Home LiteratureArticle Details
PMID: 9488449 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The regulator of nitrate assimilation in ascomycetes is a dimer which binds a nonrepeated, asymmetrical sequence.

Molecular and cellular biology ·Vol. 18 ·No. 3 ·1998-03-00 ·Pages 1339-48

Strauss J, Muro-Pastor MI, Scazzocchio C

Abstract

The regulation of nitrate assimilation seems to follow the same pattern in all ascomycetes where this process has been studied. We show here by in vitro binding studies and a number of protection and interference techniques that the transcription factor mediating nitrate induction in Aspergillus nidulans, a protein containing a binuclear zinc cluster DNA binding domain, recognizes an asymmetrical sequence of the form CTCC GHGG. We further show that the protein binds to its consensus site as a dimer. We establish the role of the putative dimerization element by its ability to replace the analogous element of the cI protein of phage lambda. Mutagenesis of crucial leucines of the dimerization element affect both the binding ability of the dimer and the conformation of the resulting protein-DNA complex. This is the first case to be described where a dimer recognizes such an asymmetrical nonrepeated sequence, presumably by each monomeric subunit making different contacts with different DNA half-sites.

MeSH Terms
Amino Acid Sequence Aspergillus nidulans/genetics,metabolism Binding Sites Chromosome Mapping DNA Footprinting DNA Probes DNA, Fungal/metabolism DNA-Binding Proteins/genetics,metabolism Dimerization Fungal Proteins/genetics,metabolism Molecular Sequence Data Mutagenesis Nitrates/metabolism Protein Binding Recombinant Fusion Proteins/genetics,metabolism Regulatory Sequences, Nucleic Acid
Chemicals
DNA Probes DNA, Fungal DNA-Binding Proteins Fungal Proteins Nitrates Recombinant Fusion Proteins NirA protein, Aspergillus nidulans
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Strauss J
Institut de Génétique et Microbiologie, Université Paris-Sud, URA D2225, Orsay, France.
Muro-Pastor M I
Scazzocchio C
References (36)
36 references, click to expand
  1. crnA encodes a nitrate transporter in Aspergillus nidulans.
    Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):204-8 PMID: 1986367
  2. Independently segregating genetic loci concerned with nitrate reductase activity in Aspergillus nidulans.
    Nature. 1963 Apr 20;198:262-3 PMID: 14023503
  3. Identification of base and backbone contacts used for DNA sequence recognition and high-affinity binding by LAC9, a transcription activator containing a C6 zinc finger.
    Mol Cell Biol. 1991 Apr;11(4):1777-84 PMID: 2005880
  4. Correct intron splicing generates a new type of a putative zinc-binding domain in a transcriptional activator of Aspergillus nidulans.
    FEBS Lett. 1991 Mar 11;280(1):11-6 PMID: 2053973
  5. nit-4, a pathway-specific regulatory gene of Neurospora crassa, encodes a protein with a putative binuclear zinc DNA-binding domain.
    Mol Cell Biol. 1991 Nov;11(11):5735-45 PMID: 1840634
  6. 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
  7. DNA recognition by GAL4: structure of a protein-DNA complex.
    Nature. 1992 Apr 2;356(6368):408-14 PMID: 1557122
  8. Identification of the promoter region involved in the autoregulation of the transcriptional activator ALCR in Aspergillus nidulans.
    Mol Cell Biol. 1992 May;12(5):1932-9 PMID: 1569930
  9. Structure of the leucine zipper.
    Curr Opin Genet Dev. 1992 Apr;2(2):205-10 PMID: 1638114
  10. Specific binding sites for the activator protein, ALCR, in the alcA promoter of the ethanol regulon of Aspergillus nidulans.
    J Biol Chem. 1992 Oct 15;267(29):21146-53 PMID: 1400424
  11. Determinants of binding-site specificity among yeast C6 zinc cluster proteins.
    Science. 1993 Aug 13;261(5123):909-11 PMID: 8346441
  12. Two different, adjacent and divergent zinc finger binding sites are necessary for CREA-mediated carbon catabolite repression in the proline gene cluster of Aspergillus nidulans.
