Abstract
Nitrogen is an essential mineral nutrient and is required in great abundance for plant growth and development. Insufficient nitrogen triggers extensive physiological and biochemical changes in plants which constitute a set of adaptive responses to nitrogen limitation. In this study, to determine the genome-wide transcriptome response to nitrogen limitation, Arabidopsis plants were grown with limiting (3 mM) and sufficient (10 mM) nitrate, respectively, and their gene expression profiles were analyzed using Affymetrix GeneChip arrays. In addition to inducing the adaptive responses in Arabidopsis, nitrogen limitation altered the expression levels of 629 genes with 340 up-regulated and 289 down-regulated. The up-regulated group included the genes involved in protein degradation and the biosynthesis of anthocyanin and phenylpropanoids. The down-regulated group contained the genes functioning in photosynthesis and in the synthesis of nitrogenous macromolecules such as chlorophyll, proteins, amino acids and nucleotides. Numerous nitrogen limitation responsive genes encode transcription factors, signal transduction components, and proteins required for hormone synthesis and response. The Arabidopsis nitrogen limitation adaptation mutant (nla) is defective in developing the nitrogen limitation adaptive responses. The microarray analysis revealed that the absence of the functional NLA in the nla mutant extensively altered its responsive transcriptome to nitrogen limitation. In this mutant 1122 genes were up-regulated and 622 repressed. It was also found that the nla mutant phenotype was associated with the early induction of senescence-associated genes. This study presents a genome-wide view of Arabidopsis transcriptome response to nitrogen limitation and its regulation by NLA, and provides information to probe the molecular mechanism controlling plant adaptability to nitrogen limitation.
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References
Arnon DI (1949) Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant Physiol 24:1–15
Bi Y-M, Zhang Y, Signorelli T, Zhao R, Zhu T, Rothstein SJ (2005) Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity. Plant J 44:680–692
Bongue-Bartelsman M, Phillips DA (1995) Nitrogen stress regulates gene expression of enzymes in the flavonoid biosynthetic pathway of tomato. Plant Physiol Biochem 33:539–546
Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C (2000) Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell 12:2383–2393
Castleberry RM, Crum CW, Krull F (1984) Genetic yield improvement of U.S. maize cultivars under varying fertility and climatic environments. Crop Sci 24:33–36
Chalker-Scott L (1999) Environmental significance of anthocyanins in plant stress responses. Photochem Photobiol 70:1–9
Crawford NM, Forde BG (2002) Molecular and developmental biology of inorganic nitrogen nutrition. In: Meyerowitz E, Somerville C (eds) The arabidopsis book, American Society of Plant Biologists, Rockville, MD, http://www.aspb.org/publications/arabidopsis
Coruzzi GM (2003) Primary N-assimilation into Amino acids in Arabidopsis. In: Meyerowitz E, Somerville C (eds) The arabidopsis book, American Society of Plant Biologists, Rockville, MD, http://www.aspb.org/publications/arabidopsis
De Angeli A, Monachello D, Ephritikhine G, Frachisse JM, Thomine S, Gambale F, Barbier-Brygoo H (2006) The nitrate/proton antiporter AtCLCa mediates nitrate accumulation in plant vacuoles. Nature 442:939–942
Diaz C, Purdy S, Christ A, Morot-Gaudry J-F, Wingler A, Masclaux-Daubresse C (2005) Characterization of markers to determine the extent and variability of leaf senescence in Arabidopsis. A metabolic profiling approach. Plant Physiol 138:898–908
Diaz C, Saliba-Colombani V, Loudet O, Belluomo P, Moreau L, Daniel-Vedele F, Morot-Gaudry JF, Masclaux-Daubresse C (2006) Leaf yellowing and anthocyanin accumulation are two genetically independent strategies in response to nitrogen limitation in Arabidopsis thaliana. Plant Cell Physiol 47:74–83
Ding L, Wang KJ, Jiang GM, Biswas DK, Xu H, Li LF, Li YH (2005) Effects of nitrogen deficiency on photosynthetic traits of maize hybrids released in different years. Ann Bot (Lond) 96:925–930
