A CELD-fusion method for rapid determination of the DNA-binding sequence specificity of novel plant DNA-binding proteins

Plant Journal

Volumn 41, Issue 4, 2005, Pages 638-649

  Xue, Gang Ping ^a  

^a CSIRO   (Australia)

Author keywords

Binding sequence specificity; DNA binding protein; Enzymatic DNA binding activity assays; High throughput; Rapid binding site selection

Indexed keywords

BIOASSAY; CROPS; DNA SEQUENCES; ELECTROPHORESIS; GROWTH KINETICS; PLANTS (BOTANY); PROTEINS;

BINDING SITES; CELLULASE D (CELD); DNA-BINDING PROTEINS (DBP); GENE REGULATORY NETWORKS;

GENETIC ENGINEERING;

CELLULASE; DNA BINDING PROTEIN; ENDOGLUCANASE CELD; HYBRID PROTEIN; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; CONSENSUS SEQUENCE; ESCHERICHIA COLI; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; TRANSGENIC ORGANISM;

BASE SEQUENCE; BINDING SITES; CELLULASE; CONSENSUS SEQUENCE; DNA-BINDING PROTEINS; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; ORGANISMS, GENETICALLY MODIFIED; PLANT PROTEINS; RECOMBINANT FUSION PROTEINS; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

BIOLOGICAL TESTS; ELECTROPHORESIS; FARM CROPS; GENETIC ENGINEERING; NUCLEIC ACIDS; PLANTS; PROTEINS;

TRITICUM AESTIVUM;

EID: 14644399302     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2004.02323.x     Document Type: Article

References (32)

