Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism

Journal of Experimental Botany

Volumn 59, Issue 10, 2008, Pages 2831-2846

  Falkenberg, Bettina ^a   Witt, Isabell ^a   Zanor, Maria Inés ^a   Steinhauser, Dirk ^a   Mueller Roeber, Bernd ^b   Hesse, Holger ^a   Hoefgen, Rainer ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b UNIVERSITY OF POTSDAM   (Germany)

Author keywords

Auxin; Sulphur metabolism; Systems biology; Transcription factors

Indexed keywords

ARABIDOPSIS PROTEIN; ARF2 PROTEIN, ARABIDOPSIS; IAA13 PROTEIN, ARABIDOPSIS; IAA28 PROTEIN, ARABIDOPSIS; INDOLEACETIC ACID DERIVATIVE; PHYTOHORMONE; REPRESSOR PROTEIN; SULFUR; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; CAULIFLOWER MOSAIC VIRUS; GENE EXPRESSION REGULATION; GENE VECTOR; GENETICS; METABOLISM; PHENOTYPE; PHYSIOLOGY; SIGNAL TRANSDUCTION; TRANSGENIC PLANT;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CAULIMOVIRUS; GENE EXPRESSION REGULATION, PLANT; GENETIC VECTORS; INDOLEACETIC ACIDS; MUTAGENESIS, INSERTIONAL; PHENOTYPE; PLANT GROWTH REGULATORS; PLANTS, GENETICALLY MODIFIED; REPRESSOR PROTEINS; SIGNAL TRANSDUCTION; SULFUR; TRANSCRIPTION FACTORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 46849110151     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/ern144     Document Type: Article

References (68)

