Subtle hydrophobic interactions between the seventh residue of the zinc finger loop and the first base of an HGATAR sequence determine promoter-specific recognition by the Aspergillus nidulans GATA factor AreA

EMBO Journal

Volumn 16, Issue 13, 1997, Pages 3974-3986

  Ravagnani, Adriana ^a,e   Gorfinkiel, Lisette ^b,f   Langdon, Timothy ^a,g   Diallinas, George ^b,h   Adjadj, Elisabeth ^c   Demais, Stéphane ^b   Gorton, Diana ^d,i   Arst Jr , Herbert N ^a   Scazzocchio, Claudio ^b,d  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b CNRS   (France)

^c INSERM   (France)

^d UNIVERSITY OF ESSEX   (United Kingdom)

^e ABERYSTWYTH UNIVERSITY   (United Kingdom)

^f UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

^g ABERYSTWYTH UNIVERSITY   (United Kingdom)

^h INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

ⁱ Enfield and Haringey Hlth Authority   (United Kingdom)

Author keywords

Aspergillus nidulans; GATA transcription factors; Molecular modelling; Promoter recognition

Indexed keywords

DNA BINDING PROTEIN; LEUCINE; METHIONINE; MUTANT PROTEIN; PERMEASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA; UNCLASSIFIED DRUG; VALINE; ZINC FINGER PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ASPERGILLUS NIDULANS; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA PROTEIN COMPLEX; GENE ACTIVATION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; HYDROPHOBICITY; MOLECULAR MODEL; NONHUMAN; NORTHERN BLOTTING; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION;

ASPERGILLUS NIDULANS; BINDING SITES; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHENOTYPE; POINT MUTATION; PROMOTER REGIONS (GENETICS); RECOMBINANT FUSION PROTEINS; REPRESSOR PROTEINS; TRANSCRIPTION FACTORS; WATER; ZINC FINGERS;

EID: 0030982626     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.13.3974     Document Type: Article

References (51)

