Characterization of a cDNA encoding cottonseed catalase. Biochim. Biophys. Acta 1049: 219-222.
34. Nyathi, Y. and Baker, A. (2006) Plant peroxisomes as a source of signalling molecules. Biochim. Biophys. Acta 1763: 1478-1495.
35. Perkins, D.N., Pappin, D.J., Creasy, D.M. and Cottrell, J.S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
36. Perrière, G. and Gouy, M. (1996) WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364-369.
37. Pertea, G., Huang, X., Liang, F., Antonescu, V., Sultana, R., et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
38. Preisig-Muller, R., Guhnemann-Schafer, K. and Kindl, H. (1994) Domains of the tetrafunctional protein acting in glyoxysomal fatty acid beta-oxidation. Demonstration of epimerase and isomerase activities on a peptide lacking hydratase activity. J. Biol. Chem. 269: 20475-20481.
39. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R. and White, J. (2001) The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29: 159-164.
40. Reumann, S., Babujee, L., Ma, C., Wienkoop, S., Siemsen, T., Antonicelli, G.E., Rasche, N., Luder, F., Weckwerth, W. and Jahn, O. (2007) Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms. Plant Cell 19: 3170-3193.
41. Reumann, S., Bettermann, M., Benz, R. and Heldt, H.W. (1997) Evidence for the presence of a porin in the membrane of glyoxysomes of castor bean. Plant Physiol. 115: 891-899.
42. Reumann, S., Maier, E., Benz, R. and Heldt, H.W. (1995) The membrane of leaf peroxisomes contains a porin-like channel. J. Biol. Chem. 270: 17559-17565.
43. Reumann, S., Maier, E., Heldt, H.W. and Benz, R. (1998) Permeability properties of the porin of spinach leaf peroxisomes. Eur. J. Biochem. 251: 359-366.
44. Richmond, T.A. and Bleecker, A.B. (1999) A defect in beta-oxidation causes abnormal inflorescence development in Arabidopsis. Plant Cell 11: 1911-1924.
45. Rylott, E.L., Eastmond, P.J., Gilday, A.D., Slocombe, S.P., Larson, T.R., Baker, A. and Graham, I.A. (2006) The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal beta-oxidation is essential for seedling establishment. Plant J. 45: 930-941.
46. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D. and Lohmann, J. (2005) A gene expression map of Arabidopsis development. Nature Genet. 37: 501-506.
47. Schneider, K., Kienow, L., Schmelzer, E., Colby, T., Bartsch, M., Miersch, O., Wasternack, C., Kombrink, E. and Stuible, H.P. (2005) A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis thaliana has the catalytic capacity to activate biosynthetic precursors of jasmonic acid. J. Biol. Chem. 280: 13962-13972.
48. Tsai, J., Sultana, R., Lee, Y., Pertea, G., Karamycheva, K., Antonescu, V., Cho, J., Parvizi, B., Cheung, F. and Quackenbush, J. (2001) RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol. 2: software0002.1-0002.4.
49. Tsugeki, R., Hara-Nishimura, I., Mori, H. and Nishimura, M. (1993) Cloning and sequencing of cDNA for glycolate oxidase from pumpkin cotyledons and northern blot analysis. Plant Cell Physiol. 34: 51-57.
50. Usami, N., Ishikura, S., Abe, H., Nagano, M., Uebuchi, M., Kuniyasu, A., Otagiri, M., Nakayama, H., Imamura, Y. and Hara, A. (2003) Cloning, expression and tissue distribution of a tetrameric form of pig carbonyl reductase. Chem. Biol. Interact. 143: 353-361.
51. Volokita, M. and Somerville, C.R. (1987) The primary structure of spinach glycolate oxidase deduced from the DNA sequence of a cDNA clone. J. Biol. Chem. 262: 15825-15828.
52. Wandrey, M., Trevaskis, B., Brewin, N. and Udvardi, M.K. (2004) Molecular and cell biology of a family of voltage-dependent anion channel porins in Lotus japonicus. Plant Physiol. 134: 182-193.
53. Wessel, D. and Flugge, U.I. (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138: 141-143.
54. Zolman, B.K., Monroe-Augustus, M., Thompson, B., Hawes, J.W., Krukenberg, K.A., Matsuda, S.P. and Bartel, B. (2001) chy1, an Arabidopsis mutant with impaired beta-oxidation, is defective in a peroxisomal beta- hydroxyisobutyryl-CoA hydrolase. J. Biol. Chem. 276: 31037-31046.