1. Alonso JM, Stepanova AN, Leisse TJ, et al. 2003. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301, 653-657.
2. Bellman R. 1961. Adaptive control processes: a guided tour. Princeton, NJ: Princeton University Press.
3. Blaszczyk A, Brodzik R, Sirko A. 1999. Increased resistance to oxidative stress in transgenic tobacco plants overexpressing bacterial serine acetyltransferase. The Plant Journal 20, 237-243.
4. Bohnert HJ, Gong QQ, Li PH, Ma SS. 2006. Unraveling abiotic stress tolerance mechanisms - getting genomics going. Current Opinion Plant Biology 9, 180-188.
5. Buchanan BB, Gruissem W, Jones RL, eds. 2000. Biochemistry and molecular biology of plants. Rockville, MD: American Society of Plant Physiologists.
6. Czechowski T, Bari RP, Stitt M, Scheible W-R, Udvardi MK. 2004. Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root-and shoot-specific genes. The Plant Journal 38, 366-379.
7. Ellis CM, Nagpal P, Young JC, Hagen G, Guilfoyle TJ, Reed JW. 2005. Auxin Response Factor1 and Auxin Response Factor2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development 132, 4563-4574.
8. Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K. 2006. Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Current Opinion Plant Biology 9, 436-442.
9. Hamann T, Benkova E, Baurle I, Kientz M, Jürgens G. 2002. The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS-mediated embryo patterning. Genes Development 16, 1610-1615.
10. Hamann T, Mayer U, Jürgens G. 1999. The auxin-sensitive bodenlos mutation affects primary root formation and apical-basal patterning in the Arabidopsis embryo. Development 126, 1387-1395.
11. Harms K, von Ballmoos P, Brunold C, Höfgen R, Hesse H. 2000. Expression of a bacterial serine acetyltransferase in transgenic potato plants leads to increased levels of cysteine and glutathione. The Plant Journal 22, 335-343.
12. Hesse H, Hoefgen R. 2003. Molecular aspects of methionine biosynthesis in Arabidopsis and potato. Trends in Plant Science 8, 259-262.
13. Hesse H, Kreft O, Maimann S, Zeh M, Hoefgen R. 2004b. Current understanding of the regulation of methionine biosynthesis in plants. Journal Experimental Botany 55, 1799-1808.
14. Hesse H, Nikiforova V, Gakière B, Hoefgen R. 2004a. Molecular analysis and control of cysteine biosynthesis: integration of nitrogen and sulfur metabolism. Journal Experimental Botany 55, 1283-1292.
15. Hirai MY, Klein M, Fujikawa Y, et al. 2005. Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. Journal Biological Chemistry 280, 25590-25595.
16. Hirai MY, Sugiyama K, Sawada Y, et al. 2007. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proceedings of the National Academy of Sciences, USA 10, 6478-6483.
17. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K. 2004. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 101, 10205-10210.
18. Hirai YM, Fujiwara T, Awazuhara M, Kimura T, Masaaki N, Saito K. 2003. Global expression profiling of sulphur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-L-serine as a general regulator of gene expression in response to sulphur nutrition. The Plant Journal 33, 651-663.
19. Howarth JR, Barraclough PB, Hawkesford MJ. 2005. A highly specific sulfate-deficiency induced gene (sdi1) from wheat. In: Saito K, De Kok LJ, Stuhlen I, Hawkesford MJ, Schnug E, Sirko A, Rennenberg H, eds. Sulfur transport and assimilation in plants in the postgenomic era. Leiden, The Netherlands: Backhuys Publishers, 153-156.
20. Kepinski S. 2006. Integrating hormone signaling and patterning mechanisms in plant development. Current Opinion in Plant Biology 9, 28-34.
21. Kim J, Harter K, Theologis A. 1997. Protein-protein interactions among the Aux/IAA proteins. Proceedings of the National Academy of Sciences, USA 94, 11786-11791.
22. Kreft O, Höfgen R, Hesse H. 2003. Functional analysis of cystathionine γ-synthase in genetically engineered potato plants. Plant Physiology 131, 1843-1854.
23. Kutz A, Müller A, Hennig P, Kaiser WM, Piotrowski M, Weiler EW. 2002. A role for nitrilase 3 in the regulation of root morphology in sulfur-starving Arabidopsis thaliana. The Plant Journal 30, 95-106.
24. Ide Y, Kato T, Sato S, Tabata S, Naito S, Fujiwara T. 2005. Screening of Arabidopsis enhancer-trap lines for sulfur-responsive genes in seeds. In: Saito K, De Kok LJ, Stuhlen I, Hawkesford MJ, Schnug E, Sirko A, Rennenberg H, eds. Sulfur transport and assimilation in plants in the postgenomic era. Leiden, The Netherlands: Backhuys Publishers, 173-176.
25. Lam HM, Coschigano KT, Oliveira IC, Melooliveira R, Coruzzi GM. 1996. The molecular genetics of nitrogen assimilation into amino acids in higher plants. Annual Review of Plant Physiology and Plant Molecular Biology 47, 569-593.
26. Lehman A, Black R, Ecker JR. 1996. HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. Cell 85, 183-194.
27. Lewandowska M, Wawrzyńska A, Kamińska J, Liszewska F, Sirko A. 2005. Identification of novel proteins of Nicotiana tabacum regulated by short term sulfur starvation. In: Saito K, De Kok LJ, Stuhlen I, Hawkesford MJ, Schnug E, Sirko A, Rennenberg H, eds. Sulfur transport and assimilation in plants in the postgenomic era. Leiden, The Netherlands: Backhuys Publishers, 153-156.
28. Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR. 2004. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Development Cell 7, 1-20.
29. Lindroth P, Mopper K. 1979. High performance liquid chromatographic determination of subpicomole amounts of amino acids by precolumn fluorescence derivatization with o-phthaldialdehyde. Analytical Chemistry 51, 1667-1674.
30. Maimann S, Höfgen R, Hesse H. 2001. Enhanced cystathionine β-lyase activity in transgenic potato plants does not force metabolite flow towards methionine. Planta 214, 163-170.
31. Maruyama-Nakashita A, Inoue E, Watanabe-Takahashi A, Yamaya T, Takahashi H. 2003. Transcriptome profiling of sulfur-responsive genes in Arabidopsis reveals global effects of sulfur nutrition on multiple metabolic pathways. Plant Physiology 132, 597-605.
32. Maruyama-Nakashita A, Nakamura Y, Tohge T, Saito K, Takahashi H. 2006. Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. The Plant Cell 18, 3235-3251.