1. Andrianopoulous, A. and Hynes, M.J. (1990) Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans. Mol. Cell. Biol., 10, 3194-3203.
2. Arst, H.N., Jr (1976) Integrator gene in Aspergillus nidulans. Nature, 262, 231-234.
3. Arst, H.N., Jr (1988) Localisation of several chromosome I genes of Aspergillus nidulans: implications for mitotic recombination. Mol. Gen. Genet., 213, 545-547.
4. Arst, H.N., Jr and Cove, D.J. (1973) Nitrogen metabolite repression in Aspergillus nidulans. Mol. Gen. Genet., 126, 111-141.
5. Arst, H.N., Jr and Scazzocchio, C. (1975) Initiator constitutive mutation with an 'up-promoter' effect in Aspergillus nidulans. Nature, 254, 31-34.
6. Ballario, P., Vittorioso, P., Magrelli, A., Talora, C., Cabibbo, A. and Macino, G. (1996) White collar-1, a central regulator of blue light responses in Neurospora is a zinc finger protein. EMBO J., 15, 1650-1657.
7. Burger, G., Strauss, J., Scazzocchio, C. and Lang, F.B. (1991) nirA, the pathway specific regulatory gene of nitrate assimilation in Aspergillus nidulans, encodes a putative GAL4-type zinc finger protein and contains four introns in highly conserved regions. Mol. Cell. Biol., 11, 5746-5755.
8. Clore, G., Bax, A., Omichinski, J.G. and Gronenborn, A. (1994) Localization of bound water in the solution structure of a complex of the erythroid transcription factor GATA-1 with DNA. Structure, 2, 89-94.
9. Clutterbuck, A.J. (1974) Aspergillus nidulans. In King, R.C. (ed.), Handbook of Genetics. Plenum Press, New York, Vol. 1, pp. 447-510.
10. Clutterbuck, A.J. (1993) Aspergillus nidulans. In O'Brien, S.J. (ed.), Genetic Maps, Locus Maps of Complex Genomes. 6th edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Vol. 3, pp. 3.71-3.84.
11. Coffman, J.A., Rai, R. and Cooper, T.G. (1995) Genetic evidence for Gln3p-independent, nitrogen catabolite repression-sensitive gene expression in Saccharomyces cerevisiae, J. Bacteriol., 177, 6910-6918.
12. Cunningham, T.S. and Cooper, T.G. (1991) Expression of the DAL80 gene whose product is homologous to the GATA factors and is a negative regulator of multiple catabolic genes in Saccharomyces cerevisiœ, is sensitive to nitrogen catabolite repression. Mol. Cell. Biol., 11, 6205-6215.
13. Davis, M.A. and Hynes, M.J. (1991) Regulatory circuits in Aspergillus nidulans. In Bennett, J.W. and Lasure, L.L. (eds), More Gene Manipulations in Fungi, Academic Press, San Diego, CA, pp. 151-189.
14. Diallinas, G., Gorfinkiel, L., Arst, H.N., Jr, Cecchetto, G. and Scazzocchio, C. (1995) Genetic and molecular characterisation of a wide specificity purine permease gene of Aspergillus nidulans reveals a novel family of transporters conserved in prokaryotes and eukaryotes. J. Biol. Chem., 270, 8610-8622.
15. Feng, B., Xiao, X. and Marzluf, G.A. (1993) Recognition of specific nucleotide bases and cooperative binding by the trans-acting nitrogen regulatory protein NIT-2 of Neurospora crassa. Nucleic Acids Res., 21, 3989-3996.
16. Fu, Y.H. and Marzluf, G.A. (1990) nit-2, the major nitrogen regulatory gene of Neurospora crassa, encodes a protein with a putative zinc finger DNA-binding domain. Mol. Cell. Biol. 10, 1056-1065.
17. Gorfinkiel, L., Diallinas, G. and Scazzocchio, C. (1993) Sequence and regulation of the uapA gene, encoding a uric acid-xanthine permease in the fungus Aspergillus nidulans. J. Biol. Chem., 268, 23376-23381.
18. Gorton, D.J. (1983) Genetical and biochemical studies of the uptake of purines and their degradation products in Aspergillus nidulans. Ph.D. Thesis, University of Essex, UK.
19. Hynes, M.J. (1975) Studies on the role of the areA gene in the regulation of nitrogen catabolism in Aspergillus nidulans. Aust. J. Biol. Sci., 28, 301-313.
20. Hynes, M.J. (1978) Multiple independent control mechanisms affecting the acetamidase of Aspergillus nidulans. Mol. Gen. Genet., 161, 59-65.
21. Hynes, M.J. and Pateman, A.J. (1970) The genetic analysis of regulation of acetamidase synthesis in Aspergillus nidulans. I Mutants able to utilise acrylamide. Mol. Gen. Genet., 108, 97-106.
22. Hynes, M.J., Corrick, C.M., Kelly, J.M. and Littlejohn, T.G. (1988) Identification of the sites of action for regulatory genes controlling the amdS gene of Aspergillus nidulans. Mol. Cell. Biol., 8, 2589-2596.
23. Ko, L. and Engel, D.J. (1993) DNA binding specificities of the GATA transcription factor family. Mol. Cell. Biol., 13, 4011-4022.
24. Kudla, B., Caddick, M.X., Langdon, T. Martinez-Rossi, N.M., Bennett, C.F., Sibley, S., Davis, R.W. and Arst, H.N., Jr (1990) The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans. Mutations affecting specific gene activation alter a loop residue of a putative zinc finger. EMBO J., 9, 1355-1364.
25. Langdon, T., Sheerins, A., Ravagnani, A., Gielkens, M., Caddick, M.X. and Arst, H.N., Jr (1995) Mutational analysis reveals dispensability of the N-terminal region of the Aspergillus transcription factor mediating nitrogen metabolite repression. Mol. Microbiol. 17, 877-888.
