Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation

Plant Journal

Volumn 42, Issue 5, 2005, Pages 618-640

  Ehlting, Jürgen ^a   Mattheus, Nathalie ^a   Aeschliman, Dana S ^a   Li, Eryang ^b   Hamberger, Britta ^a   Cullis, Ian F ^b   Zhuang, Jun ^a   Kaneda, Minako ^b   Mansfield, Shawn D ^b   Samuels, Lacey ^b   Ritland, Kermit ^b   Ellis, Brian E ^a,b   Bohlmann, Jörg ^a,b   Douglas, Carl J ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Fiber; Lignin biosynthesis; Longmer microarray; Phenylpropanoid metabolism; Shikimate pathway; Transcription factors

Indexed keywords

BIOSYNTHESIS; GENES; MATHEMATICAL MODELS; METABOLISM; NATURAL FIBERS; POLYNOMIALS; REGRESSION ANALYSIS;

ARABIDOPSIS; CANDIDATE GENES; FIBER DIFFERENTIATION; TRANSCRIPT PROFILING;

PLANTS (BOTANY);

LIGNIN; PHENYLALANINE; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; BIOSYNTHESIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYSIOLOGY; PLANT STEM; TRANSPORT AT THE CELLULAR LEVEL;

ARABIDOPSIS; BIOLOGICAL TRANSPORT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; LIGNIN; PHENYLALANINE; PLANT STEMS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BIOSYNTHESIS; FIBERS; GENES; MATHEMATICAL MODELS; METABOLISM; PLANTS; REGRESSION ANALYSIS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 20444484861     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2005.02403.x     Document Type: Article

References (112)