33. Maruyama-Nakashita A, Takahashi H. 2005. Transcriptional regulation of Sultr1. In: Saito K, De Kok LJ, Stuhlen I, Hawkesford MJ, Schnug E, Sirko A, Rennenberg H, eds. Sulfur transport and assimilation in plants in the postgenomic era. Leiden, The Netherlands: Backhuys Publishers, 43-441 and Sultr1;2 in Arabidopsis roots.
34. Maruyama-Nakashita A, Watanabe-Takahashi A, Inoue E, Yamaya T, Takahashi H. 2005. Identification of a novel cis-acting element conferring sulfur deficiency response in Arabidopsis roots. The Plant Journal 42, 305-314.
35. Mirkin B. 1996. Nonconvex optimisation and its application, mathematical classification and clustering, Vol. 3. Dordrecht, The Netherlands: Kluwer Academic Publishers.
36. Nikiforova VJ, Bielecka M, Gakière B, Krueger S, Rinder J, Kempa S, Morcuende R, Scheible W-R, Hesse H, Hoefgen R. 2006. Effect of sulfur availability on the integrity of amino acid biosynthesis in plants. Amino Acids 30, 173-183.
37. Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R. 2005b. Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulfur stress response. Journal Experimental Botany 56, 1887-1896.
38. Nikiforova V, Freitag J, Kempa S, Adamik M, Hesse H, Höfgen R. 2003. Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. The Plant Journal 33, 633-650.
39. Nikiforova VJ, Kopka J, Tolstikov V, Fiehn O, Hopkins L, Hawkesford MJ, Hesse H, Hoefgen R. 2005a. Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiology 138, 304-318.
40. Okushima Y, Mitina I, Quach HL, Theologis A. 2005b. AUXIN RESPONSE FACTOR 2 (ARF2): a pleiotropic developmental regulator. The Plant Journal 43, 29-46.
41. Okushima Y, Overvoorde PJ, Arima K, et al. 2005a. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. The Plant Cell 17, 444-463.
42. Onouchi H, Nagami Y, Haraguchi Y, Nakamoto M, Nishimura Y, Sakurai R, Nagao N, Kawasaki D, Kadokura Y, Naito S. 2005. Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis. Genes Development 19, 1799-1810.
43. Ouellet F, Overvoorde PJ, Theologis A. 2001. IAA17/AXR3: biochemical insight into an auxin mutant phenotype. The Plant Cell 13, 829-841.
44. Paciorek T, Friml J. 2006. Auxin signalling. Journal of Cell Science 119, 1199-1202.
45. Pfaffl MW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 29, 2002-2007.
46. Prusinkiewicz P, Rolland-Lagan AG. 2006. Modeling plant morphogenesis. Current Opinion in Plant Biology 9, 83-88.
47. R Development Core Team. 2007. a language and environment for statistical computing. R Foundation for Statistical Computing. Vienna: Austria. RISBN 3-900051-07-0URL http://www.Rproject.org.
48. Rademacher T, Häusler RE, Hirsch H-J, Zhang L, Lipka V, Weier D, Kreuzaler F, Peterhänsel C. 2002. An engineered phosphoenolpyruvate carboxylase redirects carbon and nitrogen flow in transgenic potato plants. The Plant Journal 32, 25-39.
49. Ramakers C, Ruijter JM, Deprez RH, Moorman AF. 2003. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neuroscience Letters 13, 62-66.
50. Reed JW. 2001. Roles and activities of Aux/IAA proteins in Arabidopsis. Trends in Plant Science 6, 420-425.
51. Remington DL, Vision TJ, Guilfoyle TJ, Reed JW. 2004. Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiology 135, 1738-1752.
52. Roger P, Hellens E, Edwards A, Leyland NR, Bean S, Mullineaux PM. 2000. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Molecular Biology 42, 819-832.
53. Rogg LE, Lasswell J, Bartel B. 2001. A gain-of-function mutation in IAA28 suppresses lateral root development. The Plant Cell 13, 465-480.
54. Scholz M, Gatzek S, Sterling A, Fiehn O, Selbig J. 2004. Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20, 2447-2454.
55. Scholz M, Kaplan F, Guy CL, Kopka J, Selbig J. 2005. Non-linear PCA: a missing data approach. Bioinformatics 21, 3887-3895.
56. Skirycz A, Reichelt M, Burow M, et al. 2006. DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. The Plant Journal 47, 10-24.
57. Sokal RR, Rohlf FJ. 1995. Biometry: the principles and practice of statistics in biological research, 3rd edn. New York, NY: W.H. Freeman and Company.
58. Takahashi H. 2005. Function and regulation of plant sulfate transporter. In: Saito K, De Kok LJ, Stuhlen I, Hawkesford MJ, Schnug E, Sirko A, Rennenberg H, eds. Sulfur transport and assimilation in plants in the postgenomic era. Leiden, The Netherlands: Backhuys Publishers, 13-21.
59. Ulmasov T, Hagen G, Guilfoyle TJ. 1999a. Activation and repression of transcription by auxin-response factors. Proceedings of the National Academy ofSciences, USA 96, 5844-5849.
60. Ulmasov T, Hagen G, Guilfoyle TJ. 1999b. Dimerization and DNA binding of auxin response factors. The Plant Journal 19, 309-319.
61. Valliyodan B, Nguyen HT. 2006. Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Current Opinion in Plant Biology 9, 189-195.
62. Van Buskirk HA, Thomashow MF. 2006. Arabidopsis transcription factors regulating cold acclimation. Physiologia Plantarum 126, 72-80.
63. Warnes GR. 2007. Includes R source code and/or documentation contributed by Ben Bolker and Thomas Lumley gplots: various R programming tools for plotting data. R package version 2.3.2.
64. Weijers D, Benkova E, Jager KE, Schlereth A, Hamann T, Kientz M, Wilmoth JC, Reed JW, Jürgens G. 2005. Developmental specificity of auxin response by pairs of ARF and Aux/ IAA transcriptional regulators. EMBO Journal 24, 1874-1885.
65. Woodward AW, Bartel B. 2005. Auxin: regulation, action, and interaction. Annals Botany 95, 707-735.
66. Worley CK, Zenser N, Ramos J, Rouse D, Leyser O, Theologis A, Callis J. 2000. Degradation of Aux/IAA proteins is essential for normal auxin signalling. The Plant Journal 21, 553-562.
67. Yamaguchi-Shinozaki K, Shinozaki K. 2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stress. Annual Review of Plant Biology 57, 781-803.
68. Yanagisawa S, Akiyama A, Kisaka H, Uchimiya H, Miwa T. 2004. Metabolic engineering with Dof1 transcription factor in plants: improved nitrogen assimilation and growth under lownitrogen conditions, 18. Proceedings of the National Academy of Sciences, USA, 7833-7838.