Arabidopsis thaliana-A model organism to study plant peroxisomes

Biochimica et Biophysica Acta - Molecular Cell Research

Volumn 1763, Issue 12, 2006, Pages 1382-1391

  Hayashi, Makoto ^a   Nishimura, Mikio ^a  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

Author keywords

Arabidopsis; Glyoxysome; Leaf peroxisome; Lipid metabolism; Photorespiration

Indexed keywords

ARABIDOPSIS; CELL FUNCTION; GENETIC ANALYSIS; GENOME; NONHUMAN; PEROXISOME; PLANT; PLANT MODEL; PRIORITY JOURNAL; REVIEW;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENOME, PLANT; MODELS, BIOLOGICAL; PEROXISOMES;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA;

EID: 33845297292     PISSN: 01674889     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamcr.2006.08.014     Document Type: Review

References (82)

1. Beevers H. Early research on peroxisomes in plants. In: Baker A., and Graham I.A. (Eds). Plant Peroxisomes (2002), Kluwer Academic publishers, Dordrecht 1-17
2. Beevers H. Glyoxysomes in higher plants. Ann. N.Y. Acad. Sci. 386 (1982) 243-251
3. Beevers H. Microbodies in higher plants. Annu. Rev. Plant Physiol. 30 (1979) 159-193
4. Nishimura M., Hayashi M., Kato A., Yamaguchi K., and Mano S. Functional transformation of microbodies in higher plant cells. Cell Struct. Funct. 21 (1996) 387-393
5. Trelease R.N., and Doman D.C. Mobilization of oil and wax reserves. In: Murray D.R. (Ed). Seed Physiology vol. 2 Germination and Reserve Mobilization (1984), Academic Press, New York 201-245
6. Hayashi H., De Bellis L., Ciurli A., Kondo M., Hayashi M., and Nishimura M. A novel acyl-CoA oxidase that can oxidize short-chain acyl-CoA in plant peroxisomes. J. Biol. Chem. 274 (1999) 12715-12721
7. Hayashi H., DeBellis L., Yamaguchi K., Kato A., Hayashi M., and Nishimura M. Molecular characterization of a glyoxysomal long chain acyl-CoA oxidase that is synthesized as a precursor of higher molecular mass in pumpkin. J. Biol. Chem. 273 (1998) 8301-8307
8. Hayashi M., Toriyama K., Kondo M., and Nishimura M. 2,4-dichlorophenoxybutyric acid-resistant mutants of Arabidopsis have defects in glyoxysomal fatty acid β-oxidation. Plant Cell 10 (1998) 183-195
9. Tolbert N.E. Leaf peroxisomes. Ann. N.Y. Acad. Sci. 386 (1982) 254-268
10. Titus D.E., and Becker W.M. Investigation of the glyoxysome-peroxisome transition in germinating cucumber cotyledons using double-label immunoelectron microscopy. J. Cell Biol. 101 (1985) 1288-1299
11. Nishimura M., Yamaguchi J., Mori H., Akazawa T., and Yokota S. Immunocytochemical analysis shows that glyoxysomes are directly transformed to leaf peroxisomes during greening of pumpkin cotyledons. Plant Physiol. 80 (1986) 313-316
12. Nishimura M., Takeuchi Y., De Bellis L., and Hara-Nishimura I. Leaf peroxisomes are directly transformed to glyoxysomes during senescence of pumpkin cotyledons. Protoplasma 175 (1993) 131-137
13. De Bellis L., Tsugeki R., and Nishimura M. Glyoxylate cycle enzymes in peroxisomes isolated from petals of pumpkin (Cucurbita sp.) during senescence. Plant Cell Physiol. 32 (1991) 1227-1235
14. De Bellis L., and Nishimura M. Development of enzymes of the glyoxylate cycle during senescence of pumpkin cotyledons. Plant Cell Physiol. 32 (1991) 555-561
15. Somerville C.R., and Ogren W.L. Photorespiration mutants of Arabidopsis thaliana deficient in serine-glyoxylate aminotransferase activity. Proc. Natl. Acad. Sci. U. S. A. 77 (1980) 2684-2687