Doelling JH, Walker JM, Friedman EM, Thompson AR, Vierstra RD (2002) The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J Biol Chem 277:33105–33114
Duvick DN (1984) Genetic contributions to yield gains of U.S. hybrid maize, 1930 to 1980. In: Fehr WR (ed) Genetic contributions to yield gains of five major crop plants, CSSA Special Publication 7. ASA and CSSA, Madison, WI, pp. 15–47
Duvick DN (1997) Review of the symposium on developing drought and low-N tolerant maize. In: Edmeades GO, Banziger M, Mickelson HR, Pena-Valdicia CB (eds) Developing drought and low N-tolerant maize El Batan. CIMMYT, Mexico, pp. 554–556
Filleur S, Dorbe MF, Cerezo M, Orsel M, Granier F, Gojon A, Daniel-Vedele F (2001) An Arabidopsis T-DNA mutant affected in Nrt2 genes is impaired in nitrate uptake. FEBS Lett 489:220–224
Frink CR, Waggoner PE, Ausubel JH (1999) Nitrogen fertilizer: retrospect and prospect. Proc Natl Acad Sci USA 96:1175–1180
Geelen D, Lurin C, Bouchez D, Frachisse JM, Lelievre F, Courtial B, Barbier-Brygoo H, Maurel C (2000) Disruption of putative anion channel gene AtCLC-a in Arabidopsis suggests a role in the regulation of nitrate content. Plant J 21:259–267
Geiger M, Walch-Liu P, Engels C, Harnecker J, Schulze E-D, Ludewig F, Sonnewald U, Scheible W-R, Stitt M (1998) Enhanced carbon dioxide leads to a modified diurnal rhythm of nitrate reductase activity in older plants, and a large stimulation of nitrate reductase activity and higher levels of amino acids in young tobacco plants. Plant Cell Environ 21:253–268
Glickman MH, Ciechanover A (2002) The ubiquitin-proteasome proteolytic pathway:destruction for the sake of construction. Physiol Rev 82:373–428
Good AG, Shrawat AK, Muench DG (2004) Can less yield more? Is reducing nutrient input into the environment compatible with maintaining crop production? Trends Plant Sci 9:597–605
Guo Y, Cai Z, Gan S (2004) Transcriptome of Arabidopsis leaf senescence. Plant Cell Environ 27:521–549
Hanaoka H, Noda T, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Ohsumi Y (2002) Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol 129:1181–1193
Harada H, Kuromori T, Hirayama T, Shinozaki K, Leigh RA (2004) Quantitative trait loci analysis of nitrate storage in Arabidopsis leading to an investigation of the contribution of the anion channel gene, AtCLC-c, to variation in nitrate levels. J Exp Bot 55:2005–2014
Kang J, Turano FJ (2003) The putative glutamate receptor 1.1 (AtGLR1.1) functions as a regulator of carbon and nitrogen metabolism in Arabidopsis thaliana. Proc Natl Acad Sci USA 100:6872–6877
Khamis S, Lamaze T, Lemoine Y, Foyer C (1990) Adaptation of the photosynthetic apparatus in maize leaves as a result of nitrogen limitation. Plant Physiol 94:1436–1443
Lea US, Slimestad R, Smedvig P, Lillo C (2007) Nitrogen deficiency enhances expression of specific MYB and bHLH transcription factors and accumulation of end products in the flavonoid pathway. Planta 225:1245–1253
Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, Li X, Yuan D, Han B, Zhang Q (2006) Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol Biol 60:617–631
McCullough DE, Girardin PH, Mihajlovic M, Aguilera A, Tollenaar M (1994) Influence of N supply on development and dry matter accumulation of an old and a new maize hybrid. Can. J. Plant Sci 74:471–477
Miyawaki K, Matsumoto-Kitano M, Kakimoto T (2004) Expression of cytokinin biosynthetic isopentenyltransferase genes in Arabidopsis: tissue specificity and regulation by auxin, cytokinin, and nitrate. Plant J 37:128–138
Noh YS, Amasino RM (1999) Identification of a promoter region responsible for the senescence-specific expression of SAG12. Plant Mol Biol 41:181–194
Noh B, Spalding EP (1998) Anion channels and the stimulation of anthocyanin accumulation by blue light in Arabidopsis seedlings. Plant Physiol 116:503–509
Okamoto M, Vidmar JJ, Glass AD (2003) Regulation of NRT1 and NRT2 gene families of Arabidopsis thaliana: responses to nitrate provision. Plant Cell Physiol 44:304–317
Ono K, Terashima I, Watanabe A (1996) Interaction between nitrogen deficit of a plant and nitrogen content in the old leaves. Plant Cell Physiol 37:1083–1089
