Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: Functional and evolutionary implications

Plant Molecular Biology

Volumn 58, Issue 2, 2005, Pages 229-245

  Gachon, Claire M M ^a   Langlois Meurinne, Mathilde ^a   Henry, Yves ^a   Saindrenan, Patrick ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

Author keywords

Arabidopsis; Functional genomics; Gene duplication; Glycosyltransferase; Microarray

Indexed keywords

BIOSYNTHESIS; DATA REDUCTION; DYNAMICS; METABOLISM; PLANTS (BOTANY); SUGARS;

ARABIDOPSIS; FUNCTIONAL GENOMICS; GENE DUPLICATION; MICROARRAYS;

ENZYMES;

ARABIDOPSIS PROTEIN; CYTOCHROME P 450 CYP71B1 (THLASPI ARVENSE); CYTOCHROME P-450 CYP71B1 (THLASPI ARVENSE); CYTOCHROME P450; FLAVONOID; GLUCOSYLTRANSFERASE; ISOENZYME; PHENYLPROPIONIC ACID DERIVATIVE; TRYPTOPHAN; UDP GLUCOSE THIOHYDROXIMATE S GLUCOSYLTRANSFERASE UGT74B1, ARABIDOPSIS; UDP-GLUCOSE THIOHYDROXIMATE S-GLUCOSYLTRANSFERASE UGT74B1, ARABIDOPSIS;

ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA MICROARRAY; ENZYMOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEIC ACID DATABASE; PHYLOGENY; STATISTICS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CLUSTER ANALYSIS; CYTOCHROME P-450 ENZYME SYSTEM; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; FLAVONOIDS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, PLANT; GLUCOSYLTRANSFERASES; ISOENZYMES; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENYLPROPIONATES; PHYLOGENY; TRANSCRIPTION, GENETIC; TRYPTOPHAN;

BIOSYNTHESIS; DYNAMICS; ENZYMES; METABOLISM; PLANTS; SUGARS;

ARABIDOPSIS;

EID: 23644461190     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-005-5346-5     Document Type: Article

References (66)

