Regulation of metabolic gene clusters in Arabidopsis thaliana

New Phytologist

Volumn 205, Issue 2, 2015, Pages 503-510

  Nützmann, Hans Wilhelm ^a   Osbourn, Anne ^a  

^a JOHN INNES CENTRE   (United Kingdom)

Author keywords

Arabidopsis thaliana; ARP6; H2A.Z; Nucleosome positioning; Plant metabolic gene clusters; Specialized metabolism; Triterpenes

Indexed keywords

ARABIDOPSIS THALIANA;

ACTIN BINDING PROTEIN; ARABIDOPSIS PROTEIN; ARP6 PROTEIN, ARABIDOPSIS; H2A.Z PROTEIN, ARABIDOPSIS; HISTONE;

ARABIDOPSIS; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MULTIGENE FAMILY; PHYSIOLOGY; PLANT GENOME;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HISTONES; MICROFILAMENT PROTEINS; MULTIGENE FAMILY;

EID: 84919683111     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.13189     Document Type: Article

References (45)

1. Bennett RN, Wenke T, Freudenberg B, Mellon FA, Ludwig-Muller J. 2005. The tu8 mutation of Arabidopsis thaliana encoding a heterochromatin protein 1 homolog causes defects in the induction of secondary metabolite biosynthesis. Plant Biology 7: 348-357.
2. Bok JW, Chiang YM, Szewczyk E, Reyes-Dominguez Y, Davidson AD, Sanchez JF, Lo HC, Watanabe K, Strauss J, Oakley BR et al. 2009. Chromatin-level regulation of biosynthetic gene clusters. Nature Chemical Biology 5: 462-464.
3. Boycheva S, Daviet L, Wolfender JL, Fitzpatrick TB. 2014. The rise of operon-like gene clusters in plants. Trends Plant Science 19: 447-459.
4. Brakhage AA. 2013. Regulation of fungal secondary metabolism. Nature Reviews Microbiology 11: 21-32.
5. Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8: e1002988.
6. Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, Young RA, Jaenisch R, Boyer LA. 2008. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 135: 649-661.
7. Deal RB, Topp CN, McKinney EC, Meagher RB. 2007. Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 19: 74-83.
8. Field B, Fiston-Lavier AS, Kemen A, Geisler K, Quesneville H, Osbourn AE. 2011. Formation of plant metabolic gene clusters within dynamic chromosomal regions. Proceedings of the National Academy of Sciences, USA 108: 16116-16121.
9. Field B, Osbourn AE. 2008. Metabolic diversification-independent assembly of operon-like gene clusters in different plants. Science 320: 543-547.
10. Frey M, Chomet P, Glawischnig E, Stettner C, Grun S, Winklmair A, Eisenreich W, Bacher A, Meeley RB, Briggs SP et al. 1997. Analysis of a chemical plant defense mechanism in grasses. Science 277: 696-699.
11. Go YS, Lee SB, Kim HJ, Kim J, Park HY, Kim JK, Shibata K, Yokota T, Ohyama K, Muranaka T et al. 2012. Identification of marneral synthase, which is critical for growth and development in Arabidopsis. Plant Journal 72: 791-804.
12. Guillemette B, Bataille AR, Gevry N, Adam M, Blanchette M, Robert F, Gaudreau L. 2005. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biology 3: e384.
13. Hong SM, Bahn SC, Lyu A, Jung HS, Ahn JH. 2010. Identification and testing of superior reference genes for a starting pool of transcript normalization in Arabidopsis. Plant and Cell Physiology 51: 1694-1706.
14. Hurst LD, Pal C, Lercher MJ. 2004. The evolutionary dynamics of eukaryotic gene order. Nature Reviews Genetics 5: 299-310.
15. Itkin M, Heinig U, Tzfadia O, Bhide AJ, Shinde B, Cardenas PD, Bocobza SE, Unger T, Malitsky S, Finkers R et al. 2013. Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes. Science 341: 175-179.
16. King AJ, Brown GD, Gilday AD, Larson TR, Graham IA. 2014. Production of bioactive diterpenoids in the Euphorbiaceae depends on evolutionarily conserved gene clusters. Plant Cell 26: 3286-3298.
17. Krokida A, Delis C, Geisler K, Garagounis C, Tsikou D, Pena-Rodriguez LM, Katsarou D, Field B, Osbourn AE, Papadopoulou KK. 2013. A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis. New Phytologist 200: 675-690.
18. Kumar SV, Wigge PA. 2010. H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 140: 136-147.
19. March-Diaz R, Garcia-Dominguez M, Lozano-Juste J, Leon J, Florencio FJ, Reyes JC. 2008. Histone H2A.Z and homologues of components of the SWR1 complex are required to control immunity in Arabidopsis. Plant Journal 53: 475-487.
20. Martin-Trillo M, Larazo A, Poethig RS, Gomez-Mena C, Pineiro MA, Martinez-Zapater JM, Jarillo JA. 2006. EARLY IN SHORT DAYS 1 (ESD1) encodes ACTIN-RELATED PROTEIN 6 (AtARP6), a putative component of chromatin remodelling complexes that positively regulates FLC accumulation in Arabidopsis. Development 133: 1241-1252.