16. Somerville C.R., and Ogren W.L. Genetic modification of photorespiration. Trends Biochem Sci. 7 (1982) 171-174
17. Somerville C.R. An early Arabidopsis demonstration. Resolving a few issues concerning photorespiration. Plant Physiol. 125 (2001) 20-24
18. Liepman A.H., and Olsen L.J. Peroxisomal alanine: glyoxylate aminotransferase (AGT1) is a photorespiratory enzyme with multiple substrates in Arabidopsis thaliana. Plant J. 25 (2001) 487-498
19. Zolman B.K., Yoder A., and Bartel B. Genetic analysis of indole-3-butyric acid responses in Arabidopsis thaliana reveals four mutant classes. Genetics 156 (2000) 1323-1337
20. Hayashi M., Nito K., Takei-Hoshi R., Yagi M., Kondo M., Suenaga A., Yamaya T., and Nishimura M. Ped3p is a peroxisomal ATP-binding cassette transporter that might supply substrates for fatty acid β-oxidation. Plant Cell Physiol. 43 (2002) 1-11
21. Hayashi M., Nito K., Toriyama-Kato K., Kondo M., Yamaya T., and Nishimura M. AtPex14p maintains peroxisomal functions by determining protein targeting to three kinds of plant peroxisomes. EMBO J. 19 (2000) 5701-5710
22. Zolman B.K., MonroeAugustus M., Thompson B., Hawes J.W., Krukenberg K.A., Matsuda S.P.T., and Bartel B. chy1, an Arabidopsis mutant with impaired β-oxidation, is defective in a peroxisomal β-hydroxyisobutyryl-CoA hydrolase. J. Biol. Chem. 276 (2001) 31037-31046
23. Zolman B.K., Silva I.D., and Bartel B. The Arabidopsis pxa1 mutant is defective in an ATP-binding cassette transporter-like protein required for peroxisomal fatty acid beta-oxidation. Plant Physiol. 127 (2001) 1266-1278
24. Zolman B.K., and Bartel B. An Arabidopsis indole-3-butyric acid-response mutant defective in PEROXIN6, an apparent ATPase implicated in peroxisomal function. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 1786-1791
25. Adham A.R., Zolman B.K., Millius A., and Bartel B. Mutations in Arabidopsis acyl-CoA oxidase genes reveal distinct and overlapping roles in beta-oxidation. Plant J. 41 (2005) 859-874
26. Woodward A.W., and Bartel B. The Arabidopsis peroxisomal targeting signal type 2 receptor PEX7 is necessary for peroxisome function and dependent on PEX5. Mol. Biol. Cell 16 (2005) 573-583
27. Zolman B.K., Monroe-Augustus M., Silva I.D., and Bartel B. Identification and functional characterization of Arabidopsis PEROXIN4 and the interacting protein PEROXIN22. Plant Cell 17 (2005) 3422-3435
28. Footitt S., Slocombe S.P., Larner V., Kurup S., Wu Y.S., Larson T., Graham I., Baker A., and Holdsworth M. Control of germination and lipid mobilization by COMATOSE, the Arabidopsis homologue of human ALDP. EMBO J. 21 (2002) 2912-2922
29. Hayashi H., De Bellis L., Hayashi Y., Nito K., Kato A., Hayashi M., Hara-Nishimura I., and Nishimura M. Molecular characterization of an Arabidopsis acyl-coenzyme A synthetase localized on glyoxysomal membranes. Plant Physiol. 130 (2002) 2019-2026
30. Fulda M., Shockey J., Werber M., Wolter F.P., and Heinz E. Two long-chain acyl-CoA synthetases from Arabidopsis thaliana involved in peroxisomal fatty acid beta-oxidation. Plant J. 32 (2002) 93-103
31. Theodoulou F.L., Slocombe S.P., Footitt S., Holdsworth M., Baker A., Larson T.R., and Grahama I.A. Jasmonoic acid levels are reduced in COMATOSE ATP-binding cassette transporter mutants. Implications for transport of jasmonate precursors into peroxisomes. Plant Physiol. 137 (2005)
