Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation

Journal of Cell Science

Volumn 116, Issue 20, 2003, Pages 4249-4259

  Vlieghe, Kobe ^a   Vuylsteke, Marnik ^a   Florquin, Kobe ^a   Rombauts, Stephane ^a   Maes, Sara ^a   Ormenese, Sandra ^b   Van Hummelen, Paul ^a   Van de Peer, Yves ^a   Inzé, Dirk ^a   De Veylder, Lieven ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Arabidopsis thaliana; Cell cycle; E2F; Microarray; Nitrogen assimilation

Indexed keywords

NITRATE; NITROGEN; NITROGEN DERIVATIVE; PLANT DNA; TRANSCRIPTION FACTOR E2F;

ARABIDOPSIS; ARTICLE; BIOSYNTHESIS; CELL WALL; CONTROLLED STUDY; DNA DETERMINATION; DNA MICROARRAY; DNA MODIFICATION; DNA REPLICATION; DOWN REGULATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENE TARGETING; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT GENETICS; PLANT GROWTH; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; SIGNAL TRANSDUCTION; TRANSGENIC PLANT; UNINDEXED SEQUENCE; WILD TYPE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; CELL CYCLE; CELL DIVISION; CELL WALL; DNA REPLICATION; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE DATA; NITROGEN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANTS, GENETICALLY MODIFIED; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 0242319625     PISSN: 00219533     EISSN: None     Source Type: Journal    
DOI: 10.1242/jcs.00715     Document Type: Article

References (42)

