Genome-wide investigation of light and carbon signaling interactions in Arabidopsis

Genome Biology

Volumn 5, Issue 2, 2004, Pages

  Thum, Karen E ^a   Shin, Michael J ^a   Palenchar, Peter M ^a   Kouranov, Andrei ^a,b   Coruzzi, Gloria M ^a  

^a NEW YORK UNIVERSITY   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Additional Data File; InterAct Class; PlantCARE Database; Quantitative Polymerase Chain Reaction; Similar Expression Profile

Indexed keywords

CARBON;

ARABIDOPSIS; ARTICLE; CARBOHYDRATE METABOLISM; DNA MICROARRAY; DNA RESPONSIVE ELEMENT; DRUG EFFECT; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; LIGHT; METABOLISM; RADIATION EXPOSURE; REGULATORY SEQUENCE; SIGNAL TRANSDUCTION;

ARABIDOPSIS; CARBOHYDRATE METABOLISM; CARBON; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; LIGHT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID; RESPONSE ELEMENTS; SIGNAL TRANSDUCTION;

EID: 1842567165     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2004-5-2-r10     Document Type: Article

References (52)

1. Fankhauser C, Chory J: Light control of plant development. Annu Rev Plant Physiol Plant Mol Biol. 1997, 13: 203-229. 10.1146/annurev.cellbio.13.1.203.
2. Neff MM, Fankhauser C, Chory J: Light: An indicator of time and place. Genes Dev. 2000, 14: 257-271.
3. Moller SG, Ingles PJ, Whitelam GC: The cell biology of phytochrome signaling. New Physiol. 2002, 154: 553-590. 10.1046/j.1469-8137.2002.00419.x. DOI: 10.1046/j.1469-8137.2002.00419.x
4. Nagy F, Schafer E: Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants. Annu Rev Plant Physiol Plant Mol Biol. 2002, 53: 329-355. 10.1146/annurev.arplant.53.100301.135302. DOI: 10.1146/annurev.arplant.53.100301.135302
5. 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. DOI: 10.1146/annurev.arplant.47.1.509
6. Rolland F, Moore B, Sheen J: Sugar sensing and signaling in plants. Plant Cell Supp. 2002, 2002: S185-S205.
7. Sheen J, Zhou L, Jang J-C: Sugars as signaling molecules. Curr Opin Plant Biol. 1999, 2: 410-418. 10.1016/S1369-5266(99)00014-X. DOI: 10.1016/S1369-5266(99)00014-X
8. Barnes SA, Nishizawa NK, Quaggio RB, Whitelam GC, Chua NH: Far-red light blocks greening of Arabidopsis seedlings via a phytochrome A-mediated change in plastid development. Plant Cell. 1996, 8: 601-615. 10.1105/tpc.8.4.601.
9. Dijkwel PP, Huijser C, Weisbeek PJ, Chua NH, Smeekens S: Sucrose control of phytochrome A signaling in Arabidopsis. Plant Cell. 1997, 9: 583-595. 10.1105/tpc.9.4.583. DOI: 10.1105/tpc.9.4.583
10. Short T: Over-expression of Arabidopsis phytochrome B inhibits phytochrome A function in the presence of sucrose. Plant Physiol. 1999, 119: 1497-1506. 10.1104/pp.119.4.1497. DOI: 10.1104/pp.119.4.1497
11. Thum KE, Shasha DE, Lejay LV, Coruzzi GM: Light and carbon signaling pathways. Modeling circuits of interactions. Plant Physiol. 2003, 132: 440-452. 10.1104/pp.103.022780. DOI: 10.1104/pp.103.022780
12. Lam HM, Hsieh MH, Coruzzi GM: Reciprocal regulation of distinct asparagine synthetase genes by light and metabolites in Arabidopsis thaliana. Plant J. 1998, 16: 345-353. 10.1046/j.1365-313x.1998.00302.x. DOI: 10.1046/j.1365-313x.1998.00302.x
13. Oliveira IC, Coruzzi GM: Carbon and amino acids reciprocally modulate the expression of glutamine synthetase in Arabidopsis. Plant Physiol. 1999, 121: 301-309. 10.1104/pp.121.1.301. DOI: 10.1104/pp.121.1.301
14. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270: 467-470. DOI: 10.1126/science.270.5235.467
15. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA: Orchestrated transcription of a key pathway in Arabidopsis by the circadian clock. Science. 2000, 290: 2110-2113. 10.1126/science.290.5499.2110. DOI: 10.1126/science.290.5499.2110
16. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E: Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell. 2001, 13: 113-123. 10.1105/tpc.13.1.113. DOI: 10.1105/tpc.13.1.113
17. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH: Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci USA. 2001, 98: 9437-9442. 10.1073/pnas.161300998. DOI: 10.1073/pnas.161300998
18. Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng XW: Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell. 2001, 13: 2589-2607. 10.1105/tpc.13.12.2589. DOI: 10.1105/tpc.13.12.2589
19. Ma L, Gao Y, Qu L, Chen Z, Li J, Zhao H, Deng XW: Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell. 2002, 14: 2383-2398. 10.1105/tpc.004416. DOI: 10.1105/tpc.004416
20. Wang R, Guegler K, LaBrie ST, Crawford NM: Genomic evidence of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell. 2000, 12: 1491-1509. 10.1105/tpc.12.8.1491. DOI: 10.1105/tpc.12.8.1491
21. Wang YH, Garvin DF, Kochian LV: Rapid induction of regulatory and transporter genes in response to phosphorus, potassium, and iron deficiencies in tomato roots. Evidence for cross talk and root/rhizosphere-mediated signals. Plant Physiol. 2002, 130: 1361-1370. 10.1104/pp.008854. DOI: 10.1104/pp.008854
22. Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Caminic P, Hayashizaki Y, Shinozaki K: Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell. 2001, 13: 61-72. 10.1105/tpc.13.1.61. DOI: 10.1105/tpc.13.1.61
23. Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet. 2001, 27: 167-171. 10.1038/84792. DOI: 10.1038/84792
24. Keles S, Van Der Laan M, Eisen MB: Identification of regulatory elements using a feature selection method. Bioinformatics. 2002, 18: 1167-1175. 10.1093/bioinformatics/18.9.1167. DOI: 10.1093/bioinformatics/18.9.1167
25. Conlon EM, Liu XS, Lieb JD, Liu JS: Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci USA. 2003, 100: 3339-3344. 10.1073/pnas.0630591100. DOI: 10.1073/pnas.0630591100
26. Quackenbush J: Computational analysis of microarray data. Nat Rev Genet. 2001, 2: 418-427. 10.1038/35076576. DOI: 10.1038/35076576
27. Details on microarray gene expression classification using InterAct Class. [http://www.cs.nyu.edu/~pathexp]
28. MAtDB entry page. [http://mips.gsf.de/proj/thal/db/]
29. Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer FX: MIPS Arabidopsis thaliana database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 2002, 30: 91-93. 10.1093/nar/30.1.91. DOI: 10.1093/nar/30.1.91
30. AlignACE homepage. [http://atlas.med.harvard.edu]
31. Roth FP, Hughes JD, Estep PW, Church GA: Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol. 1998, 16: 939-945. 10.1038/nbt1098-939. DOI: 10.1038/nbt1098-939
32. Regulatory sequence analysis tools. [http://rsat.ulb.ac.be/rsat/]
33. van Helden J: Regulatory sequence analysis tools. Nucleic Acids Res. 2003, 31: 3593-3596. 10.1093/nar/gkg567. DOI: 10.1093/nar/gkg567
34. PlantCARE, a database of plant promoters and their cis-regulatory elements. [http://oberon.fvms.ugent.be:8080/PlantCARE/]
35. Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts S: PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30: 325-327. 10.1093/nar/30.1.325. DOI: 10.1093/nar/30.1.325
36. Bolle C, Kusnetsov VV, Herrmann RG, Oelmuller R: The spinach AtpC and AtpD genes contain elements for light-regulated, plastid-dependent and organ-specific expression in the vicinity of the transcription start sites. Plant J. 1996, 9: 21-30. 10.1046/j.1365-313X.1996.09010021.x. DOI: 10.1046/j.1365-313X.1996.09010021.x