21. Matsuba Y, Nguyen TT, Wiegert K, Falara V, Gonzales-Vigil E, Leong B, Schafer P, Kudrna D, Wing RA, Bolger AM et al. 2013. Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell 25: 2022-2036.
22. Meneghini MD, Wu M, Madhani HD. 2003. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112: 725-736.
23. Michalak P. 2008. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91: 243-248.
24. Miyamoto K, Matsumoto T, Okada A, Komiyama K, Chujo T, Yoshikawa H, Nojiri H, Yamane H, Okada K. 2014. Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells. PLoS ONE 9: e105823.
25. Murashige T, Skoog F. 1962. A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiologia Plantarum 15: 473-497.
26. Mylona P, Owatworakit A, Papadopoulou K, Jenner H, Qin B, Findlay K, Hill L, Qi X, Bakht S, Melton R et al. 2008. Sad3 and Sad4 are required for saponin biosynthesis and root development in oat. Plant Cell 20: 201-212.
27. Nützmann HW, Osbourn A. 2014. Gene clustering in plant specialized metabolism. Current Opinion in Biotechnology 26: 91-99.
28. Nützmann HW, Reyes-Dominguez Y, Scherlach K, Schroeckh V, Horn F, Gacek A, Schumann J, Hertweck C, Strauss J, Brakhage AA. 2011. Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proceedings of the National Academy of Sciences, USA 108: 14282-14287.
29. Osbourn AE, Field B. 2009. Operons. Cellular and Molecular Life Sciences 66: 3755-3775.
30. Petter M, Selvarajah SA, Lee CC, Chin WH, Gupta AP, Bozdech Z, Brown GV, Duffy MF. 2013. H2A.Z and H2B.Z double-variant nucleosomes define intergenic regions and dynamically occupy var gene promoters in the malaria parasite Plasmodium falciparum. Molecular Microbiology 87: 1167-1182.
31. Qi X, Bakht S, Leggett M, Maxwell C, Melton R, Osbourn A. 2004. A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants. Proceedings of the National Academy of Sciences, USA 101: 8233-8238.
32. Reyes-Dominguez Y, Bok JW, Berger H, Shwab EK, Basheer A, Gallmetzer A, Scazzocchio C, Keller N, Strauss J. 2010. Heterochromatic marks are associated with the repression of secondary metabolism clusters in Aspergillus nidulans. Molecular Microbiology 76: 1376-1386.
33. Rider SD Jr, Hemm MR, Hostetler HA, Li HC, Chapple C, Ogas J. 2004. Metabolic profiling of the Arabidopsis pkl mutant reveals selective derepression of embryonic traits. Planta 219: 489-499.
34. Scholl RL, May ST, Ware DH. 2000. Seed and molecular resources for Arabidopsis. Plant Physiology 124: 1477-1480.
35. Shimura K, Okada A, Okada K, Jikumaru Y, Ko KW, Toyomasu T, Sassa T, Hasegawa M, Kodama O, Shibuya N et al. 2007. Identification of a biosynthetic gene cluster in rice for momilactones. Journal of Biological Chemistry 282: 34013-34018.
36. Song J, Rutjens B, Dean C. 2014. Detecting histone modifications in plants. In: Spillane C, McKeown PC, eds. Plant epigenetics and epigenomics. New York, NY, USA: Humana Press, 165-175.
37. Takos AM, Knudsen C, Lai D, Kannangara R, Mikkelsen L, Motawia MS, Olsen CE, Sato S, Tabata S, Jorgensen K et al. 2011. Genomic clustering of cyanogenic glucoside biosynthetic genes aids their identification in Lotus japonicus and suggests the repeated evolution of this chemical defence pathway. Plant Journal 68: 273-286.
38. Walley JW, Rowe HC, Xiao Y, Chehab EW, Kliebenstein DJ, Wagner D, Dehesh K. 2008. The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathogens 4: e1000237.
39. Wegel E, Koumproglou R, Shaw P, Osbourn A. 2009. Cell type-specific chromatin decondensation of a metabolic gene cluster in oats. Plant Cell 21: 3926-3936.
40. Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. 2008. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genetics 4: e1000187.
41. Wilderman PR, Xu M, Jin Y, Coates RM, Peters RJ. 2004. Identification of syn-pimara-7, 15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin/allelochemical biosynthesis. Plant Physiology 135: 2098-2105.
42. Winzer T, Gazda V, He Z, Kaminski F, Kern M, Larson TR, Li Y, Meade F, Teodor R, Vaistij FE et al. 2012. A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine. Science 336: 1704-1708.
43. Wong S, Wolfe KH. 2005. Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nature Genetics 37: 777-782.
44. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. 2007. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biology 5: e129.
45. Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456: 125-129.