1. S. Bak R. Feyereisen 2001 The involvement of two P450 enzymes, CYP83B1 and CYP83A1, in auxin homeostasis and glucosinolate biosynthesis Plant Physiol. 127 108 118
2. A. Baudry M.H. Heim B. Dubreucq M. Caboche B. Weisshaar L. Lepiniec 2004 TT2, TT8, and TTG1 synergistically specify the expression of Bayals and protoanthocyanidin synthesis in Arabidopsis thaliana Plant J. 39 366 380
3. G. Blanc K. Hokamp K.H. Wolfe 2003 A recent polyploidy superimposed in older large-scale duplication events in the Arabidopsis genome Genome Res 13 137 144
4. G. Blanc K.H. Wolfe 2004 Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution Plant Cell 16 1679 1691
5. S.J. Bloor S. Abrahams 2002 The structure of the major anthocyanin in Arabidopsis thaliana Phytochemistry 59 343 346
6. J.O. Borevitz Y. Xia J. Blount R.A. Dixon C. Lamb 2000 Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis Plant Cell 12 2383 2393
7. N. Bouché D. Bouchez 2001 Arabidopsis gene knock-out: phenotypes wanted Curr. Opin. Plant Biol. 4 111 117
8. J.E. Bowers B.A. Chapman J. Rong A.H. Paterson 2003 Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events Nature 422 433 438
9. G. Brader E. Tas E.T. Palva 2001 Jasmonate-dependent induction of indole glucosinolates in Arabidopsis by culture filtrates of the nonspecific pathogen Erwinia amylovora Plant Physiol. 126 849 860
10. S.B. Cannon A. Mitra A. Baumgarten N.D. Young M. Georgiana 2004 The role of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana BMC Plant Biol. 4 10
11. S. Chen E. Glawischnig K. Jorgensen P. Naur B. Jorgensen C.E. Olsen C.H. Hansen H. Rasmussen J. Pickett B.A. Halkier 2003 CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis Plant J. 33 923 937
12. J. Ehlting D. Büttner Q. Wang C.J. Douglas I.E. Somssich E. Kombrink 1999 Three coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in Angiosperms Plant J. 19 9 20
13. J. Felsenstein 1989 PHYLIP - Phylogeny inference package (Version 3.2) Cladistics 5 164 166
14. A. Force M. Lynch F.B. Pickett A. Amores Yan Y.-l. J. Postlethwait 1999 Preservation of duplicate genes by complementary, degenerative mutations Genetics 151 1531 1545
15. K. Freudenberg J.M. Harkin 1963 The glucosides of cambial sap of spruce Phytochemistry 2 189 193
16. M. Frey P. Chomet E. Glawischnig C. Stettner S. Grün A. Winklmair W. Eisenreich A. Bacher R.B. Meeley S.P. Briggs K. Simcox A. Gierl 1997 Analysis of a chemical plant defense mechanism in grasses Science 277 696 699
17. M. Frey C. Stettner E.A. Schmelz J.H. Tumlinson A. Gierl 2000 An herbivore elicitor activates the gene for indole synthesis emission in maize Proc. Natl. Acad. Sci. USA 97 14801 14806
18. C.D. Grubb B. Zipp J. Ludwig-Müller M.N. Masuno T.F. Molinski S. Abel 2004 Arabidopsis glucosyltransferase ugt74b1 functions in glucosinolate biosynthesis and auxin homeostasis Plant J. 40 893 908
19. Z. Gu S.A. Rifkin K.P. White W.-H. Li 2004 Duplicate genes increase gene expression diversity within and between species Nat. Genet. 36 577 579
20. Z. Gu L.M. Steinmetz X. Gu C. Scharfe R.W. Davis W.-H. Li 2003 Role of duplicate genes in genetic robustness against null mutations Nature 421 63 66
21. C.H. Hansen U. Wittstock C.E. Olsen A.J. Hick J.A. Pickett B.A. Halkier 2001 Cytochrome P450 CYP79F1 from Arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates J. Biol. Chem. 276 11078 11085
22. M.R. Hemm M.O. Ruegger C. Chapple 2003 The Arabidopsis ref2 mutant is defective in the gene encoding CYP83A1 and shows both phenylpropanoid and glucosinolate phenotypes Plant Cell 15 179 194
23. Z. Hong Z. Zhang J.M. Olson D.P.S. Verma 2001 A novel UDP-glucose transferase is part of the callose synthase complex and interacts with phragmoplastin at the forming cell plate Plant Cell 13 769 779