37. Kusnetsov V, Bolle C, Lubberstedt T, Sopory S, Herrman RG, Oelmuller R: Evidence that the plastid signal and light operate via the same cis-acting elements in the promoters of nuclear genes for plastid proteins. Mol Gen Genet. 1996, 252: 631-639. 10.1007/s004380050271.
38. Kusnetsov V, Landsgerger M, Meurer J, Oelmuller R: The assembly of the CAAT-box binding complex at a photosynthesis gene promoter is regulated by light, cytokinin, and the stage of the plastids. J Biol Chem. 1999, 274: 36009-36014. 10.1074/jbc.274.50.36009. DOI: 10.1074/jbc.274.50.36009
39. Coschigano KT, Melo-Oliveira R, Lim J, Coruzzi GM: Arabidopsis gls mutants and distinct Fd-GOGAT genes: Implications for photorespiration and primary nitrogen assimilation. Plant Cell. 1998, 10: 741-752. 10.1105/tpc.10.5.741.
40. Lam HM, Coschigano K, Oliveira IC, Melo-Oliverira R, Coruzzi GM: The molecular-genetics of nitrogen assimilation into amino acids in higher plants. Annu Rev Plant Physiol Plant Mol Biol. 1996, 47: 569-593. 10.1146/annurev.arplant.47.1.569. DOI: 10.1146/annurev.arplant.47.1.569
41. Melo-Oliveira R, Oliveira IC, Coruzzi G: Arabidopsis mutant analysis and gene regulation define a non-redundant role for glutamate dehydrogenase in nitrogen assimilation. Proc Natl Acad Sci USA. 93: 4718-4723. 10.1073/pnas.93.10.4718. DOI: 10.1073/pnas.93.10.4718
42. Arguello-Astorga GR, Herrera-Estrella LR: Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways. Plant Physiol. 1996, 112: 1151-1166. 10.1104/pp.112.3.1151. DOI: 10.1104/pp.112.3.1151
43. Hartman U, Valentine WJ, Christie JM, Hays J, Jenkins GI, Weisshaar B: Identification of UV/blue light response elements in the Arabidopsis thaliana chalcone synthase promoter using a homologous protoplast transient expression system. Plant Mol Biol. 1998, 36: 741-754. 10.1023/A:1005921914384. DOI: 10.1023/A:1005921914384
44. Terzaghi WB, Cashmore AR: Light-regulated transcription. Annu Rev Plant Physiol Plant Mol Biol. 1995, 46: 445-474. 10.1146/annurev.pp.46.060195.002305. DOI: 10.1146/annurev.pp.46.060195.002305
45. Bezhani S, Sherameti I, Pfannschmidt T, Oelmuller R: A repressor with similarities to prokaryotic and eukaryotic DNA helicases controls the assembly of the CAAT box binding complex at a photosynthesis gene promoter. J Biol Chem. 2001, 276: 23785-23789. 10.1074/jbc.M010945200. DOI: 10.1074/jbc.M010945200
46. Yu LM, Lamb CJ, Dixon RA: Purification and biochemical characterization of proteins which bind to the H-box cis-element implicated in transcriptional activation of plant defense genes. Plant J. 1993, 3: 805-816. 10.1046/j.1365-313X.1993.03060805.x. DOI: 10.1111/j.1365-313X.1993.00805.x
47. Loake GJ, Faktor O, Lamb CJ, Dixon RA: Combination of H-box [CCTACC(N)7CT] and G-box (CACGTG) cis elements is necessary for feed-forward stimulation of a chalcone synthase promoter by the phenylpropanoid-pathway intermediate p-courmaric acid. Proc Natl Acad Sci USA. 1992, 89: 9230-9234. DOI: 10.1073/pnas.89.19.9230
48. Kuno N, Furuya M: Phytochrome regulation of nuclear gene expression in plants. Semin Cell Dev Biol. 2000, 11: 485-493. 10.1006/scdb.2000.0205. DOI: 10.1006/scdb.2000.0205
49. Bruce WB, Deng XW, Quail PH: A negatively acting DNA sequence element mediates phytochrome-directed repression of phyA gene transcription. EMBO J. 1991, 10: 3015-3024.
50. Zhou DX: Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends Plant Sci. 1999, 4: 210-214. 10.1016/S1360-1385(99)01418-1. DOI: 10.1016/S1360-1385(99)01418-1
51. Jackson AO, Larkins BA: Influence of ionic strength, pH and chelation of divalent metals on isolation of polyribosomes from tobacco leaves. Plant Physiol. 1976, 57: 5-10. DOI: 10.1104/pp.57.1.5
52. Exact binomial probability calculator. [http://faculty.vassar.edu/lowry/binom_stats.html]