1. Ackerman, S.H., Martin, J. and Tzagoloff, A. (1992) Characterization of ATP11 and detection of the encoded protein in mitochondria of Saccharomyces cerevisiae. J. Biol. Chem. 267, 7386-7394.
2. Baima, S., Possenti, M., Matteucci, A., Wisman, E., Altamura, M.M., Ruberti, I. and Morelli, G. (2001) The Arabidopsis ATHB-8 HD-Zip protein acts as a differentiation-promoting transcription factor of the vascular meristems. Plant Physiol. 126, 643-655.
3. Baudry, A., Heim, M.A., Dubreucq, B., Caboche, M., Weisshaar, B. and Lepiniec, L. (2004) TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J. 39, 366-380.
4. Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W. and Benfey, P.N. (2003) A gene expression map of the Arabidopsis root. Science, 302, 1956-1960.
5. Blee, K.A., Choi, J.W., O'Connell, A.P., Schuch, W., Lewis, N.G. and Bolwell, G.P. (2003) A lignin-specific peroxidase in tobacco whose antisense suppression leads to vascular tissue modification. Phytochemistry, 64, 163-176.
6. Boerjan, W., Cervera, M.T., Delarue, M., Beeckman, T., Dewitte, W., Bellini, C., Caboche, M., Van Onckelen, H., Van Montagu, M. and Inze, D. (1995) Superroot, a recessive mutation in Arabidopsis, confers auxin overproduction. Plant Cell, 7, 1405-1419.
7. Boerjan, W., Ralph, J. and Baucher, M. (2003) Lignin biosynthesis. Physiol. Plant. 54, 519-546.
8. Bonke, M., Thitamadee, S., Mahonen, A.P., Hauser, M.-T. and Helariutta, Y. (2003) APL regulates vascular tissue identity in Arabidopsis. Nature, 426, 181-186.
9. Borevitz, J.O., Xia, Y., Blount, J., Dixon, R.A. and Lamb, C. (2000) Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell, 12, 2383-2394.
10. van den Brûle, S., Muller, A., Fleming, A.J. and Smart, C.C. (2002) The ABC transporter SpTUR2 confers resistance to the antifungal diterpene sclareol. Plant J. 30, 649-662.
11. Bryan, J. (2004) Problems in gene clustering based on gene expression data. J. Multivariate Anal. 90, 44-66.
12. Burk, D.H., Liu, B., Zhong, R., Morrison, W.H. and Ye, Z.-H. (2001) A katanin-like protein regulates normal cell wall biosynthesis and cell elongation. Plant Cell, 13, 807-828.
13. Carter, C., Graham, R.A. and Thornburg, R.W. (1998) Arabidopsis thaliana contains a large family of germin-like proteins:characterization of cDNA and genomic sequences encoding 12 unique family members. Plant Mol. Biol. 38, 929-943.
14. Celenza, J.L. Jr, Grisafi, P.L. and Fink, G.R. (1995) A pathway for lateral root formation in Arabidopsis thaliana. Genes Dev. 9, 2131-2134.
15. Chaffey, N., Cholewa, E., Regan, S. and Sundberg, B. (2002) Secondary xylem development in Arabidopsis: a model for wood formation. Physiol. Plant. 114, 594-600.
16. Chapple, C.C., Vogt, T., Ellis, B.E. and Somerville, C.R. (1992) An Arabidopsis mutant defective in the general phenylpropanoid pathway. Plant Cell, 4, 1413-1424.
17. Christensen, J.H., Overney, S., Rohde, A., Diaz, W.A., Bauw, G., Simon, P., van Montagu, M. and Boerjan, W. (2001) The syringaldazine-oxidizing peroxidase PXP3-4 from poplar xylem: cDNA isolation, characterization and expression. Plant Mol. Biol. 47, 581-593.
18. Costa, M.A., Collins, R.E., Anterola, A.M., Cochrane, F.C., Davin, L.B. and Lewis, N.G. (2003) An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof. Phytochemistry, 64, 1097-1112.
19. Cukovic, D., Ehlting, J., VanZiffle, J.A. and Douglas, C.J. (2001) Structure and evolution of 4-coumarate:coenzyme A ligase (4CL) gene families. Biol. Chem. 382, 645-654.
20. Davin, L.B., Wang, H.-B., Crowell, A.L., Bedgar, D.L., Martin, D.M., Sarkanen, S. and Lewis, N.G. (1997) Stereoselective bimolecular phenoxy radical coupling by an auxiliary (dirigent) protein without an active center. Science, 275, 362-367.
21. Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M. and Grotewold, E. (2003) AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics, 4, 25.
22. De-Eknamkul, W. and Ellis, B.E. (1988) Purification and characterization of prephenate aminotransferase from Anchusa officinalis cell cultures. Arch. Biochem. Biophys. 267, 87-94.
