Qualitative network models and genome-wide expression data define carbon/ nitrogen-responsive molecular machines in Arabidopsis

Genome Biology

Volumn 8, Issue 1, 2007, Pages

  Gutiérrez, Rodrigo A ^a,b   Lejay, Laurence V ^a,e   Dean, Alexis ^a   Chiaromonte, Francesca ^c   Shasha, Dennis E ^d   Coruzzi, Gloria M ^a  

^a NEW YORK UNIVERSITY   (United States)

^b PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE   (Chile)

^c Department of Statistics ^*  (United States)

^d NEW YORK UNIVERSITY   (United States)

^e INRA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AUXIN; CARBON; MICRORNA; NITROGEN; TRANSCRIPTOME; INDOLEACETIC ACID DERIVATIVE;

ANALYSIS OF VARIANCE; ARABIDOPSIS; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENE INTERACTION; NONHUMAN; PLANT CELL; PLANT GENETICS; PLANT METABOLISM; PLANT RESPONSE; PLANT ROOT; PROTEIN DEGRADATION; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; CLUSTER ANALYSIS; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GENOME; METABOLISM; TIME;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS; CARBON; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENES, PLANT; GENOME, PLANT; INDOLEACETIC ACIDS; MODELS, GENETIC; NITROGEN; PLANT ROOTS; TIME FACTORS;

EID: 34147133691     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-1-r7     Document Type: Article

References (32)

1. Wang R Guegler K LaBrie ST Crawford NM Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes that are induced by nitrate. Plant Cell 2000 12 1491-1510 149118 10948265 10.1105/tpc.12.8.1491
2. Wang R Okamoto M Xing X Crawford NM 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 2003 132 556-567 166997 12805587 10.1104/pp.103.021253
3. Stitt M Muller C Matt P Gibon Y Carillo P Morcuende R Scheible WR Krapp A Steps towards an integrated view of nitrogen metabolism. J Exp Bot 2002 53 959-970 10.1093/jexbot/53.370.959 11912238
4. Rolland F Moore B Sheen J Sugar sensing and signaling in plants. Plant Cell 2002 14 S185-S205 151255 12045277
5. Price J Laxmi A St Martin SK Jang JC Global transcription profiling reveals multiple sugar signal transduction mechanisms in Arabidopsis. Plant Cell 2004 16 2128-2150 519203 15273295 10.1105/tpc.104.022616
6. Palenchar P Kouranov A Lejay L Coruzzi G Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol 2004 5 R91 545782 15535867
7. Schneper L Duvel K Broach JR Sense and sensibility: Nutritional response and signal integration in yeast. Curr Opin Microbiol 2004 7 624 10.1016/ j.mib.2004.10.002 15556035
8. Forchhammer K Global carbon/nitrogen control by PII signal transduction in cyanobacteria: From signals to targets. FEMS Microbiol Rev 2004 28 319 10.1016/j.femsre.2003.11.001 15449606
9. Corbesier L Lejeune P Bernier G The role of carbohydrates in the induction of flowering in Arabidopsis thaliana: Comparison between the wild type and a starchless mutant. Planta 1998 206 131-137 10.1007/ s004250050383 9715535
10. Lynch J Root architecture and plant productivity. Plant Physiol 1995 109 7-13 157559 12228579
11. Koch KE Carbohydrate-modulated gene expression in plants. Annu Rev Plant Physiol Plant Mol Biol 1996 47 509-540 10.1146/annurev.arplant.47.1.509 15012299
12. Stitt M Nitrate regulation of metabolism and growth. Curr Opin Plant Biol 1999 2 178-186 10.1016/S1369-5266(99)80033-8 10375569
13. Scheible WR Morcuende R Czechowski T Fritz C Osuna D Palacios-Rojas N Schindelasch D Thimm O Udvardi MK Stitt M 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 2004 136 2483-2499 523316 15375205 10.1104/ pp.104.047019
14. Wang R Tischner R Gutierrez RA Hoffman M Xing X Chen M Coruzzi G Crawford NM Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol 2004 136 2512-2522 523318 15333754 10.1104/pp.104.044610
15. Thum KE Shin MJ Palenchar PM Kouranov A Coruzzi GM Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol 2004 5 R10 395748 14759260 10.1186/gb-2004-5-2-r10
16. Palenchar PM Kouranov A Lejay LV Coruzzi GM Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol 2004 5 R91 545782 15535867
17. Price J Laxmi A St Martin SK Jang JC Global transcription profiling reveals multiple sugar signal transduction mechanisms in Arabidopsis. Plant Cell 2004 16 2128-2150 519203 15273295 10.1105/tpc.104.022616
18. Venables WN Ripley BD S Programming New York: Springer-Verlag 2000
19. Accompanying Website: Arabidopsis Gene Networks http://virtualplant.bio.nyu.edu/cgi-bin/networks/index.cgi
20. The VirtualPlant System http://www.virtualplant.org
21. Ferro A Pigola G Pulvirenti A Shasha D Fast clustering and minimum weight matching algorithms for very large mobile backbone wireless networks. Int J Found Comput Sci 2003 14 223-236 10.1142/ S0129054103001698
22. Li C Potuschak T Colon-Carmona A Gutierrez RA Doerner P Arabidopsis TCP20 links regulation of growth and cell division control pathways. Proc Natl Acad Sci USA 2005 102 12978-12983 1200278 16123132 10.1073/ pnas.0504039102
23. Martin T Oswald O Graham IA Arabidopsis seedling growth, storage lipid mobilization, and photosynthetic gene expression are regulated by carbon:nItrogen availability. Plant Physiol 2002 128 472-481 148910 11842151 10.1104/pp.128.2.472
24. Kepinski S Leyser O The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 2005 435 446-451 10.1038/nature03542 15917798
25. Forde BG Local and long-range signaling pathways regulating plant responses to nitrate. Annu Rev Plant Biol 2002 53 203-224 10.1146/ annurev.arplant.53.100301.135256 12221973
26. Lejay L Tillard P Lepetit M Olive F Filleur S Daniel-Vedele F Gojon A Molecular and functional regulation of two NO3-uptake systems by N- and C-status of Arabidopsis plants. Plant J 1999 18 509-519 10.1046/ j.1365-313X.1999.00480.x 10417701
27. Lobreaux S Massenet O Briat JF Iron induces ferritin synthesis in maize plantlets. Plant Mol Biol 1992 19 563-572 10.1007/BF00026783 1627771
28. ArrayExpress http://www.ebi.ac.uk/arrayexpress/
29. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Statistical Soc B 1995 57 289-300
30. Lejay LV Shasha DE Palenchar PM Kouranov AY Cruikshank AA Chou MF Coruzzi GM Adaptive combinatorial design to explore large experimental spaces: Approach and validation. Systems Biol (Stevenage) 2004 1 2 206-212
31. Schoof H Zaccaria P Gundlach H Lemcke K Rudd S Kolesov G Arnold R Mewes HW Mayer KF MIPS Arabidopsis thaliana database (MAtDB): An integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res 2002 30 91-93 99069 11752263 10.1093/nar/30.1.91
32. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003 13 2498-2504 403769 14597658 10.1101/gr.1239303