26. Martin, D.I.K., Tsai, S.F. and Orkin, S.H. (1989) Increased γ-globin expression in a nondeletion HPFH mediated by an erythroid-specific DNA-binding factor. Nature, 338, 435-438.
27. Maxam, A.M. and Gilbert, W. (1977) A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA. 74, 560-564.
28. Merika, M. and Orkin, S.H. (1993) DNA-binding specificity of GATA family transcription factors. Mol. Cell. Biol., 13, 3999-4010.
29. Minehart, P.L. and Magasanik, B. (1991) Sequence and expression of GLN3, a positive nitrogen regulatory gene of Saccharomyces cerevisiae encoding a protein with a putative zinc finger DNA-binding domain. Mol. Cell. Biol., 11, 6216-6228.
30. Monod, J. (1970) L'Hasard et la Nécessité. Editions du Seuil, Paris.
31. Oestreicher, N. and Scazzocchio, C. (1995) A single amino acid change in a pathway-specific transcription factor results in differing degrees of constitutivity, hyperinducibility and derepression of several structural genes. J. Mol. Biol., 249, 693-699.
32. Omichinski, J.G., Clore, G.M., Schaad, O., Felsenfeld, G., Trainor, C., Appella, E., Stahl, S.J. and Gronenborn, A.M. (1993) NMR structure of a specific DNA complex of Zn-containing DNA-binding domain of GATA-1. Science, 261, 438-446.
33. Platt, A., Langdon, T., Arst, H.N., Jr. Kirk, D., Tollervey, D., Mates Sanchez, J.M. and Caddick, M.X. (1996a) Nitrogen metabolite signalling involves the C-terminus and the GATA domain of the Aspergillus transcription factor AREA and the 3′ untranslated region of its mRNA. EMBO J., 15, 2791-2801.
34. Platt, A., Ravagnani, A., Arst, H.N., Jr, Kirk, D., Langdon, T. and Caddick, M.X. (1996b) Mutational analysis of the C-terminal region of AREA, the transcription factor mediating nitrogen metabolite repression in Aspergillus nidulans. Mol. Gen. Genet., 250, 106-114.
35. Polkinghorne, M. and Hynes, M.J. (1975) Mutants affecting histidine utilization in Aspergillus nidulans. Genet. Res. Camb., 25, 119-135.
36. Pontecorvo, G., Roper, J.A., Hemmons, L.M., Macdonald, K.D. and Bufton, A.W.J. (1953) The genetics of Aspergillus nidulans. Adv. Genet., 5, 141-238
37. Pu, W.T. and Struhl, K. (1992) Uracil interference, a rapid and general method for defining protein-DNA interactions involving the 5-methyl group of thymines: the GCN4-DNA complex. Nucleic Acids Res., 20, 771-775.
38. Rand, K.M. and Arst, H.N., Jr (1977) A mutation in Aspergillus nidulans which affects the regulation of nitrate reductase and is tightly linked to its structural gene. Mol. Gen. Genet., 155, 67-75.
39. Rand, K.N. and Arst, H.N., Jr (1978) Mutations in nirA gene of Aspergillus nidulans and nitrogen metabolism. Nature, 272, 732-734.
40. 2+ chelation. Nucleic Acids Res., 23, 3069-3070.
41. Sanger, F., Nickels, S. and Coulson, A.R. (1977) DNA sequencing with chain termination inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
42. Scazzocchio, C. (1990) Of moulds and men, or two fingers are not better than one. Trends Genet., 6, 311-313.
43. Scazzocchio, C. and Arst, H.N., Jr. (1978) The nature of an initiator constitutive mutation in Aspergillus nidulans. Nature, 274, 177-179.
44. Stanbrough, M., Rowen, D.W. and Magasanik, B. (1995) Role of the GATA factors Gln3p and Ni11p of Saccharomyces cerevisiae in the expression of nitrogen regulated genes. Proc. Natl Acad. Sci. USA, 92, 9450-9454.
45. Stankovich, M. Platt, A., Caddick, M.X., Langdon, T., Shaffer, P.M. and Arst, H.N., Jr (1993) C-terminal truncation of the transcriptional activator encoded by areA in Aspergillus nidulans results in both loss-of-function and gain-of-function phenotypes. Mol. Microbiol., 7, 81-87.
46. Strauss, E.C., Andrews, N.C., Higgs, D.R. and Orkin, S.H. (1992) In vivo footprinting of the human α-globin locus upstream regulatory element by guanine and adenine ligation-mediated polymerase chain reaction. Mol. Cell. Biol., 12, 2135-2142.
47. Suárez, T., Oestreicher, N., Kelly, J., Ong, G., Sankarsing, T. and Scazzocchio, C. (1991) The uaY positive control gene of Aspergillus nidulans: fine structure, isolation of constitutive mutants and reversion patterns. Mol. Gen. Genet., 230, 359-368.
48. Suárez, T., Vieira de Queiroz, M., Oestreicher, N. and Scazzocchio, C. (1995) The sequence and binding specificity of UaY, the specific regulator of the purine utilisation pathway in Aspergillus nidulans, suggest an evolutionary relationship with the PPR1 protein of Saccharomyces cerevisiae. EMBO J., 14, 1453-1467.
49. Tilburn, J., Scazzocchio, C., Taylor, G.G., Zabicky-Zissman, J.H., Lockington, R.A. and Davies, R.W. (1983) Transformation by integration in Aspergillus nidulans. Gene, 26, 205-221.
50. Tilburn, J., Sarkar, S., Widdick, D.A., Espeso, E.A., Orejas, M. Mungroo, J., Peñalva, M.A. and Arst, H.N., Jr (1995) The Aspergillus PacC zinc finger transcription factor mediates regulation of both acid- and alkaline-expressed genes by ambient pH. EMBO J., 14, 779-790.
51. Tollervey, D.W. and Arst, H.N., Jr (1981) Mutations to constitutivity and derepression are separate and separable in a regulatory gene of Aspergillus nidulans. Curr. Genet., 4, 63-68.