23. Demura, T., Tashiro, G., Horiguchi, G. et al. (2002) Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl Acad. Sci. USA, 99, 15794-15799.
24. Després, C., Chubak, C., Rochon, A., Clark, R., Bethune, T., Desveaux, D. and Fobert, P.R. (2003) The Arabidopsis NPR1 disease resistance protein is a novel cofactor that confers redox regulation of DNA binding activity to the basic domain/leucine zipper transcription factor TGA1. Plant Cell, 15, 2181-2191.
25. Dharmawardhana, D.P., Ellis, B.E. and Carlson, J.E. (1992) Characterization of vascular lignification in Arabidopsis thaliana. Can. J. Bot. 70, 2238-2244.
26. Di Laurenzio, L., Wysocka-Diller, J., Malamy, J.E., Pysh, L., Helariutta, Y., Freshour, G., Hahn, M.G., Feldmann, K.A. and Benfey, P.N. (1996) The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell, 86, 423-433.
27. Dixon, R.A., Achnine, L., Kota, P., Liu, C.-J., Reddy, M.S.S. and Wang, L. (2002) The phenylpropanoid pathway and plant defence - a genomics perspective. Mol. Plant Pathol. 3, 371-390.
28. Eberhard, J., Raesecke, H.-R., Schmid, J. and Amrhein, N. (1993) Cloning and expression in yeast of a higher plant chorismate mutase. Molecular cloning, sequencing of the cDNA and characterization of the Arabidopsis thaliana enzyme expressed in yeast. FEBS Lett. 334, 233-236.
29. Eberhard, J., Ehrler, T.T., Epple, P., Felix, G., Raesecke, H.-R., Amrhein, N. and Schmid, J. (1996) Cytosolic and plastidic chorismate mutase isozymes from Arabidopsis thaliana: molecular characterization and enzymatic properties. Plant J. 10, 815-821.
30. Emery, J.F., Floyd, S.K., Alvarez, J., Eshed, Y., Hawker, N.P., Izhaki, A., Baum, S.F. and Bowman, J.L. (2003) Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13, 1768-1774.
31. Gang, D.R., Costa, M.A., Fujita, M., Dinkova-Kostova, A.T., Wang, H.-B., Burlat, V., Martin, W., Sarkanen, S., Davin, L.B. and Lewis, N.G. (1999) Regiochemical control of monolignol radical coupling: a new paradigm for lignin and lignan biosynthesis. Chem. Biol. 6, 143-151.
32. Garcia, O., Bouige, P., Forestier, C. and Dassa, E. (2004) Inventory and comparative analysis of rice and Arabidopsis ATP-binding cassette (ABC) systems. J. Mol. Biol. 343, 249-265.
33. Gaskin, B.J., Adcock, H.J., Buckberry, L.D., Teesdale-Spittle, P.H. and Shaw, P.M. (1995) The C-S lysis of L-cysteine conjugates by aspartate and alanine aminotransferace enzymes. Hum. Exp. Toxicol. 14, 422-427.
34. Gavnholt, B. and Larsen, K. (2002) Molecular biology of plant laccases in relation to lignin formation. Physiol. Plant, 116, 273-280.
35. Gavnholt, B., Larsen, K. and Rasmussen, S.K. (2002) Isolation and characterisation of laccase cDNAs from meristematic and stem tissues of ryegrass (Lolium perenne). Plant Sci. 162, 873-885.
36. Goff, S.A., Cone, K.C. and Chandler, V.L. (1992) Functional analysis of the transcriptional activator encoded by the maize B gene: evidence for a direct functional interaction between two classes of regulatory proteins. Genes Dev. 6, 864-875.
37. Goodman, C.D., Casati, P. and Walbot, V. (2004) A multidrug resistance-associated protein involved in anthocyanin transport in Zea mays. Plant Cell, 16, 1812-1826.
38. Goujon, T., Sibout, R., Eudes, A., MacKay, J. and Jouanin, L. (2003) Genes involved in the biosynthesis of lignin precursors in Arabidopsis thaliana. Plant Physiol. Biochem. 41, 677-687.
39. Gutterson, N. and Reuber, T.L. (2004) Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7, 465-471.
40. Hahlbrock, K. and Scheel, D. (1989) Physiology and molecular biology of phenylpropanoid metabolism. Annu. Rev. Plant Physiol. 40, 347-369.
41. Hardtke, C.S. and Berleth, T. (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J. 17, 1405-1411.
42. Hertzberg, M., Aspeborg, H., Schrader, J. et al. (2001) A transcriptional roadmap to wood formation. Proc. Natl Acad. Sci. USA, 98, 14732-14737.
43. Higgins, C.F. (2001) ABC transporters: physiology, structure and mechanism - an overview. Res. Microbiol. 152, 205-210.