1. Aida, M., Ishida, T., Fukaki, H., Fujisawa, H. and Tasaka, M. (1997) Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell, 9, 841-857.
2. Alex, R., Sozeri, O., Meyer, S. and Dildrop, R. (1992) Determination of the DNA sequence recognized by the bHLH-zip domain of the N-Myc protein. Nucleic Acids Res. 20, 2257-2263.
3. Choi, H.-I., Hong, J.-H., Ha, J.-O., Kang, J.-Y. and Kim, S.Y. (2000) ABFs, a family of ABA-responsive element binding factors. J. Biol. Chem. 215, 1723-1730.
4. Collinge, M. and Boller, T. (2001) Differential induction of two potato genes, Stprx2 and StNAC, in response to infection by Phytophthora infestans and to wounding. Plant Mol. Biol. 46, 521-529.
5. De Borja, P.F., Collins, N.K., Du, P., Azizkhan-Clitford, J. and Mudryj, M. (2001) Cyclin A-CDK phosphorylates Sp1 and enhances Sp1-mediated transcription. EMBO J. 20, 5737-5747.
6. Duval, M., Hsieh, T.F., Kim, S.Y. and Thomas, T.L. (2002) Molecular characterization of AtNAM: a member of the Arabidopsis thaliana NAC domain superfamily. Plant Mol. Biol. 50, 237-248.
7. Emmerich, R., Strehler, P., Hennecke, H. and Fischer, H.M. (2000) An imperfect inverted repeat is critical for DNA binding of the response regulator RegR of Bradyrhizobium japonicum. Nucleic Acids Res. 28, 4166-4171.
8. Gilmour, S.J., Zarka, D.G., Stockinger, E.J., Salazar, M.P., Houghton, J.M. and Thomashow, M.F. (1998) Low temperature regulation of the Arabidopsis CBF family of AP2 transcription activators as an early step in cold-induced COR gene expression. Plant J. 16, 433-442.
9. Grant, C.E., May, D.L. and Deeley, R.G. (2000) DNA binding and transcription activation by chicken interferon regulatory factor-3 (chlRF-3). Nucleic Acids Res. 28, 4790-4799.
10. Hosoda, K., Imamura, A., Katoh, E., Hatta, T., Tachiki, M., Yamada, H., Mizuno, T. and Yamazaki, T. (2002) Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. Plant Cell, 14, 2015-2029.
11. Hsu, S.-H., Shyu, H.-W., Hsieh-Li, H.-M. and Li, H. (2001) Spz1, a novel bHLH-Zip protein, is specifically expressed in testis. Mech. Dev. 100, 177-187.
12. Johannesson, H., Wang, Y. and Engstrom, P. (2001) DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro. Plant Mol. Biol. 45, 63-73.
13. Kawagoe, N. and Murai, Y. (1996) A novel basic region/helix-loop-helix protein binds to a G-box motif CACGTG of the bean seed storage protein beta-phaseolin gene. Plant Sci. 116, 47-57.
14. Kikuchi, K., Ueguchi-Tanaka, M., Yoshida, K.T., Nagato, Y., Matsusoka, M. and Hirano, H.Y. (2000) Molecular analysis of the NAC gene family in rice. Mol. Gen. Genet. 262, 1047-1051.
15. Koering, C.E., Fourel, G., Binet-Brasselet, E., Laroche, T., Klein, F. and Gilson, E. (2000) Identification of high affinity Tbf1p-binding sites within the budding yeast genome. Nucleic Acids Res. 28, 2519-2526.
16. Kosugi, S. and Ohashi, Y. (2000) Cloning and DNA-binding properties of a tobacco Ethylene-Insensitive3 (EIN3) homolog. Nucleic Acids Res. 28, 960-967.
17. Kosugi, S. and Ohashi, Y. (2002) DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 30, 337-348.
18. Liu, Q., Xia, Z.-Q. and Case, C.C. (2002) Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol. Chem. 277, 3850-3856.
19. Marè, C., Mazzucotelli, E., Crosatti, C., Francia, E., Stanca, A.M. and Cattivelli, L. (2004) Hv-WRKY38: a new transcription factor involved in cold- and drought-response in barley. Plant Mol. Biol. 55, 399-416.
20. Niu, X.P., Helentjaris, T. and Bate, N.J. (2002) Maize ABI4 binds coupling element1 in abscisic acid and sugar response genes. Plant Cell, 14, 2565-2575.
21. Riechmann, J.L and Ratclitfe, O.J. (2000) A genomic perspective on plant transcription factors. Curr. Opin. Plant Biol. 3, 423-434.
22. Röttgers, K., Krohn, N.M., Lichota, J., Stemmer, C., Merkle, T. and Grasser, K.D. (2000) DNA interactions and nuclear localisation of the chromosomal HMG domain protein SSRP1 from maize. Plant J. 23, 395-405.
23. Roulet, E., Bucher, P., Schneider, R., Wingender, E., Dusserre, Y., Werner, T. and Mermod, N. (2000) Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J. Mol. Biol. 297, 833-848.
24. Rubio, V., Linhares, F., Solano, R., Martin, A.C., Iglesias, J., Leyva, A. and Paz-Ares, J. (2001) A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 15, 2122-2133.
25. Souer, E., Houwelingen, A., van Kloos, D., Mol, J. and Koes, R. (1996) The no apical meristem gene of petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell, 85, 159-170.
26. Tang, W.N. and Perry, S.E. (2003) Binding site selection for the plant MADS domain protein AGL15: an in vitro and in vivo study. J. Biol. Chem. 278, 28154-28159.
27. Tronche, F., Ringeisen, F., Blumenfeld, M., Yaniv, M. and Pontoglio, M. (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 266, 231-245.
28. Xue, G.P. (2002a) Characterisation of the DNA-binding profile of barley HvCBF1 using an enzymatic method for rapid, quantitative and high-throughput analysis of the DNA-binding activity. Nucleic Acids Res. 30, e77.
29. Xue, G.P. (2002b) An AP2 domain transcription factor HvCBF1 activate expression of cold-responsive genes in barley through interaction with a (G/a)(C/t)CGAC motif. Biochim. Biophys. Acta, 1577, 63-72.
30. Xue, G.P. (2003) The DNA-binding activity of an AP2 transcriptional activator HvCBF2 involved in regulation of low-temperature responsive genes in barley is modulated by temperature. Plant J. 33, 373-383.
31. Xue, G.P. and Loveridge, C.W. (2004) HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably to a CT-rich element. Plant J. 37, 326-339.
32. Xue, G.P., Gobius, K.S. and Orpin, C.G. (1992) A novel polysaccharide hydrolase cDNA (celD) from Neocallimastix patriciarum encoding three multi-functional catalytic domains with high endoglucanase, cellobiohydrolase and xylanase activities. J. Gen. Microbiol. 138, 2397-2403.