32. Germain V., Rylott E.L., Larson T.R., Sherson S.M., Bechtold N., Carde J.P., Bryce J.H., Graham I.A., and Smith S.M. Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings. Plant J. 28 (2001) 1-12
33. Hayashi Y., Hayashi H., Hayashi M., Hara-Nishimura I., and Nishimura M. Direct interaction between glyoxysomes and lipid bodies in cotyledons of the Arabidopsis thaliana ped1 mutant. Protoplasma 218 (2001) 83-94
34. Eastmond P.J., Hooks M.A., Williams D., Lange P., Bechtold N., Sarrobert C., Nussaume L., and Graham I.A. Promoter trapping of a novel medium-chain acyl-CoA oxidase, which is induced transcriptionally during Arabidopsis seed germination. J. Biol. Chem. 275 (2000) 34375-34381
35. Hooks M.A., Kellas F., and Graham I.A. Long-chain acyl-CoA oxidases of Arabidopsis. Plant J. 20 (1999) 1-13
36. Rylott E.L., Rogers C.A., Gilday A.D., Edgell T., Larson T.R., and Graham I.A. Arabidopsis mutants in short- and medium-chain acyl-CoA oxidase activities accumulate acyl-CoAs and reveal that fatty acid beta-oxidation is essential for embryo development. J. Biol. Chem. 278 (2003) 21370-21377
37. Froman B.E., Edwards P.C., Bursch A.G., and Dehesh K. ACX3, a novel medium-chain acyl-coenzyme A oxidase from Arabidopsis. Plant Physiol. 123 (2000) 733-741
38. Will G.K., Soukupova M., Hong X., Erdmann K.S., Kiel J., Dodt G., Kunau W.H., and Erdmann R. Identification and characterization of the human orthologue of yeast pex14p. Mol. Cell. Biol. 19 (1999) 2265-2277
39. Albertini M., Rehling P., Erdmann R., Girzalsky W., Kiel J.A.K.W., Veenhuis M., and Kunau W.H. Pex14p, a peroxisomal membrane protein binding both receptors of the two PTS-dependent import pathways. Cell 89 (1997) 83-92
40. Nito K., Hayashi M., and Nishimura M. Direct interaction and determination of binding domains among peroxisomal import factors in Arabidopsis thaliana. Plant Cell Physiol. 43 (2002) 355-366
41. Otera H., Harano T., Honsho M., Ghaedi K., Mukai S., Tanaka A., Kawai A., Shimizu N., and Fujiki Y. The mammalian peroxin Pex5pL, the longer isoform of the mobile peroxisome targeting signal (PTS) type 1 transporter, translocates the Pex7p center dot PTS2 protein complex into peroxisomes via its initial docking site, Pex14p. J. Biol. Chem. 275 (2000) 21703-21714
42. Mano S., and Nishimura M. Plant peroxisomes. Vitam. Horm. 72 (2005) 111-154
43. Mano S., Nakamori C., Hayashi M., Kato A., Kondo M., and Nishimura M. Distribution and characterization of peroxisomes in Arabidopsis by visualization with GFP: dynamic morphology and actin-dependent movement. Plant Cell Physiol. 43 (2002) 331-341
44. Mano S., Nakamori C., Hayashi C., Nito K., Kondo M., and Nishimura M. The Arabidopsis pex12 and pex13 mutants are defective in both PTS1- and PTS2-dependent protein transport to peroxisomes. Plant J. 47 (2006) 604-618
45. Mano S., Nakamori C., Kondo M., Hayashi M., and Nishimura M. An Arabidopsis dynamin-related protein, DRP3A, controls both peroxisomal and mitochondrial division. Plant Cell Physiol. 38 (2004) 487-498
46. Richmond T.A., and Bleecker A.B. A defect in β-oxidation causes abnormal inflorescence development in Arabidopsis. Plant Cell 11 (1999) 1911-1923
47. Rylott E.L., Eastmond P.J., Gilday A.D., Slocombe S.P., Larson T.R., Baker A., and Graham I.A. The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal β-oxidation is essential for seedling establishment. Plant J. 45 (2006) 903-941