1. Albani, D., Mariconti, L., Ricagno, S., Pitto, L., Moroni, C., Helin, K. and Cella, R. (2000). DcE2F, a functional plant E2F-like transcriptional activator from Daucus carota. J. Mol. Chem. 275, 19258-19267.
2. Campbell, P. and Braam, J. (1999). Xyloglucan endotransglycosylases: diversity of genes, enzymes and potential wall-modifying functions. Trends Plant Sci. 4, 361-366.
3. Cannons, A. C. and Shiflett, S. D. (2001). Transcriptional regulation of the nitrate reductase gene in Chlorella vulgaris: identification of regulatory elements controlling expression. Curr. Genet. 40, 128-135.
4. Castellano, M. M., del Pozo, J. C., Ramirez-Parra, E., Brown, S. and Gutierrez, C. (2001). Expression and stability of Arabidopsis CDC6 are associated with endoreplication. Plant Cell 13, 2671-2686.
5. Chabouté, M.-E., Clément, B., Sekine, M., Philipps, G. and Chaubet-Gigot, N. (2000). Cell cycle regulation of the tobacco ribonucleotide reductase small subunit gene is mediated by E2F-like elements. Plant Cell 12, 1987-1999.
6. de Jager, S. M., Menges, M., Bauer, U.-M. and Murray, J. A. H. (2001). Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol. Biol. 47, 555-568.
7. De Veylder, L., Beeckman, T., Beemster, G. T. S., de Almeida Engler, J., Ormenese, S., Maes, S., Naudts, M., Van Der Schueren, E., Jacqmard, A., Engler, G. and Inzé, D. (2002). Control of proliferation, endoreduplication and differentiation by the Arabidopsis E2Fa/DPa transcription factor. EMBO J. 21, 1360-1368.
8. AtSKP2 pathway in response to light. Plant Cell 14, 3057-3071.
9. Egelkrout, E. M., Robertson, D. and Hanley-Bowdoin, L. (2001). Proliferating cell nuclear antigen transcription is repressed through an E2F consensus element and activated by geminivirus infection in mature leaves. Plant Cell 13, 1437-1452.
10. Fanutti, C., Gidley, M. J. and Reid, J. S. G. (1993). Action of a pure xyloglucan endo-transglycosylase (formerly called xyloglucan-specific endo-(1→4)-β-D-glucanase) from the cotyledons of germinated nasturtium seeds. Plant J. 3, 691-700.
11. Farkas, V., Sulova, Z., Stratilova, E., Hanna, R. and Maclachlan, G. (1992). Cleavage of xyloglucan by nasturtium seed xyloglucanase and transglycosylation to xyloglucan subunit oligosaccharides. Arch. Biochem. Biophys. 298, 365-370.
12. Fu, Y.-H. and Marzluf, G. A. (1990). nit-2, the major positive-acting nitrogen regulatory gene of Neurospora crassa, encodes a sequence-specific DNA-binding protein. Proc. Natl. Acad. Sci. USA 87, 5331-5335.
13. Ishida, S., Huang, E., Zuzan, H., Spang, R., Leone, G., West, M. and Nevins, J. R. (2001). Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol. Cell. Biol. 21, 4684-4699.
14. Kel, A. E., Kel-Margoulis, O. V., Farnham, P. J., Bartley, S. M., Wingender, E. and Zhang, M. Q. (2001). Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. J. Mol. Biol. 309, 99-120.
15. Kiyosue, T., Yamaguchi-Shinozaki, K. and Shinozaki, K. (1994). Cloning of cDNAs for genes that are early-responsive to dehydration stress (ERDs) in Arabidopsis thaliana L.: identification of three ERDs as HSP cognate genes. Plant Mol. Biol. 25, 791-798.
16. Koprivova, A., Suter, M., Op den Camp, R., Brunold, C. and Kopriva, S. (2000). Regulation of sulfate assimilation by nitrogen in Arabidopsis. Plant Physiol. 122, 737-746.
17. Kosugi, S. and Ohashi, Y. (2002a). E2F sites that can interact with E2F proteins cloned from rice are required for meristematic tissue-specific expression of rice and tobacco proliferating cell nuclear antigen promoters. Plant J. 29, 45-59.
18. Kosugi, S. and Ohashi, Y. (2002b). E2Ls, E2F-like repressors of Arabidopsis that bind to E2F sites in a monomeric form. J. Biol. Chem. 277, 16553-16558.
19. Lancien, M., Gadal, P. and Hodges, M. (2000). Enzyme redundancy and the importance of 2-oxoglutarate in higher plant ammonium assimilation. Plant Physiol. 123, 817-824.
20. Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P. and Rombauts, S. (2002). PlantCare: a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30, 325-327.
21. Lusser, A., Eberharter, A., Loidl, A., Goralik-Schramel, M., Horngacher, M., Haas, H. and Loidl, P. (1999). Analysis of the histone acetyltransferase B complex of maize embryos. Nucleic Acids Res. 27, 4427-4435.
22. Magyar, Z., Atanassova, A., De Veylder, L., Rombauts, S. and Inzé, D. (2000). Characterization of two distinct DP-related genes from Arabidopsis thaliana. FEBS Lett. 486, 79-87.
23. Mariconti, L., Pellegrini, B., Cantoni, R., Stevens, R., Bergounioux, C., Cella, R. and Albani, D. (2002). The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J. Biol. Chem. 277, 9911-9919.
24. Medford, J. I., Elmer, J. S. and Klee, H. J. (1991). Molecular cloning and characterization of genes expressed in shoot apical meristems. Plant Cell 3, 359-370.
25. Menges, M. and Murray, J. A. H. (2002). Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity. Plant J. 20, 203-212.
26. Menges, M., Hennig, L., Gruissem, W. and Murray, J. A. H. (2002). Cell cycle-regulated gene expression in Arabidopsis. J. Biol. Chem. 277, 41987-42002.
27. Müller, H., Bracken, A. P., Vernell, R., Moroni, M. C., Christians, F., Grassilli, E., Prosperini, E., Vigo, E., Oliner, J. D. and Helin, K. (2001). E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev. 15, 267-285.
28. Porceddu, A., De Veylder, L., Hayles, J., Van Montagu, M., Inzé, D. and Mironov, V. (1999). Mutational analysis of two Arabidopsis thaliana cyclin-dependent kinases in fission yeast. FEBS Lett. 446, 182-188.
29. Puskás, L. G., Zvara, A., Hackler, L. J. and Van Hummelen, P. (2002). RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 32, 1330-1341.
30. Ramirez-Parra, E. and Gutierrez, C. (2000). Characterization of wheat DP, a heterodimerization partner of the plant E2F transcription factor which stimulates E2F-DNA binding. FEBS Lett. 486, 73-78.
31. Ramirez-Parra, E., Fründt, C. and Gutierrez, C. (2003). A genome-wide identification of E2F-regulated genes in Arabidopsis. Plant J. 33, 801-811.
32. 1/S regulators. Nucleic Acids Res. 27, 3527-3533.
33. 2/M checkpoints. Genes Dev. 16, 245-256.
34. Sekine, M., Ito, M., Uemukai, K., Maeda, Y., Nakagami, H. and Shinmyo, A. (1999). Isolation and characterization of the E2F-like gene in plants. FEBS Lett. 460, 117-122.
35. Stevens, R., Mariconti, L., Rossignol, P., Perennes, C., Cella, R. and Bergounioux, C. (2002). Two E2F sites in the Arabidopsis MCM3 promoter have different roles in cell cycle activation and meristematic expression. J. Biol. Chem. 277, 32978-32984.
36. Trimarchi, J. M. and Lees, J. A. (2002). Sibling rivalry in the E2F family. Nature Rev. Mol. Cell. Biol. 3, 11-20.
37. Valvekens, D., Van Montagu, M. and Van Lijsebettens, M. (1988). Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc. Natl. Acad. Sci. USA 85, 5536-5540.
38. Vandepoele, K., Raes, J., De Veylder, L., Rouzé, P., Rombauts, S. and Inzé, D. (2002). Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell 14, 903-916.
39. Weinmann, A., Bartley, S. M., Zhang, T., Zhang, M. Q. and Farnham, P. J. (2001). Use of chromatin immumoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21, 6820-6832.
40. Wittstock, U. and Halkier, B. A. (2002). Glucosinolate research in the Arabidopsis era. Trends Plant Sci. 7, 263-270.
41. Wolfinger, R. D., Gibson, G., Wolfinger, E. D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C. and Paules, R. S. (2001). Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol. 8, 625-637.
42. Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J. and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.