Finding and analyzing plant metabolic gene clusters

Methods in Enzymology

Volumn 517, Issue , 2012, Pages 113-138

  Osbourn, Anne ^a   Papadopoulou, Kalliopi K ^b   Qi, Xiaoquan ^c   Field, Ben ^d   Wegel, Eva ^e  

^a JOHN INNES CENTRE   (United Kingdom)

^b UNIVERSITY OF THESSALY   (Greece)

^c INSTITUTE OF BOTANY   (China)

^d CNRS   (France)

^e UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

FISH; Gene cluster; Genome mining; Plants; Secondary metabolism

Indexed keywords

2,4 DIHYDROXY 7 METHOXY 1,4 BENZOXAZIN 3 ONE; ACYLTRANSFERASE; BETA AMYRIN; CHALCONE SYNTHASE; CYCLOARTENOL SYNTHASE; CYTOCHROME P450; GLYCOSYLTRANSFERASE; LINAMARIN; METHYLTRANSFERASE; MOLECULAR SCAFFOLD; OXIDOREDUCTASE; SAPONIN;

AGAR GEL ELECTROPHORESIS; ARABIDOPSIS; ARTICLE; CONFOCAL MICROSCOPY; DNA PROBE; ESCHERICHIA COLI; FLUORESCENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CLUSTER; GENE EXPRESSION; GENE MAPPING; GENE MUTATION; GENETIC ANALYSIS; GENOTYPE; HARVESTING; IMMUNODETECTION; LOTUS JAPONICUS; MAIZE; MUTANT; NICOTIANA BENTHAMIANA; NONHUMAN; OAT; PHENOTYPE; PLANT GROWTH; PRIORITY JOURNAL; PROTEIN PURIFICATION; RESTRICTION FRAGMENT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; YEAST;

EID: 84867657458     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-404634-4.00006-1     Document Type: Chapter

References (45)