44. Hiraga, S., Sasaki, K., Ito, H., Ohashi, Y. and Matsui, H. (2001) A large family of class III plant peroxidases. Plant Cell Physiol. 42, 462-468.
45. Hsieh, M.-H. and Goodman, H.M. (2002) Molecular characterization of a novel gene family encoding ACT domain repeat proteins in Arabidopsis. Plant Physiol. 130, 1797-1806.
46. Hu, Y., Zhong, R., Morrison, W.H., III and Ye, Z.-H. (2003) The Arabidopsis RHD3 gene is required for cell wall biosynthesis and actin organization. Planta, 217, 912-921.
47. Humphreys, J.M. and Chapple, C. (2002) Rewriting the lignin roadmap. Curr. Opin. Plant Biol. 5, 224-229.
48. Huntley, S.K., Ellis, D., Gilbert, M., Chapple, C., and Mansfield, S.D. (2003) Improved pulping efficiency in C4H-F5H transformed poplar. J. Agric. Food Chem. 51, 6178-6183.
49. Iraqui, I., Vissers, S., Cartiaux, M. and Urrestarazu, A. (1998) Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily. Mol. Gen. Genet. 257, 238-248.
50. Jakoby, M., Weisshaar, B., Droge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T. and Parcy, F. (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci. 7, 106-111.
51. Jasinski, M., Stukkens, Y., Degand, H., Purnelle, B., Marchand-Brynaert, J. and Boutry, M. (2001) A plant plasma membrane ATP binding cassette-type transporter is involved in antifungal terpenoid secretion. Plant Cell, 13, 1095-1107.
52. Jin, H., Cominelli, E., Bailey, P., Parr, A., Mehrtens, F., Jones, J., Tonelli, C., Weisshaar, B. and Martin, C. (2000) Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis. EMBO J. 19, 6150-6161.
53. Jofuku, K.D., den Boer, B.G.W., Montagu, M.V. and Okamuro, J.K. (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell, 6, 1211-1225.
54. Jones, M.G., Hughes, J., Tregova, A., Milne, J., Tomsett, A.B. and Collin, H.A. (2004) Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot. 55, 1903-1918.
55. Keith, B., Dong, X., Ausubel, F. and Fink, G. (1991) Differential induction of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase genes in Arabidopsis thaliana by wounding and pathogenic attack. PNAS, 88, 8821-8825.
56. Kiefer-Meyer, M.-C., Gomord, V., O'Connell, A., Halpin, C. and Faye, L. (1996) Cloning and sequence analysis of laccase-encoding cDNA clones from tobacco. Gene, 178, 205-207.
57. Kim, M.K., Jeon, J.-H., Davin, L.B. and Lewis, N.G. (2002) Monolignol radical-radical coupling networks in western red cedar and Arabidopsis and their evolutionary implications. Phytochemistry, 61, 311-322.
58. King, J.J., Stimart, O.P., Fisher, R.H. and Bleecker, A.B. (1995) A mutation altering auxin homeostasis and plant morphology in Arabidopsis. Plant Cell, 7, 2023-2037.
59. Ko, J.-H., Han, K.-H., Park, S. and Yang, J. (2004) Plant body weight-induced secondary growth in Arabidopsis and its transcription phenotype revealed by whole-transcriptome profiling. Plant Physiol. 135, 1069-1083.
60. LaFayette, P.R., Eriksson, K.-E.L. and Dean, J.F.D. (1999) Characterization and heterologous expression of laccase cDNAs from xylem tissues of yellow-poplar (Liriodendron tulipifera). Plant Mol. Biol. 40, 23-35.
61. Lancaster, J.E., Shaw, M.J. and Walton, E.F. (2000) S-alk(en)yl-L- cysteine sulfoxides, allinase and aroma in Leucocoryne. Phytochemistry. 55, 127-130.
62. Lapierre, C., Pollet, B., Petit-Conil, M. et al. (1999) Structural alterations of lignins in transgenic poplars with depressed cinnamyl alcohol dehydrogenase or caffeic acid O-methyltransferase activity have an opposite impact on the efficiency of industrial kraft pulping. Plant Physiol. 119, 153-164.
63. Lee, D., Meyer, K., Chapple, C. and Douglas, C.J. (1997) Antisense suppression of 4-Coumarate:Coenzyme A ligase activity in Arabidopsis leads to altered lignin subunit composition. Plant Cell, 9, 1985-1998.
64. Lehman, A., Black, R. and Ecker, J.R. (1996) HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. Cell. 85, 183-194.
65. 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.
66. Lim, E.-K., Li, Y., Parr, A., Jackson, R., Ashford, D.A. and Bowles, D.J. (2001) Identification of glucosyltransferase genes involved in sinapate metabolism and lignin synthesis in Arabidopsis. J. Biol. Chem. 276, 4344-4349.
