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PMID: 15075269 Published · ppublish English Journal Article

A paradoxical mutant GATA factor.

Eukaryotic cell ·Vol. 3 ·No. 2 ·2004-04-00 ·Pages 393-405

Muro-Pastor MI, Strauss J, Ramón A, Scazzocchio C

Abstract

The niiA (nitrite reductase) and niaD (nitrate reductase) genes of Aspergillus nidulans are subject to both induction by nitrate and repression by ammonium or glutamine. The intergenic region between these genes functions as a bidirectional promoter. In this region, nucleosomes are positioned under nonexpression conditions. On nitrate induction under derepressing conditions, total loss of positioning occurs. This is independent of transcription and of the NirA-specific transcription factor but absolutely dependent on the wide-domain GATA-binding AreA factor. We show here that a 3-amino-acid deletion in the basic carboxy-terminal sequence of the DNA-binding domain results in a protein with paradoxical properties. Its weak DNA binding is consistent with its loss-of-function phenotype on most nitrogen sources. However, it results in constitutive expression and superinducibility of niiA and niaD. Nucleosome loss of positioning is also constitutive. The mutation partially suppresses null mutations in the transcription factor NirA. AreA binds NirA in vitro, and the mutation does not affect this interaction. The in vivo methylation pattern of the promoter is drastically altered, suggesting the recruitment of one or more unknown transcription factors and/or a local distortion on the DNA double helix.