24. T. Imayama N. Yoshihara M. Fukuchi-Mizutani Y. Tanaka I. Ino T. Yabuya 2004 Isolation and characterization of a cDNA clone of UDP-glucose:anthocyanin 5-O-glucosyltransferase in Iris hollandica Plant Sci. 167 1243 1248
25. R.G. Jackson M. Kowalczyk Y. Li G. Higgins J. Ross G. Sandberg D.J. Bowles 2002 Over-expression of an Arabidopsis gene encoding a glucosyltransferase of indole-3-acetic acid: phenotypic characterisation of transgenic lines Plant J. 32 573 583
26. R.G. Jackson E.-K. Lim Y. Li M. Kowalczyk G. Sandberg J. Hoggett D.A. Ashford D.J. Bowles 2001 Identification and biochemical characterization of an Arabidopsis indole-3-acetic acid glucosyltransferase J. Biol. Chem. 276 4350 4356
27. C.S. Johnson B. Kolevski D.R. Smyth 2002 TRANSPARENT TESTA GLABRA 2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor Plant Cell 14 1359 1375
28. P.R. Jones B. Messner J. Nakajima A.R. Schäffner K. Saito 2003 UGT73C6 and UGT78D1, glycosyltransferases involved in flavonol glycoside biosynthesis in Arabidopsis thaliana J. Biol. Chem. 278 43910 43918
29. P.R. Jones T. Vogt 2001 Glycosyltransferases in secondary plant metabolism: tranquilizers and stimulant controllers Planta 213 164 174
30. M. Kellis B.W. Birren E.S. Lander 2004 Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae Nature 428 617 624
31. M. Kita Y. Hirata T. Moriguchi T. Endo-Inagaki R. Matsumoto S. Hasegawa C.G. Suhayda M. Omura 2000 Molecular cloning and characterization of a novel gene encoding limonoid UDP-glucosyltransferase in Citrus FEBS Lett. 469 173 178
32. D.J. Kliebenstein V.M. Lambrix M. Reichelt J. Gershenzon T. Mitchell-Olds 2001 Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis Plant Cell 13 681 693
33. Kreps, J.A., Wu, Y., Chang, H.-S., Zhu, T., Wang, X. and Harper, J.F. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 130: 2129-2141
34. E.-K. Lim D.J. Bowles 2004 A class of plant glycosyltransferases involved in cellular homeostasis EMBO J. 23 2915 2922
35. E.-K. Lim C.J. Doucet Y. Li L. Elias D. Worrall S.P. Spencer J. Ross D.J. Bowles 2002 The activity of Arabidopsis glucosyltransferases toward salicylic acid, 4-hydroxybenzoic acid, and other benzoates J. Biol. Chem. 277 586 592
36. E.-K. Lim Y. Li A. Parr R. Jackson D.A. Ashford D.J. Bowles 2001 Identification of glucosyltransferase genes involved in sinapate metabolism and lignin synthesis in Arabidopsis J. Biol. Chem. 276 4344 4349
37. M. Lynch J.S. Conery 2000 The evolutionary fate and consequences of duplicate genes Science 290 1151 1155
38. E.-F. Marillia J.M. MacPherson E.W.T. Tsang K. Van Audenhove W.A. Keller J.W.D. GrootWassink 2001 Molecular cloning of a Brassica napus gene and its expression in Escherichia coli Physiol. Plant 113 176 184
39. F. Martz S. Maury G. Pinçon M. Legrand 1998 cDNA cloning, substrate specificity and expression study of tobacco caffeoyl-CoA 3-O-methyltransferase, a lignin biosynthetic enzyme Plant Mol. Biol. 36 427 437
40. M.D. Mikkelsen B.L. Petersen E. Glawischnig A.B. Jensen E. Andreasson B.A. Halkier 2003 Modulation of CYP79 genes and glucosinolates profiles in Arabidopsis by defense signaling pathways Plant Physiol. 131 298 308
41. E.M. Mobley B.N. Kunkel B. Keith 1999 Identification, characterization and comparative analysis of a novel chorismate mutase gene in Arabidopsis thaliana Gene 240 115 123
42. K.K. Niyogi G.R. Fink 1992 Two anthranilate synthase genes in Arabidopsis: defense-related regulation of the tryptophan pathway Plant Cell 4 721 733
43. S. Paquette B.L. Moller S. Bak 2003 On the origin of family 1 glycosyltransferases Phytochemistry 62 399 413
44. M.K. Pelletier I.E. Burbulis B. Winkel-Shirley 1999 Disruption of specific flavonoid genes enhances the accumulation of flavonoid enzymes and end-products in Arabidopsis seedlings Plant Mol. Biol. 40 45 54