1. S. Allouis, G. Moore, A. Bellec, R. Sharp, R.P. Faivre, and K. Mortimer Construction and characterisation of a hexaploid wheat BAC library from the reference germplasm 'Chinese Spring' Cereal Research Communications 31 2003 331 338 (Pubitemid 37358434)
2. S. Bak, F. Beisson, G. Bishop, B. Hamberger, R. Höfer, and S. Paquette Cytochromes p450 Arabidopsis Book 9 2011 e0144 [Epub 2011 Oct 6]
3. S. Chen, L. Xiang, X. Guo, and Q. Li An introduction to the medicinal plant genome project Frontiers of Medicine 5 2011 178 184
4. H.-Y. Chu, E. Wegel, and A. Osbourn From hormones to secondary metabolism: The emergence of secondary metabolic gene clusters in plants The Plant Journal 66 2011 66
5. A. Cyr, P.R. Wilderman, M. Determan, and R.J. Peters A modular approach for facile biosynthesis of labdane-related diterpenes Journal of the American Chemical Society 129 2007 6684 6685 (Pubitemid 46847494)
6. J.C. D'Auria, and J. Gershenzon The secondary metabolism of Arabidopsis thaliana: Growing like a weed Current Opinion in Plant Biology 8 2005 308 316 (Pubitemid 40599984)
7. J.H. de Jong, P. Fransz, and P. Zabel High resolution FISH in plants - Techniques and applications Trends in Plant Science 4 1999 258 263 (Pubitemid 29319501)
8. R.A. Dixon, L. Achnine, B.E. Deavours, and M. Naoumkina Metabolomics and gene identification in plant natural product pathways Biotechnology in Agriculture and Forestry 57 2006 243 259
9. J. Ehlting, V. Sauveplane, A. Olry, J.F. Ginglinger, N.J. Provart, and D. Werck-Reichhart An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana BMC Plant Biology 8 2008 47
10. V. Falara, T.A. Akhtar, T.T. Nguyen, E.A. Spyropoulou, P.M. Bleeker, and I. Schauvinhold The tomato terpene synthase gene family Plant Physiology 157 2011 770 789
11. B. Field, A.S. Fiston-Lavier, A. Kemen, K. Geisler, H. Quesneville, and A.E. Osbourn Formation of plant metabolic gene clusters within dynamic chromosomal regions Proceedings of the National Academy of Sciences of the United States of America 108 2011 16116 16121
12. B. Field, and A.E. Osbourn Metabolic diversification - Independent assembly of operon-like gene clusters in different plants Science 320 2008 543 547 (Pubitemid 351590669)
13. M. Frey, P. Chomet, E. Glawischnig, C. Stettner, S. Grun, and A. Winklmair Analysis of a chemical plant defense mechanism in grasses Science 277 1997 696 699 (Pubitemid 27373917)
14. M. Frey, K. Huber, J.P. Woong, D. Sicker, P. Lindberg, and R.B. Meeley A 2-oxoglutarate-dependent dioxygenase is integrated in DIMBOA-biosynthesis Phytochemistry 62 2003 371 376 (Pubitemid 36168939)
15. M. Frey, R. Kliem, H. Saedler, and A. Gierl Expression of a cytochrome P450 gene family in maize Molecular & General Genetics 246 1995 100 109
16. M. Frey, K. Schullehner, R. Dick, A. Fiesselmann, and A. Gierl Benzoxazinoid biosynthesis, a model for evolution of secondary metabolic pathways in plants Phytochemistry 70 2009 1645 1651
17. K. Haralampidis, G. Bryan, X. Qi, K. Papadopoulou, S. Bakht, and R. Melton A new class of oxidosqualene cyclases directs synthesis of antimicrobial phytoprotectants in monocots Proceedings of the National Academy of Sciences of the United States of America 98 2001 13431 13436 (Pubitemid 33051380)
18. S. Huang, R. Li, Z. Zhang, L. Li, X. Gu, and W. Fan The genome of the cucumber, Cucumis sativus L Nature Genetics 41 2009 1275 1281
19. R. Jonczyk, H. Schmidt, A. Osterrieder, A. Fiesselmann, K. Schullehner, and M. Haslbeck Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: Characterization of Bx6 and Bx7 Plant Physiology 146 2008 1053 1063 (Pubitemid 352844122)
20. T. Kushiro, M. Shibuya, and Y. Ebizuka Beta-amyrin synthase - Cloning of oxidosqualene cyclase that catalyzes the formation of the most popular triterpene among higher plants European Journal of Biochemistry 256 1998 238 244 (Pubitemid 28399118)
21. G. Mao, H. Buschmann, J. Doonan, and C.W. Lloyd The role of MAP65-1 in microtubule bundling during Zinnia tracheary element formation Journal of Cell Science 119 2006 753 758
22. C.M. McCallum, L. Comai, E.A. Greene, and S. Henikoff Targeted screening for induced mutations Nature Biotechnology 18 2000 455 457 (Pubitemid 30217538)
23. S.T. Mugford, X. Qi, S. Bakht, L. Hill, E. Wegel, and R.K. Hughes A serine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compounds and disease resistance in oats The Plant Cell 21 2009 2473 2484
