Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen

Transcriptome analysis, using Affymetrix ATH1 arrays and a real-time reverse transcription-PCR platform for >1,400 transcription factors, was performed to identify processes affected by long-term nitrogen-deprivation or short-term nitrate nutrition in Arabidopsis. Two days of nitrogen deprivation...

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Published in:	Plant physiology (Bethesda) Vol. 136; no. 1; pp. 2483 - 2499
Main Authors:	Scheible, W.R, Morcuende, R, Czechowski, T, Fritz, C, Osuna, D, Palacios-Rojas, N, Schindelasch, D, Thimm, O, Udvardi, M.K, Stitt, M
Format:	Journal Article
Language:	English
Published:	Rockville, MD American Society of Plant Biologists 01.09.2004 American Society of Plant Physiologists
Series:	Focus Issue on Plant Nutrition
Subjects:	Agricultural and forest climatology and meteorology. Irrigation. Drainage Agricultural and forest meteorology Agronomy. Soil science and plant productions Amino acids Arabidopsis Arabidopsis - genetics Arabidopsis - growth & development Arabidopsis - metabolism Arabidopsis Proteins Arabidopsis Proteins - biosynthesis Arabidopsis thaliana assimilation (physiology) Biological and medical sciences biosynthesis carbohydrate metabolism Cell biochemistry cell growth Cell physiology Cell Wall Cell Wall - metabolism cell walls chlorophyll Climatic adaptation. Acclimatization Economic plant physiology flavonoids Focus Issue on Plant Nutrition Fundamental and applied biological sciences. Psychology Gene Expression Profiling gene expression regulation Gene Expression Regulation, Plant General agronomy. Plant production Genes Genes. Genome genetics genome Genome Analysis Genome, Plant growth & development homeodomain proteins Lipid Metabolism Metabolism microarray technology Molecular and cellular biology Molecular genetics Nitrates nitrogen Nitrogen - metabolism Nitrogen metabolism and other ones (excepting carbon metabolism) Nutrition. Photosynthesis. Respiration. Metabolism Nutritional Physiological Phenomena Oligonucleotide Array Sequence Analysis organic acids and salts Oxidation-Reduction phenylpropanoids Plant cells plant nutrition Plant physiology and development plant proteins Plant roots Plants post-translational modification protein degradation Protein Processing, Post-Translational Protein synthesis redox reactions Reverse transcriptase polymerase chain reaction Seedlings shikimate pathway Signal Transduction transcription (genetics) transcriptome trehalose Chlorophyll Transcription Enzyme Arabidopsis Growth Transferases Phosphoric monoester hydrolases Esterases Biosynthesis Plastid Organic acids Gene Cruciferae Kinase Protein kinase Protein synthesis Dicotyledones Aminoacid Angiospermae Hydrolases Spermatophyta Transcription factor Photosynthesis Secondary metabolism
ISSN:	0032-0889, 1532-2548
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Summary:	Transcriptome analysis, using Affymetrix ATH1 arrays and a real-time reverse transcription-PCR platform for >1,400 transcription factors, was performed to identify processes affected by long-term nitrogen-deprivation or short-term nitrate nutrition in Arabidopsis. Two days of nitrogen deprivation led to coordinate repression of the majority of the genes assigned to photosynthesis, chlorophyll synthesis, plastid protein synthesis, induction of many genes for secondary metabolism, and reprogramming of mitochondrial electron transport. Nitrate readdition led to rapid, widespread, and coordinated changes. Multiple genes for the uptake and reduction of nitrate, the generation of reducing equivalents, and organic acid skeletons were induced within 30 min, before primary metabolites changed significantly. By 3 h, most genes assigned to amino acid and nucleotide biosynthesis and scavenging were induced, while most genes assigned to amino acid and nucleotide breakdown were repressed. There was coordinate induction of many genes assigned to RNA synthesis and processing and most of the genes assigned to amino acid activation and protein synthesis. Although amino acids involved in central metabolism increased, minor amino acids decreased, providing independent evidence for the activation of protein synthesis. Specific genes encoding expansin and tonoplast intrinsic proteins were induced, indicating activation of cell expansion and growth in response to nitrate nutrition. There were rapid responses in the expression of many genes potentially involved in regulation, including genes for trehalose metabolism and hormone metabolism, protein kinases and phosphatases, receptor kinases, and transcription factors.
Bibliography:	http://www.plantphysiol.org/ ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Review-3 The work was supported by the Max-Planck-Society and the Bundesministerium für Bildung und Forschung-funded project GABI Verbund Arabidopsis III Gauntlets (“Carbon and Nutrient Signaling: Test Systems, and Metabolite and Transcript Profiles”; 0312277A). The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.104.047019. Present address: Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain. Corresponding author; e-mail scheible@mpimp-golm.mpg.de; fax 49–331–567–8101.
ISSN:	0032-0889 1532-2548
DOI:	10.1104/pp.104.047019