45. M.K. Pelletier J.R. Murrell B.W. Shirley 1997 Characterization of flavonol synthase and leucoanthocyanidin dioxygenase genes in Arabidopsis Plant Physiol 113 1437 1445
46. M.K. Pelletier B.W. Shirley 1996 Analysis of flavanone 3-hydroxylase in Arabidopsis seedlings Plant Physiol 111 339 345
47. B.L. Petersen S. Chen C.H. Hansen C.E. Olsen B.A. Halkier 2002 Composition and content of glucosinolates in developing Arabidopsis thaliana Planta 214 562 571
48. J.A. Quiel J. Bender 2003 Glucose conjugation of anthranilate by the Arabidopsis UGT74F2 glucosyltransferase is required for tryptophan mutant blue fluorescence J Biol Chem 278 6275 6281
49. J.C. Redman B.J. Haas G. Tanimoto C.D. Town 2004 Development and evaluation of an Arabidopsis whole genome Affymetrix probe array Plant J. 38 545 561
50. B. Reintanz M. Lehnen M. Reichelt J. Gershenzon M. Kowalczyk G. Sandberg M. Godde R. Uhl K. Palme 2001 bus, a bushy CYP79F1 knock-out mutant with abolished synthesis of short-chain aliphatic glucosinolates Plant Cell 13 351 367
51. A. Rohde K. Morreel J. Ralph G. Goeminne V. Hostyn R. de Rycke S. Kushnir J. Van Doorsselaere J.-P. Joseleau M. Vuylsteke G. Van Driessche J. Van Beumen E. Messens W. Boerjan 2004 Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism Plant Cell 16 2749 2771
52. A. Saeed V. Sharov J. White J. Li W. Liang N. Bhagabati J. Braisted M. Klapa T. Currier M. Thiagarajan A. Sturn M. Snuffin A. Rezantsev D. Popov A. Ryltsov E. Kostukovich I. Borisovsky Z. Liu A. Vinsavich V. Trush J. Quackenbush 2003 TM4: a free, open-source system for microarray data management and analysis Biotechniques 24 374 378
53. W. Schwab 2003 Metabolome diversity: too few genes, too many metabolites? Phytochemistry 62 837 849
54. G. Sembdner R. Atzorn G. Schneider 1994 Plant hormone conjugation Plant. Mol. Biol. 26 1459 1481
55. G. Taguchi T. Ubukata N. Hayashida H. Yamamoto M. Okazaki 2003 Cloning and characterization of a glucosyltransferase that reacts on 7-hydroxyl groups of flavonol and 3-hydroxyl group of coumarin from tobacco cells Arch. Biochem. Biophys. 420 95 102
56. J. Tsuji E.P. Jackson A.G. Douglas R. Hammerschmidt S.C. Somerville 1992 Phytoalexin accumulation in Arabidopsis thaliana Plant Physiol. 98 1304 1309
57. Turner, J.G., Ellis, C. and Devoto, A. 2002. The jasmonate signal pathway. Plant Cell Suppl. S153-S164.
58. M.J. Van der Laan J. Bryan 2001 Gene expression analysis with the parametric bootstrap Biostatistics 2 445 461
59. V. van Noort B. Snel M.A. Huynen 2003 Predicting gene function by conserved co-expression Trends. Genet. 19 238 242
60. T. Vogt 2002 Substrate specificity and sequence analysis define a polyphyletic origin of betanidin 5- and 6-O-glucosyltransferase from Dorotheanthus bellidiformis Planta 214 492 495
61. G.A. Wray M.W. Hahn E. Abouheif J.P. Balhoff M. Pizer M.V. Rockman L.A. Romano 2003 The evolution of transcriptional regulation in Eukaryotes Mol. Biol. Evol. 20 1377 1419
62. M. Yamazaki Z. Gong M. Fukuchi-Mizutani Y. Fukui Y. Tanaka T. Kusumi K. Saito 1999 Molecular cloning and biochemical characterization of a novel anthocyanin 5-O-glucosyltransferase by mRNA differential display for plant forms regarding anthocyanin J. Biol. Chem. 274 7405 7411
63. K. Zhang H. Zhao 2000 Assessing reliability of gene clusters from gene expression data Funct. Integr. Genom. 1 156 173
64. P. Zhang Z. Gu W.-H. Li 2003 Different evolutionary patterns between young duplicate genes in the human genome Genome Biol. 4 R56
65. J. Zhao R.L. Last 1996 Coordinate regulation of the tryptophan biosynthetic pathway and indolic phytoalexin accumulation in Arabidopsis Plant Cell 8 2235 2244
66. J. Zhao C.C. Williams R.L. Last 1998 Induction of Arabidopsis tryptophan pathway enzymes and camalexin by amino acid starvation, oxidative stress, and an abiotic elicitor Plant Cell 10 359 370