MeSH Terms
Binding Sites Chromatin/metabolism DNA Footprinting DNA-Binding Proteins/genetics Electrophoretic Mobility Shift Assay Fungal Proteins/genetics,metabolism,physiology Gene Expression Regulation, Fungal/genetics Genes, Reporter Nitrate Reductase Nitrate Reductases/genetics Nitrates/metabolism Nitrite Reductases/genetics Phenotype Promoter Regions, Genetic Protein Binding Sequence Deletion Transcription Factors/genetics,physiology beta-Galactosidase/analysis
Chemicals
AreA protein, Aspergillus nidulans Chromatin DNA-Binding Proteins Fungal Proteins Nitrates Transcription Factors NirA protein, Aspergillus nidulans Nitrate Reductases Nitrite Reductases Nitrate Reductase beta-Galactosidase
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Muro-Pastor M Isabel
Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621, 91405 Orsay Cedex, France.
Strauss Joseph
Ramón Ana
Scazzocchio Claudio
References (62)
62 references, click to expand
  1. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase.
    Gene. 1988 Jul 15;67(1):31-40 PMID: 3047011
  2. Mutations in nirA gene of Aspergillus nidulans and nitrogen metabolism.
    Nature. 1978 Apr 20;272(5655):732-4 PMID: 347305
  3. Hematopoietic-specific activators establish an overlapping pattern of histone acetylation and methylation within a mammalian chromatin domain.
    Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14309-14 PMID: 12379744
  4. Autoregulation of the synthesis of nitrate reductase in Aspergillus nidulans.
    J Bacteriol. 1969 Mar;97(3):1374-8 PMID: 5776531
  5. Mutational analysis of AREA, a transcriptional activator mediating nitrogen metabolite repression in Aspergillus nidulans and a member of the "streetwise" GATA family of transcription factors.
    Microbiol Mol Biol Rev. 1998 Sep;62(3):586-96 PMID: 9729601
  6. The GATA factor AreA is essential for chromatin remodelling in a eukaryotic bidirectional promoter.
    EMBO J. 1999 Mar 15;18(6):1584-97 PMID: 10075929
  7. The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors.
    J Mol Biol. 1998 Apr 3;277(3):605-20 PMID: 9533883
  8. In situ detection of protein-DNA interactions in filamentous fungi by in vivo footprinting.
    Nucleic Acids Res. 1998 Aug 15;26(16):3862-4 PMID: 9685506
  9. Sequence, exon-intron organization, transcription and mutational analysis of prnA, the gene encoding the transcriptional activator of the prn gene cluster in Aspergillus nidulans.
    Mol Microbiol. 1998 Apr;28(2):355-70 PMID: 9622360
  10. The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity.
    J Mol Biol. 1998 Apr 3;277(3):621-34 PMID: 9533884
  11. The purine degradation pathway, genetics, biochemistry and regulation.
    Prog Ind Microbiol. 1994;29:221-57 PMID: 7765126
  12. The genetics of Aspergillus nidulans.
    Adv Genet. 1953;5:141-238 PMID: 13040135
  13. Positive regulation in a eukaryote, a study of the uaY gene of Aspergillus nidulans: I. Characterization of alleles, dominance and complementation studies, and a fine structure map of the uaY--oxpA cluster.
    Genetics. 1982 Feb;100(2):185-208 PMID: 7049832
  14. Initiator constitutive mutation with an 'up-promoter' effect in Aspergillus nidulans.
    Nature. 1975 Mar 6;254(5495):31-4 PMID: 1089904
  15. Genetic regulation of nitrogen metabolism in the fungi.
    Microbiol Mol Biol Rev. 1997 Mar;61(1):17-32 PMID: 9106362
  16. 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. 1995 Jun 16;249(4):693-9 PMID: 7602582
  17. NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region.
    EMBO J. 1995 Jan 3;14(1):106-16 PMID: 7828582
  18. The intergenic region between the divergently transcribed niiA and niaD genes of Aspergillus nidulans contains multiple NirA binding sites which act bidirectionally.
    Mol Cell Biol. 1995 Oct;15(10):5688-99 PMID: 7565720
  19. The sequence and binding specificity of UaY, the specific regulator of the purine utilization pathway in Aspergillus nidulans, suggest an evolutionary relationship with the PPR1 protein of Saccharomyces cerevisiae.
    EMBO J. 1995 Apr 3;14(7):1453-67 PMID: 7729421
  20. Nitrogen metabolite repression in Aspergillus nidulans.
    Mol Gen Genet. 1973 Nov 2;126(2):111-41 PMID: 4591376
  21. A gene coding for the uric acid-xanthine permease of Aspergillus nidulans: inactivational cloning, characterization, and sequence of a cis-acting mutation.
    Genetics. 1989 Jun;122(2):341-50 PMID: 2670668
  22. PrnA, a Zn2Cys6 activator with a unique DNA recognition mode, requires inducer for in vivo binding.
    Mol Microbiol. 2002 Apr;44(2):585-97 PMID: 11972793
  23. Chromatin rearrangements in the prnD-prnB bidirectional promoter: dependence on transcription factors.
    Eukaryot Cell. 2004 Feb;3(1):144-56 PMID: 14871945
  24. Multiple independent control mechanisms affecting the acetamidase of Aspergillus nidulans.
    Mol Gen Genet. 1978 Apr 25;161(1):59-65 PMID: 353500
  25. Regulation of arginine catabolism in Aspergillus nidulans.
    Nature. 1974 Aug 16;250(467):590-2 PMID: 4602656
  26. Suppressible alleles in a wide domain regulatory gene in Aspergillus nidulans.
    Curr Genet. 1984 May;8(4):245-51 PMID: 24177791
  27. 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 J. 1997 Jul 1;16(13):3974-86 PMID: 9233807
  28. Product induction of purine hydroxylase II in Asperigillus nidulans.
    Mol Gen Genet. 1979 Jul 2;174(1):105-6 PMID: 384157