Paul MJ, Driscoll SP (1997) Sugar repression of photosynthesis: the role of carbohydrates in signalling nitrogen deficiency through source:sink imbalance. Plant Cell Environ 20:110–116
Peng M, Hannam C, Gu H, Bi Y-M, Rothstein SJ (2007) A mutation in NLA, which encodes a RING-type ubiquitin ligase, disrupts Arabidopsis adaptability to nitrogen limitation. Plant J 50:320–337
Remans T, Nacry P, Pervent M, Girin T, Tillard P, Lepetit M, Gojon A (2006) A central role for the nitrate transporter NRT2.1 in the integrated morphological and physiological responses of the root system to nitrogen limitation in Arabidopsis. Plant Physiol 140:909–921
Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10:603–609
Robatzek S, Somssich IE (2001) A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence- and defence-related processes. Plant J 28:123–133
Robatzek S, Somssich IE (2002) Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev 16:1139–1149
Sakakibara H (2003) Nitrate-specific and cytokinin-mediated nitrogen signaling pathways in plants. J Plant Res 116:253–257
Scazzocchio C (2000) The fungal GATA factors. Curr Opin Microbiol 3:126–131
Scheible WR, Morcuende R, Czechowski T, Fritz C, Osuna D, Palacios-Rojas N, Schindelasch D, Thimm O, Udvardi MK, Stitt M (2004) Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol 136:2483–2499
Slavikova S, Shy G, Yao Y, Glozman R, Levanony H, Pietrokovski S, Elazar Z, Galili G (2005) The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants. J Exp Bot 56:2839–2849
Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic pathway. Ann Rev Plant Biol 55:555–590
Socolow RH (1999) Nitrogen management and the future of food: lessons from the management of energy and carbon. Proc Natl Acad Sci USA 96:6001–6008
Takei K, Ueda N, Aoki K, Kuromori T, Hirayama T, Shinozaki K, Yamaya T, Sakakibara H (2004) AtIPT3 is a key determinant of nitrate-dependent cytokinin biosynthesis in Arabidopsis. Plant Cell Physiol 45:1053–1062
Tilman D (1999) Global environmental impacts of agricultural expansion: the need for sustainable and efficient practices. Proc Natl Acad Sci USA 96:5995–6000
Thompson AR, Vierstra RD (2005) Autophagic recycling: lessons from yeast help define the process in plants. Curr Opin Plant Biol 8:165–173
Tollenaar M, Wu J (1999) Yield improvement in temperate maize is attributable to greater stress tolerance. Crop Sci 39:1597–1604
Vierstra RD (1996) Proteolysis in plants: mechanisms and functions. Plant Mol Biol 32:275–302
Wang R, Guegler K, LaBrie ST, Crawford NM (2000) Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell 12:1491–1509
Wang RC, Okamoto M, Xing XJ, Crawford NM (2003) Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol 132:556–567
Wang YH, Garvin DF, Kochian LV (2001) Nitrate-induced genes in tomato roots. Array analysis reveals novel genes that may play a role in nitrogen nutrition. Plant Physiol 127:345–359
Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM (2004) Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol 136:2512–2522
Wingler A, Purdy S, MacLean JA, Pourtau N (2006) The role of sugars in integrating environmental signals during the regulation of leaf senescence. J Exp Bot 57:391–399
Zhu T, Budworth P, Han B, Brown D, Chang HS, Zou GZ, Wang X (2001) Toward elucidating the global gene expression patterns of developing Arabidopsis: parallel analysis of 8 300 genes by a high-density oligonucleotide probe array. Plant Physiol Biochem 39:221–242
Zhu T (2003) Global analysis of gene expression using GeneChip microarrays. Curr Opin Plant Biol 6:1–8
Acknowledgements
We are grateful to Ms. Christina Shenton (Syngenta Inc., USA) for microarray hybridization. This work is funded by the Natural Sciences and Engineering Research Council of Canada, Syngenta Inc., and the Ontario Research and Development Challenge Fund to S. Rothstein.
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Peng, M., Bi, YM., Zhu, T. et al. Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA . Plant Mol Biol 65, 775–797 (2007). https://doi.org/10.1007/s11103-007-9241-0
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DOI: https://doi.org/10.1007/s11103-007-9241-0