Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Obertello, Mariana ^a,c   Krouk, Gabriel ^a,b   Katari, Manpreet S ^a   Runko, Suzan J ^a   Coruzzi, Gloria M ^a  

^a NEW YORK UNIVERSITY   (United States)

^b CNRS   (France)

^c INSTITUTO DE INVESTIGACIONES EN INGENIERÍA GENÉTICA Y BIOLOGÍA MOLECULAR   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS;

ARABIDOPSIS PROTEIN; BACTERIAL DNA; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; BZIP1 PROTEIN, ARABIDOPSIS; NITROGEN; T DNA; T-DNA;

ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; CYTOLOGY; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; LIGHT; METABOLISM; MUTATION; PLANT GENOME; RADIATION EXPOSURE; SIGNAL TRANSDUCTION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; DNA, BACTERIAL; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GENOMICS; LIGHT; MODELS, BIOLOGICAL; MUTATION; NITROGEN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

EID: 77955406540     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-111     Document Type: Article

References (29)

1. Palenchar PM, Kauranov 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 Biology 2004, 5(11):R91. 545782, 15535867.
2. Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biology 2007, 8(1):R7. 10.1186/gb-2007-8-1-r7, 1839130, 17217541.
3. Price J, Laxmi A, St Martin SK, Jang JC. Global transcription profiling reveals multiple sugar signal transduction mechanisms in Arabidopsis. Plant Cell 2004, 16(8):2128-2150. 10.1105/tpc.104.022616, 519203, 15273295.
4. 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(2):R10. 10.1186/gb-2004-5-2-r10, 395748, 14759260.
5. Thum K, Shin M, Gutierrez R, Mukherjee I, Katari M, Nero D, Shasha D, Coruzzi G. An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Systems Biology 2008, 2(1):31. 10.1186/1752-0509-2-31, 2335094, 18387196.
6. Blasing OE, Gibon Y, Gunther M, Hohne M, Morcuende R, Osuna D, Thimm O, Usadel B, Scheible WR, Stitt M. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 2005, 17(12):3257-3281. 10.1105/tpc.105.035261, 1315368, 16299223.
7. Usadel B, Blasing OE, Gibon Y, Retzlaff K, Hohne M, Gunther M, Stitt M. Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol 2008, 146(4):1834-1861. 10.1104/pp.107.115592, 2287354, 18305208.
8. Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutierrez RA. A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis. PLoS Comput Biol 2009, 5(3):e1000326. 10.1371/journal.pcbi.1000326, 2652106, 19300494.
9. Ruffel S, Krouk G, Coruzzi GM. A Systems View of Responses to Nutritional Cues in Arabidopsis: Towards a Paradigm Shift for Predictive Network Modeling. Plant Physiol 2010, 152(2):445-452. 10.1104/pp.109.148502, 2815908, 19939945.
10. Gutierrez RA, Stokes T, Thum KE, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero D, McClung C, et al. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock gene CCA1. PNAS 2008, 105(12):4939-4944. 10.1073/pnas.0800211105, 2290744, 18344319.
11. Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, et al. A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development. Plant Physiol 2003, 133(4):1480-1493. 10.1104/pp.103.029439, 300705, 14605227.
12. Baena-Gonzalez E, Rolland F, Thevelein JM, Sheen J. A central integrator of transcription networks in plant stress and energy signalling. Nature 2007, 448(7156):938-942. 10.1038/nature06069, 17671505.
13. Krouk G, Crawford NM, Coruzzi GM, Tsay Y-F. Nitrate signaling: adaptation to fluctuating environments. Current Opinion in Plant Biology 2010, 13(3):266-273. 10.1016/j.pbi.2009.12.003, 20093067.
14. Schütze K, Harter K, Chaban C. Post-translational regulation of plant bZIP factors. Trends In Plant Science 2008, 13(5):247-255. 10.1016/j.tplants.2008.03.002, 18424222.
15. Nijhawan A, Jain M, Tyagi AK, Khurana JP. Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in Rice. Plant Physiol 2008, 146(2):333-350. 10.1104/pp.107.112821, 2245831, 18065552.
16. Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F. bZIP transcription factors in Arabidopsis. Trends In Plant Science 2002, 7(3):106-111. 10.1016/S1360-1385(01)02223-3, 11906833.
17. Deppmann CD, Acharya A, Rishi V, Wobbes B, Smeekens S, Taparowsky EJ, Vinson C. Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs. Nucl Acids Res 2004, 32(11):3435-3445. 10.1093/nar/gkh653, 443529, 15226410.
18. Schindler U, Menkens AE, Ahmad M, Ecker JR, Cashmore AR. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF-like bZip proteins. EMBO 1992, 11:1261-1273.
19. de Vetten NC, Ferl RJ. Characterization of a maize G-box binding factor that is induced by hypoxia. The Plant Journal 1995, 7(4):589-601. 10.1046/j.1365-313X.1995.7040589.x, 7742856.
20. Rodriguez-Uribe L, O'Connell MA. A root-specific bZIP transcription factor is responsive to water deficit stress in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris). J Exp Bot 2006, 57(6):1391-1398. 10.1093/jxb/erj118, 16531461.
21. Meshi T, Taoka K, Iwabuchi M. Regulation of histone gene expression during the cell cycle. Plant Molecular Biology 2000, 43(5-6):643-657. 10.1023/A:1006421821964, 11089867.
22. Vincentz M, Bandeira-Kobarg C, Gauer L, Schlögl P, Leite A. Evolutionary Pattern of Angiosperm bZIP Factors Homologous to the Maize Opaque2 Regulatory Protein. Journal of Molecular Evolution 2002, 56(1):105-116.
23. Kang SG, Price J, Lin P-C, Hong JC, Jang J-C. The Arabidopsis bZIP1 Transcription Factor Is Involved in Sugar Signaling, Protein Networking, and DNA Binding. Mol Plant 2010, 3(2):361-373. 10.1093/mp/ssp115, 20080816.
24. Murashige T, Skoog F. A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 1962, 15(3):473-497.
25. Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, et al. VirtualPlant: A software platform to support Systems Biology research. Plant Physiol 2010, 152(2):500-515. 10.1104/pp.109.147025, 2815851, 20007449.
26. Sulpice R, Pyl ET, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, Gibon Y, Usadel B, Poree F, Piques MC, et al. Starch as a major integrator in the regulation of plant growth. Proc Natl Acad Sci USA 2009, 106(25):10348-10353. 10.1073/pnas.0903478106, 2693182, 19506259.
27. Wang R, Liu D, Crawford NM. The Arabidopsis CHL1 protein plays a major role in high-affinity nitrate uptake. Proc Natl Acad Sci USA 1998, 95(25):15134-15139. 10.1073/pnas.95.25.15134, 24588, 9844028.
28. Yeung KY, Haynor DR, Ruzzo WL. Validating clustering for gene expression data. Bioinformatics 2001, 17(4):309-318. 10.1093/bioinformatics/17.4.309, 11301299.
29. Hartigan JA, Wong MA. A K-means clustering algorithm. Applied Statistics 1979, 28:100-108.