24. P. Mylona, A. Owatworakit, K. Papadopoulou, H. Jenner, B. Qin, and K. Findlay Sad3 and Sad4 are required for saponin biosynthesis and root development in oat The Plant Cell 20 2008 201 212 (Pubitemid 352844043)
25. A. Osbourn, and B. Field Operons Cellular and Molecular Life Sciences 66 2009 37555 37575
26. A. Osbourn Secondary metabolic gene clusters: Evolutionary toolkits for chemical innovation Trends in Genetics 26 2010 449 457
27. K. Papadopoulou, R. Melton, M. Leggett, M.J. Daniels, and A.E. Osbourn Compromised disease resistance in saponin deficient plants Proceedings of the National Academy of Sciences of the United States of America 96 1999 12923 12928 (Pubitemid 29513604)
28. B. Prasad, A. Garg, H. Takwani, and S. Singh Metabolite identification by liquid chromatography-mass spectrometry Trends in Analytical Chemistry 30 2011 360 387
29. X. Qi, S. Bakht, M. Leggett, C. Maxwell, R. Melton, and A. Osbourn A gene cluster for secondary metabolism in oat: Implications for the evolution of metabolic diversity in plants Proceedings of the National Academy of Sciences of the United States of America 101 2004 8233 8238 (Pubitemid 38698083)
30. X. Qi, S. Bakht, B. Qin, M. Leggett, A. Hemmings, and F. Mellon A different function for a member of an ancient and highly conserved cytochrome P450 family: From essential sterol to plant defense Proceedings of the National Academy of Sciences of the United States of America 103 2006 18848 18853 (Pubitemid 44913498)
31. B. Qin, J. Eagles, F.A. Mellon, P. Mylona, L. Peña-Rodriguez, and A.E. Osbourn High throughput screening of mutants of oat that are defective in triterpene synthesis Phytochemistry 71 2010 1245 1252
32. F. Sainsbury, E.C. Thuenemann, and G.P. Lomonossoff pEAQ: Versatile expression vectors for easy and quick transient expression of heterologous proteins in plants Plant Biotechnology Journal 7 2009 682 693
33. T. Sakamoto, K. Miura, H. Itoh, T. Tatsumi, M. Ueguchi-Tanaka, and K. Ishiyama An overview of gibberellin metabolism enzyme genes and their related mutants in rice Plant Physiology 134 2004 1642 1653 (Pubitemid 38527372)
34. K. Shimura, A. Okada, K. Okada, Y. Jikumaru, K.W. Ko, and T. Toyomasu Identification of a biosynthetic gene cluster in rice for momilactones The Journal of Biological Chemistry 282 2007 34013 34018 (Pubitemid 350159470)
35. P. Stam Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP The Plant Journal 3 1993 739 744
36. S.E. Stein An integrated method for spectrum extraction and compound identification from GC/MS data Journal of American Society of Mass Spectrometry 10 1999 770 781 (Pubitemid 34506228)
37. S. Swaminathan, D. Morrone, Q. Wang, D.B. Fulton, and R.J. Peters CYP76M7 is an ent-cassadiene C11 alpha-hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice The Plant Cell 21 2009 3315 3325
38. A.M. Takos, C. Knudsen, D. Lai, R. Kannangara, L. Mikkelsen, and M.S. Motawia Genomic clustering of cyanogenic glucoside biosynthetic genes aids their identification in Lotus japonicus and suggests the repeated evolution of this chemical defence pathway The Plant Journal 68 2011 273 286
39. U. von Rad, R. Hüttl, F. Lottspeich, A. Gierl, and M. Frey Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize The Plant Journal 28 2001 633 642 (Pubitemid 34114970)
40. Q. Wang, M.L. Hillwig, and R.J. Peters CYP99A3: Functional identification of a diterpene oxidase from the momilactone biosynthetic gene cluster in rice The Plant Journal 65 2011 87 95
41. E. Wegel, R. Koumproglou, P. Shaw, and A. Osbourn Cell type-specific chromatin decondensation of a metabolic gene cluster in oats The Plant Cell 21 2009 3926 3936
42. P.R. Wilderman, M. Xu, Y. Jin, R.M. Coates, and R.J. Peters Identification of Syn -imara-7,15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin/allelochemical biosynthesis Plant Physiology 135 2004 2098 2105 (Pubitemid 39182789)
43. Y. Wu, M.L. Hillwig, Q. Wang, and R.J. Peters Parsing a multifunctional biosynthetic gene cluster from rice: Biochemical characterization of CYP71Z6 & 7 FEBS Letters 585 2011 3446 3451
44. K. Yonekura-Sakakibara, and K. Saito Functional genomics for plant natural product synthesis Natural Product Reports 26 2009 1466 1487
45. G.X. Yu, and R.P. Wise An anchored AFLP- and retrotransposon-based map of diploid Avena Genome 43 2000 736 749