48. Sanders P.M., Lee P.Y., Biesgen C., Boone J.D., Beals T.P., Weiler E.W., and Goldberg R.B. The Arabidopsis DELAYED DEHISCENCE1 gene encodes an enzyme in the jasmonic acid synthesis pathway. Plant Cell 12 (2000) 1041-1061
49. Stintzi A., and Browse J. The Arabidopsis male-sterile mutant, opr3, lacks the 12-oxophytodienoic acid reductase required for jasmonate synthesis. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 10625-10630
50. Strassner J., Schaller F., Frick U.B., Howe G.A., Weiler E.W., Amrhein N., Macheroux P., and Schaller A. Characterization and cDNA-microarray expression analysis of 12-oxophytodienoate reductases reveals differential roles for octadecanoid biosynthesis in the local versus the systemic wound response. Plant J. 32 (2002) 585-601
51. Lin Y., Sun L., Nguyen L.V., Rachubinski R.A., and Goodman H.M. The pex16p homolog SSE1 and storage organelle formation in Arabidopsis seeds. Science 284 (1999) 328-330
52. Lin Y., Cluette-Brown J.E., and Goodman H.M. The peroxisome deficient Arabidopsis mutant sse1 exhibits impaired fatty acid synthesis. Plant Physiol. 135 (2004) 814-827
53. Eitzen G.A., Szilard R.K., and Rachubinski R.A. Enlarged peroxisomes are present in oleic acid-grown Yarrowia lipolytica overexpressing the PEX16 gene encoding an intraperoxisomal peripheral membrane peroxin. J. Cell Biol. 137 (1997) 1265-1278
54. Schwechjeimer C., and Deng X.W. The COP/DET/FUS proteins-Regulators of eukaryotic growth and development. Semin. Cell Dev. Biol. 11 (2000) 495-503
55. Hu J.P., Aguirre M., Peto C., Alonso J., Ecker J., and Chory J. A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science 297 (2002) 405-409
56. Huang Y., Ito R., Miura S., Hashimoto T., and Ito M. A missense mutation in the RING finger motif of PEX2 protein disturbs the import of peroxisome targeting signal 1 (PTS1)-containing protein but not the PTS2-containing protein. Biochem. Biophys. Res. Commun. 270 (2000) 717-721
57. Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 796-815
58. Alonso J.M., Stepanova A.N., Leisse T.J., et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301 (2003) 653-657
59. Fulda M., Schnurr J., Abbadi A., Heinz E., and Browse J. Peroxisomal Acyl-CoA synthetase activity is essential for seedling development in Arabidopsis thaliana. Plant Cell 16 (2004) 394-405
60. Igarashi D., Miwa T., Seki M., Kobayashi M., Kato T., Tabata S., Shinozaki K., and Ohsumi C. Identification of photorespiratory glutamate: glyoxylate aminotransferase (GGAT) gene in Arabidopsis. Plant J. 33 (2003) 975-987
61. Eastmond P.J., Germain V., Lange P.R., Bryce J.H., Smith S.M., and Graham I.A. Postgerminative growth and lipid catabolism in oilseeds lacking the glyoxylate cycle. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 5669-5674
62. Cornah J.E., Germain V., Ward J.L., Beale M.H., and Smith S.M. Lipid utilization, gluconeogenesis and seedling growth in Arabidopsis mutants lacking the glyoxylate cycle enzyme malate synthase. J. Biol. Chem. 279 (2004) 42916-42923
63. Pracharoenwattana I., Cornah J.E., and Smith S.M. Arabidopsis peroxisomal citrate synthase is required for fatty acid respiration and seed germination. Plant Cell 17 (2005) 2037-2048
64. Mullen R.T., Flynn C.R., and Trelease R.N. How are peroxisomes formed? The role of the endoplasmic reticulum and peroxins. Trends Plant Sci. 6 (2001) 256-261