    EMBO J. 1994 Jan 15;13(2):407-15 PMID: 8313886
  13. Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop.
    J Mol Biol. 1994 Apr 8;237(4):378-87 PMID: 8151699
  14. Genetic tests to reveal TAT homodimer formation and select TAT homodimer inhibitor.
    Biochem Biophys Res Commun. 1994 Jun 15;201(2):701-8 PMID: 8003005
  15. Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer.
    Genes Dev. 1994 Apr 15;8(8):970-80 PMID: 7926781
  16. The yeast activator HAP1--a GAL4 family member--binds DNA in a directly repeated orientation.
    Genes Dev. 1994 Sep 1;8(17):2110-9 PMID: 7958882
  17. Cleavage of structural proteins during the assembly of the head of bacteriophage T4.
    Nature. 1970 Aug 15;227(5259):680-5 PMID: 5432063
  18. Sequencing end-labeled DNA with base-specific chemical cleavages.
    Methods Enzymol. 1980;65(1):499-560 PMID: 6246368
  19. Nucleotide sequence of the operators of lambda ultravirulent mutants.
    Nucleic Acids Res. 1980 May 24;8(10):2147-64 PMID: 6448986
  20. Rapid and efficient site-specific mutagenesis without phenotypic selection.
    Proc Natl Acad Sci U S A. 1985 Jan;82(2):488-92 PMID: 3881765
  21. The molecular origin of DNA-drug specificity in netropsin and distamycin.
    Proc Natl Acad Sci U S A. 1985 Mar;82(5):1376-80 PMID: 2983343
  22. An amino-terminal fragment of GAL4 binds DNA as a dimer.
    J Mol Biol. 1989 Oct 5;209(3):423-32 PMID: 2511324
  23. Sequence requirements for coiled-coils: analysis with lambda repressor-GCN4 leucine zipper fusions.
    Science. 1990 Dec 7;250(4986):1400-3 PMID: 2147779
  24. Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster.
    Genes Dev. 1994 Oct 15;8(20):2504-12 PMID: 7958913
  25. 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
  26. Sequence-specific DNA binding by NIT4, the pathway-specific regulatory protein that mediates nitrate induction in Neurospora.
    Mol Microbiol. 1995 Mar;15(5):935-42 PMID: 7596294
  27. 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
  28. DNA sequence preferences of GAL4 and PPR1: how a subset of Zn2 Cys6 binuclear cluster proteins recognizes DNA.
    Mol Cell Biol. 1996 Jul;16(7):3773-80 PMID: 8668194
  29. The C6 zinc cluster dictates asymmetric binding by HAP1.
    EMBO J. 1996 Sep 2;15(17):4676-81 PMID: 8887558
  30. A novel DNA binding motif for yeast zinc cluster proteins: the Leu3p and Pdr3p transcriptional activators recognize everted repeats.
    Mol Cell Biol. 1996 Nov;16(11):6096-102 PMID: 8887639
  31. Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators.
    Nucleic Acids Res. 1996 Dec 1;24(23):4599-607 PMID: 8967907
  32. In vitro recognition of specific DNA targets by AlcR, a zinc binuclear cluster activator different from the other proteins of this class.
    J Biol Chem. 1997 Jun 13;272(24):15521-6 PMID: 9182587
  33. The Aspergillus nidulans transcription factor AlcR forms a stable complex with its half-site DNA: a NMR study.
    FEBS Lett. 1997 May 19;408(2):235-40 PMID: 9187374
  34. The zinc binuclear cluster activator AlcR is able to bind to single sites but requires multiple repeated sites for synergistic activation of the alcA gene in Aspergillus nidulans.
    J Biol Chem. 1997 Sep 5;272(36):22859-65 PMID: 9278448
  35. Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster.
    Nat Struct Biol. 1997 Sep;4(9):751-9 PMID: 9303004
  36. Molecular cloning and functional characterization of the pathway-specific regulatory gene nirA, which controls nitrate assimilation in Aspergillus nidulans.
    Mol Cell Biol. 1991 Feb;11(2):795-802 PMID: 1990284
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.18.3.1339
Published
1998-03-00
Pages
1339-48
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC108847
Subset
IM
External Links
PubMed source DOI: 10.1128/MCB.18.3.1339 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2