67. Little, C.H.A., MacDonald, J.E. and Olsson, O. (2002) Involvement of indole-3-acetic acid in fascicular and interfascicular cambial growth and interfascicular extraxylary fiber differentiation in Arabidopsis thaliana inflorescence stems. Int. J. Plant Sci. 163, 519-529.
68. Mackenzie, S.M., Howells, A.J., Cox, G.B. and Ewart, G.D. (2000) Sub-cellular localisation of the White/Scarlet ABC transporter to pigment granule membranes within the compound eye of Drosophila melanogaster. Genetica, 108, 239-252.
69. Mele, G., Ori, N., Sato, Y. and Hake, S. (2003) The knotted1-like homeobox gene BREVIPEDICELLUS regulates cell differentiation by modulating metabolic pathways. Genes Dev. 17, 2088-2093.
70. Mikkelsen, M.D., Naur, P. and Halkier, B.A. (2004) Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis. Plant J. 37, 770-777.
71. Mizutani, M. and Ohta, D. (1998) Two isoforms of NADPH:cytochrome P450 reductase in Arabidopsis thaliana. Gene structure, heterologous expression in insect cells, and differential regulation. Plant Physiol. 116, 357-367.
72. Mobley, E.M., Kunkel, B.N. and Keith, B. (1999) Identification, characterization and comparative analysis of a novel chorismate mutase gene in Arabidopsis thaliana. Gene, 240, 115-123.
73. Morgenstern, B., Frech, K., Dress, A. and Werner, T. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290-294.
74. Newman, L.J., Perazza, D.E., Juda, L. and Campbell, M.M. (2004) Involvement of the R2R3-MYB, AtMYB61, in the ectopic lignification and dark-photomorphogenic components of the det3 mutant phenotype. Plant J. 37, 239-250.
75. Nieminen, K.M., Kauppinen, L. and Helariutta, Y. (2004) A weed for wood? Arabidopsis as a genetic model for xylem development. Plant Physiol. 135, 653-659.
76. Oh, S., Park, S. and Han, K.-H. (2003) Transcriptional regulation of secondary growth in Arabidopsis thaliana. J. Exp. Bot. 54, 2709-2722.
77. Ohkawa, J., Okada, N., Shinmyo, A. and Takano, M. (1989) Primary structure of cucumber (Cucumis sativus) ascorbate oxidase deduced from cDNA sequence: homology with blue copper proteins and tissue-specific expression. Proc. Natl Acad. Sci. USA, 86, 1239-1243.
78. Østergaard, L., Teilum, K., Mirza, O., Mattsson, O., Petersen, M., Welinder, K.G., Mundy, J., Gajhede, M. and Henriksen, A. (2000) Arabidopsis ATP A2 peroxidase. Expression and high-resolution structure of a plant peroxidase with implications for lignification. Plant Mol. Biol. 44, 231-243.
79. Payne, C.T., Zhang, F. and Lloyd, A.M. (2000) GL3 encodes a bHLH protein that regulates trichome development in Arabidopsis through interaction with GL1 and TTG1. Genetics, 156, 1349-1362.
80. Penfield, S., Meissner, R.C., Shoue, D.A., Carpita, N.C. and Bevan, M.W. (2001) MYB61 is required for mucilage deposition and extrusion in the Arabidopsis seed coat. Plant Cell, 13, 2777-2791.
81. Pighin, J.A., Zheng, H., Balakshin, L.J., Goodman, I.P., Western, T.L., Jetter, R., Kunst, L. and Samuels, A.L. (2004) Plant cuticular lipid export requires an ABC transporter. Science, 306, 702-704.
82. Putterill, J., Robson, F., Lee, K., Simon, R. and Coupland, G. (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell, 80, 847-857.
83. Raes, J., Rohde, A., Christensen, J.H., van de Peer, Y. and Boerjan, W. (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 133, 1051-1071.
84. Ranocha, P., Chabannes, M., Chamayou, S., Danoun, S., Jauneau, A., Boudet, A.-M. and Goffner, D. (2002) Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar. Plant Physiol. 129, 145-155.
85. Riechmann, J.L. and Meyerowitz, E.M. (1998) The AP2/EREBP family of plant transcription factors. Biol. Chem. 379, 633-646.
86. Rippert, P. and Matringe, M. (2002a) Molecular and biochemical characterization of an Arabidopsis thaliana arogenate dehydrogenase with two highly similar and active protein domains. Plant Mol. Biol. 48, 361-368.
87. Rippert, P. and Matringe, M. (2002b) Purification and kinetic analysis of the two recombinant arogenate dehydrogenase isoforms of Arabidopsis thaliana. Eur. J. Biochem. 269, 4753-4761.
