DNA-binding specificity of the IDI-4 basic leucine zipper factor of Podospora anserina defined by systematic evolution of ligands by exponential enrichment (SELEX)

Eukaryotic Cell

Volumn 4, Issue 2, 2005, Pages 476-483

  Dementhon, Karine ^a,b   Saupe, Sven J ^a  

^a Institut de Biochimie et Genetique Cellulaires   (France)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; FUNGAL PROTEIN; LEUCINE ZIPPER PROTEIN; LIGAND;

AMINO ACID SEQUENCE; ARTICLE; AUTOPHAGY; BINDING SITE; DIMERIZATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PODOSPORA; PROMOTER REGION; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; AUTOPHAGY; BASE SEQUENCE; BINDING SITES; DIMERIZATION; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; LEUCINE ZIPPERS; LIGANDS; MOLECULAR SEQUENCE DATA; PODOSPORA; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

FUNGI; PODOSPORA ANSERINA;

EID: 13844308292     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.4.2.476-483.2005     Document Type: Article

References (27)

1. Bailey, T. L., and C. Elkayn. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2:28-36.
2. Bourges, N., A. Groppi, C. Barreau, C. Clave, and J. Begueret. 1998. Regulation of gene expression during the vegetative incompatibility reaction in Podospora anserina. Characterization of three induced genes. Genetics 150:633-641.
3. Cuervo, A. M. 2004. Autophagy: in sickness and in health. Trends Cell Biol. 14:70-77.
4. Dementhon, K., M. Paoletti, B. Pinan-Lucarre, N. Loubradou-Bourges, M. Sabourin, S. J. Saupe, and C. Clave. 2003. Rapamycin mimics the incompatibility reaction in the fungus Podospora anserina. Eukaryot. Cell 2:238-246.
5. Dementhon, K., S. J. Saupe, and C. Clave. 2004. Characterization of IDI-4, a bZIP transcription factor inducing autophagy and cell death in the fungus Podospora anserina. Mol. Microbiol. 53:1625-1640.
6. Ellenberger, T. E., C. J. Brandl, K. Struhl, and S. C. Harrison. 1992. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell 71:1223-1237.
7. Glass, N. L., and I. Kaneko. 2003. Fatal attraction: nonself recognition and heterokaryon incompatibility in filamentous fungi. Eukaryot. Cell 2:1-8.
8. Hill, D. E., I. A. Hope, J. P. Macke, and K. Struhl. 1986. Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein. Science 234:451-457.
9. Hinnebusch, A. G., and K. Natarajan. 2002. Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot. Cell 1:22-32.
10. Hoffmann, B., O. Valerius, M. Andermann, and G. H. Braus. 2001. Transcriptional autoregulation and inhibition of mRNA translation of amino acid regulator gene cpcA of filamentous fungus Aspergillus nidulans. Mol. Biol. Cell 12:2846-2857.
11. Keller, W., P. König, and T. J. Richmond. 1995. Crystal structure of a bZIP/DNA complex at 2.2 Å: determinants of DNA specific recognition. J. Mol. Biol. 254:657-667.
12. König, P., and T. J. Richmond. 1993. The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility. J. Mol. Biol. 233:139-154.
13. Krappmann, S., E. M. Bignell, U. Reichard, T. Rogers, K. Haynes, and G. H. Braus. 2004. The Aspergillus fumigatus transcriptional activator CpcA contributes significantly to the virulence of this fungal pathogen. Mol. Microbiol. 52:785-799.
14. Kubota, H., T. Obata, K. Ota, T. Sasaki, and T. Ito. 2003. Rapamycin-induced translational derepression of GCN4 mRNA involves a novel mechanism for activation of the eIF2α kinase GCN2. J. Biol. Chem. 278:20457-20460.
15. Levine, B., and D. J. Klionsky. 2004. Development by self-digestion: molecular mechanisms and biological functions of autophagy. Dev. Cell. 6:463-477.
16. Lockshin, R. A., and Z. Zakeri. 2004. Apoptosis, autophagy, and more. Int. J. Biochem. Cell Biol. 36:2405-2419.
17. Natarajan, K., M. R. Meyer, B. M. Jackson, D. Slade, C. Roberts, A. G. Hinnebusch, and M. J. Marton. 2001. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21:4347-4368.
18. Oliphant, A. R., C. J. Brandi, and K. Struhl. 1989. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 9:2944-2949.
19. Pinan-Lucarre, B., M. Paoletti, K. Dementhon, B. Coulary-Salin, and C. Clave. 2003. Autophagy is induced during cell death by incompatibility and is essential for differentiation in the filamentous fungus Podospora anserina. Mol. Microbiol. 47:321-333.
20. Strittmatter, A. W., S. Irniger, and G. H. Braus. 2001. Induction of jlbA mRNA synthesis for a putative bZIP protein of Aspergillus nidulans by amino acid starvation. Curr. Genet. 39:327-334.
21. Suckow, M., B. von Wilcken-Bergmann, and B. Muller-Hill. 1993. Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding. EMBO J. 12:1193-1200.
22. Tallóczy, Z., W. Jiang, H. W. Virgin IV, D. A. Leib, D. Scheuner, R. J. Kaufman, E.-L. Eskelinen, and B. Levine. 2002. Regulation of starvation- and virus-induced autophagy by the eIF2α kinase signaling pathway. Proc. Natl. Acad. Sci. USA 99:190-195.
23. Valenzuela, L., C. Aranda, and A. Gonzalez. 2001. TOR modulates GCN4-dependent expression of genes turned on by nitrogen limitation. J. Bacteriol. 183:2331-2334.
24. Wang, C. W., and D. J. Klionsky. 2003. The molecular mechanism of autophagy. Mol. Med. 9:65-76.
25. Wang, P., T. G. Larson, C. H. Chen, D. M. Pawlyk, J. A. Clark, and D. L. Nuss. 1998. Cloning and characterization of a general amino acid control transcriptional activator from the chestnut blight fungus Cryphonectria parasitica. Fungal Genet. Biol. 23:81-94.
26. Weiss, M. A. 1990. Thermal unfolding studies of a leucine zipper domain and its specific DNA complex: implications for scissor's grip recognition. Biochemistry 29:8020-8024.
27. Weiss, M. A., T. Ellenberger, C. R. Wobbe, J. P. Lee, S. C. Harrison, and K. Struhl. 1990. Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA. Nature 347:575-578.