  29. The product of the regulatory gene of the proline catabolism gene cluster of Aspergillus nidulans is a positive-acting protein.
    Curr Genet. 1985;9(4):299-304 PMID: 3916725
  30. The regulator of nitrate assimilation in ascomycetes is a dimer which binds a nonrepeated, asymmetrical sequence.
    Mol Cell Biol. 1998 Mar;18(3):1339-48 PMID: 9488449
  31. Regulation of nitrate reduction in Aspergillus nidulans.
    Nature. 1967 Sep 16;215(5107):1234-7 PMID: 6052720
  32. Interaction between major nitrogen regulatory protein NIT2 and pathway-specific regulatory factor NIT4 is required for their synergistic activation of gene expression in Neurospora crassa.
    Mol Cell Biol. 1998 Jul;18(7):3983-90 PMID: 9632783
  33. A rapid method for chromatin structure analysis in the filamentous fungus Aspergillus nidulans.
    Nucleic Acids Res. 1997 Oct 1;25(19):3955-6 PMID: 9380523
  34. Acetylation of GATA-3 affects T-cell survival and homing to secondary lymphoid organs.
    EMBO J. 2000 Sep 1;19(17):4676-87 PMID: 10970860
  35. CREB-Binding protein acetylates hematopoietic transcription factor GATA-1 at functionally important sites.
    Mol Cell Biol. 1999 May;19(5):3496-505 PMID: 10207073
  36. A method for the selection of deletion mutations in the L-proline catabolism gene cluster of Aspergillus nidulans.
    Genet Res. 1981 Oct;38(2):171-95 PMID: 7035292
  37. Studies on the role of the areA gene in the regulation of nitrogen catabolism in Aspergillus nidulans.
    Aust J Biol Sci. 1975 Jun;28(3):301-13 PMID: 52352
  38. 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. 1991 Nov;11(11):5746-55 PMID: 1922075
  39. Perturbation of nucleosome structure by the erythroid transcription factor GATA-1.
    J Mol Biol. 1998 Jun 12;279(3):529-44 PMID: 9641976
  40. Mutations to constitutivity and derepression are separate and separable in a regulatory gene of Aspergillus nidulans.
    Curr Genet. 1981 Sep;4(1):63-8 PMID: 24185869
  41. Sequence and regulation of the uapA gene encoding a uric acid-xanthine permease in the fungus Aspergillus nidulans.
    J Biol Chem. 1993 Nov 5;268(31):23376-81 PMID: 8226862
  42. Distinct mechanisms control RNA polymerase II recruitment to a tissue-specific locus control region and a downstream promoter.
    Mol Cell. 2001 Aug;8(2):465-71 PMID: 11545748
  43. Integrator gene in Aspergillus nidulans.
    Nature. 1976 JUL 15;262(5565):231-4 PMID: 778641
  44. Aspergillus nidulans contains a single actin gene which has unique intron locations and encodes a gamma-actin.
    Gene. 1988 Oct 30;70(2):283-93 PMID: 2975248
  45. Zinc fingers are sticking together.
    Trends Biochem Sci. 1998 Jan;23(1):1-4 PMID: 9478126
  46. A promoter region mutation affecting replication of the Tetrahymena ribosomal DNA minichromosome.
    Mol Cell Biol. 1998 May;18(5):3021-33 PMID: 9566921
  47. The fungal GATA factors.
    Curr Opin Microbiol. 2000 Apr;3(2):126-31 PMID: 10745000
  48. Topological unwinding of strong and weak promoters by RNA polymerase. A comparison between the lac wild-type and the UV5 sites of Escherichia coli.
    J Mol Biol. 1987 Jun 20;195(4):795-808 PMID: 3309341
  49. Nitrate and the GATA factor AreA are necessary for in vivo binding of NirA, the pathway-specific transcriptional activator of Aspergillus nidulans.
    Mol Microbiol. 2002 Apr;44(2):573-83 PMID: 11972792
  50. Multiple GATA sites: protein binding and physiological relevance for the regulation of the proline transporter gene of Aspergillus nidulans.
    Mol Microbiol. 2003 Oct;50(1):277-89 PMID: 14507380
  51. Regulation of activity of the transcription factor GATA-1 by acetylation.
    Nature. 1998 Dec 10;396(6711):594-8 PMID: 9859997
  52. Heterologous expression of the Aspergillus nidulans regulatory gene nirA in Fusarium oxysporum.
    Gene. 1991 Dec 20;109(1):155-60 PMID: 1756977
  53. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction.
    Anal Biochem. 1987 Apr;162(1):156-9 PMID: 2440339
  54. A twin-reporter vector for simultaneous analysis of expression signals of divergently transcribed, contiguous genes in filamentous fungi.
    Gene. 1991 Jul 31;104(1):119-22 PMID: 1916271
  55. Sequencing end-labeled DNA with base-specific chemical cleavages.
    Methods Enzymol. 1980;65(1):499-560 PMID: 6246368
  56. Linkage map and locus list.
    Prog Ind Microbiol. 1994;29:791-824 PMID: 7765147
  57. The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans. Mutations affecting specificity of gene activation alter a loop residue of a putative zinc finger.
    EMBO J. 1990 May;9(5):1355-64 PMID: 1970293
  58. Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site.
    EMBO J. 1996 May 15;15(10):2496-507 PMID: 8665857
  59. Formation of a tissue-specific histone acetylation pattern by the hematopoietic transcription factor GATA-1.
    Mol Cell Biol. 2003 Feb;23(4):1334-40 PMID: 12556492
  60. Isolation and characterisation of the crnA-niiA-niaD gene cluster for nitrate assimilation in Aspergillus nidulans.
    Gene. 1990 Jun 15;90(2):181-92 PMID: 2205530
  61. 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. 1996 Jun 3;15(11):2791-801 PMID: 8654376
  62. Nitrogen regulation in Saccharomyces cerevisiae.
    Gene. 2002 May 15;290(1-2):1-18 PMID: 12062797
Article Info
Journal
Eukaryotic cell
Abbr.
Eukaryot Cell
ISSN
1535-9778
Published
2004-04-00
Pages
393-405
Language
English
Region
United States
NLM ID
101130731
PMCID
PMC387643
Subset
IM
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