88. Rohde, A., Morreel, K., Ralph, J. et al. (2004) Molecular phenotyping of the pal 1 and pa/2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. Plant Cell, 16, 2749-2771.
89. Ruepp, A., Zollner, A., Maier, D. et al., (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32, 5539-5545.
90. Samuels, A., Rensing, K., Douglas, C.J., Mansfield, S., Dharmawardhana, D. and Ellis, B.E. (2002) Cellular machinery of wood production: differentiation of secondary xylem in Pinus contorta var. latifolia. Planta, 216, 72-82.
91. Sánchez-Fernández, R., Davies, T.G.E., Coleman, J.O.D. and Rea, P.A. (2001) The Arabidopsis thaliana ABC protein superfamily, a complete inventory. J. Biol. Chem. 276, 30231-30244.
92. Schmid, J., Schaller, A., Leibinger, U., Boll, W. and Amrhein, N. (1992) The in-vitro synthesized tomato shikimate kinase precursor is enzymatically active and is imported and processed to the mature enzyme by chloroplasts. Plant J. 2, 375-383.
93. Schoof, H., Zaccaria, P., Gundlach, H., Lemcke, K., Rudd, S., Kolesov, G., Arnold, R., Mewes, H.W. and Mayer, K.F. (2002) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 30, 91-93.
94. Serikawa, K.A., Martinez-Laborda, A. and Zambryski, P. (1996) Three knotted1-like homeobox genes in Arabidopsis. Plant Mol. Biol. 32, 673-683.
95. Shitan, N., Bazin, I., Dan, K., Obata, K., Kigawa, K., Ueda, K., Sato, F., Forestier, C. and Yazaki, K. (2003) Involvement of CjMDR1, a plant multidrug-resistance-type ATP-binding cassette protein, in alkaloid transport in Coptis japonica. Proc. Natl Acad. Sci. USA, 100, 751-756.
96. Shockey, J.M., Fulda, M.S. and Browse, J. (2003) Arabidopsis contains a large superfamily of acyl-activating enzymes. Phylogenetic and biochemical analysis reveals a new class of acylcoenzyme A synthetases. Plant Physiol. 132, 1065-1076.
97. Siehl, D.L. and Conn, E.E. (1988) Kinetic and regulatory properties of arogenate dehydratase in seedlings of Sorghum bicolor (L.) Moench. Arch. Biochem. Biophys. 260, 822-929.
98. Siehl, D.L., Connelly, J.A. and Conn, E.E. (1986) Tyrosine biosynthesis in Sorghum bicolor. characteristics of prephenate aminotransferase. Z. Naturforsch. 41, 79-86.
99. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
100. Stracke, R., Werber, M. and Weisshaar, B. (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr. Opin. Plant Biol. 4, 447-456.
101. Taylor, N.G., Howells, R.M., Huttly, A.K., Vickers, K. and Turner, S.R. (2003) Interactions among three distinct CesA proteins essential for cellulose synthesis. Proc. Natl Acad. Sci. USA, 100, 1450-1455.
102. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
103. phox). Plant J. 14, 365-370.
104. Tsiantis, M. (2001) Control of shoot cell fate: beyond homeoboxes. Plant Cell, 13, 733-738.
105. Welinder, K.G., Justesen, A.F., Kjaersgard, I.V.H., Jensen, R.B., Rasmussen, S.K., Jespersen, H.M. and Duroux, L. (2002) Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana. Eur. J. Biochem. 269, 6063-6081.
106. Whetten, R.W., MacKay, J.J. and Sederoff, R.R. (1998) Recent advances in understanding lignin biosynthesis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49, 585-609.
107. Winicov, I. (2000) Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. Planta, 210, 416-422.
108. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J. and Speed, T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.
109. Ye, Z.-H., Freshour, G., Hahn, M.G., Burk, D.H. and Zhong, R. (2002) Vascular development in Arabidopsis. Int. Rev. Cytol. 220, 225-238.
110. Zhong, R. and Ye, Z.-H. (1999) IFL1, a gene regulating interfascicular fiber differentiation in Arabidopsis, encodes a homeodomain-leucine zipper protein. Plant Cell, 11, 2139-2152.
111. Zhong, R. and Ye, Z.-H. (2001) Alteration of auxin polar transport in the Arabidopsis ifl1 mutants. Plant Physiol. 126, 549-563.
112. Zhong, R., Taylor, J.J. and Ye, Z.H. (1997) Disruption of interfascicular fiber differentiation: in an Arabidopsis mutant. Plant Cell, 9, 2159-2170.