65. Charlton W., and Lopez-Huertas E. PEX genes in plants and other organisms. In: Baker A., and Graham I.A. (Eds). Plant peroxisomes (2002), Kluwer Academic Publishers, Dordrecht 385-426
66. Sparkes I.A., Brandizzi F., Slocombe S.P., El-Shami M., Hawes C., and Baker A. An Arabidopsis pex10 null mutant is embryo lethal, implicating peroxisomes in an essential role during plant embryogenesis. Plant Physiol. 133 (2003) 1809-1819
67. Schumann U., Wanner G., Veenhuis M., Schmid M., and Gietl C. AthPEX10, ariuclear gene essential for peroxisome and storage organelle formation during Arabidopsis embryogenesis. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9626-9631
68. Fan J.L., Quan S., Orth T., Awai C., Chory J., and Hu J.P. The Arabidopsis PEX12 gene is required for peroxisome biogenesis and is essential for development. Plant Physiol. 139 (2005) 231-239
69. Wang M.B., and Waterhouse P.M. Application of gene silencing in plants. Curr. Opin. Plant Biol. 5 (2002) 146-150
70. Levin J.Z., de Framond A.J., Tuttle A., Bauser M.W., and Heifetz P.B. Methods of double-stranded RNA-mediated gene inactivation in Arabidopsis and their use to define an essential gene in methionine biosynthesis. Plant Mol. Biol. 44 (2000) 759-775
71. Chuang C.-F., and Meyerowitz E.M. Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 4985-4990
72. Smith N.A., Singh S.P., Wang M.B., Stoutjesdijk P.A., Green A.G., and Waterhouse P.M. Gene expression-Total silencing by intron-spliced hairpin RNAs. Nature 407 (2000) 319-320
73. Hayashi M., Yagi M., Nito K., Kamada T., and Nishimura M. Differential contribution of two peroxisomal protein receptors to the maintenance of peroxisomal functions in Arabidopsis. J. Biol. Chem. 280 (2005) 14829-14835
74. Lingard M.J., and Trelease R.N. Five Arabidopsis peroxin 11 homologs individually promote peroxisome elongation, duplication or aggregation. J. Cell Sci. 11 (2006) 961-972
75. Hadden D.A., Phillipson B.A., Johnston K.A., Brown L.-A., Manfield I.W., El-Shami M., Sparkes I.A., and Baker A. Arabidopsis PEX19 is a dimeric protein that binds the peroxin PEX10. Mol. Membr. Biol. 23 (2006) 325-336
76. Hayashi M., Aoki M., Kato A., Kondo M., and Nishimura M. Transport of chimeric proteins that contain a carboxy-terminal targeting signal into plant microbodies. Plant J. 10 (1996) 225-234
77. Hayashi M., Aoki M., Kondo M., and Nishimura M. Changes in targeting efficiencies of proteins to plant microbodies caused by amino acid substitutions in the carboxy-terminal tripeptide. Plant Cell Physiol. 38 (1997) 759-768
78. Kamada T., Nito K., Hayashi H., Mano S., Hayashi M., and Nishimura M. Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana. Plant Cell Physiol. 44 (2003) 1275-1289
79. Reumann S. Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses. Plant Physiol. 135 (2004) 783-800
80. Emanuelsson O., Elofsson A., von Heijne G., and Cristóbal S. In silico prediction of the peroxisomal proteome in fungi, plants and animals. J. Mol. Biol. 330 (2003) 443-456
81. Fukao Y., Hayashi Y., Mano M., Hayashi M., and Nishimura M. Developmental analysis of a putative ATP/ADP carrier protein localized on glyoxysomal membranes during the peroxisome transition in pumpkin cotyledons. Plant Cell Physiol. 42 (2001) 835-841
82. Fukao Y., Hayashi M., and Nishimura M. Proteomic analysis of leaf peroxisomal proteins in greening cotyledons of Arabidopsis thaliana. Plant Cell Physiol. 43 (2002) 689-696