The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding

We previously reported that either oxidation or alkylation of NF-kappa B in vitro abrogates DNA binding. We used this phenomenon to help elucidate structural determinants of NF-kappa B binding. We now demonstrate that Cys-62 of NF-kappa B p50 mediates the redox effect and lies within an N-terminal region required for DNA binding but not for dimerization. Several point mutations in this region confer a transdominant negative binding phenotype to p50. The region is highly conserved in all Rel family proteins, and we have determined that it is also critical for DNA binding of NF-kappa B p65. Replacement of the N-terminal region of p65 with the corresponding region from p50 changes its DNA-binding specificity towards that of p50. These data suggest that the N-terminal regions of p50 and p65 are critical for DNA binding and help determine the DNA-binding specificities of p50 and p65. We have defined within the N-terminal region a sequence motif, R(F/G)(R/K)YXCE, which is present in Rel family proteins and also in zinc finger proteins capable of binding to kappa B sites. The potential significance of this finding is discussed.

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An interaction between the DNA-binding domains of RelA(p65) and Sp1 mediates human immunodeficiency virus gene activation

Molecular and Cellular Biology ◽

10.1128/mcb.14.10.6570-6583.1994 ◽

1994 ◽

Vol 14 (10) ◽

pp. 6570-6583 ◽

Cited By ~ 3

Author(s):

N D Perkins ◽

A B Agranoff ◽

E Pascal ◽

G J Nabel

Keyword(s):

Human Immunodeficiency Virus ◽

Transcription Factors ◽

Dna Binding ◽

Binding Sites ◽

Nf Kappa B ◽

Dna Binding Domains ◽

Amino Terminal ◽

Binding Domains ◽

Immunodeficiency Virus ◽

Hiv 1

Induction of human immunodeficiency virus type 1 (HIV-1) gene expression in stimulated T cells has been attributed to the activation of the transcription factor NF-kappa B. The twice-repeated kappa B sites within the HIV-1 long terminal repeat are in close proximity to three binding sites for Sp1. We have previously shown that a cooperative interaction of NF-kappa B with Sp1 is required for the efficient stimulation of HIV-1 transcription. In this report, we define the domains of each protein responsible for this effect. Although the transactivation domains seemed likely to mediate this interaction, we find, surprisingly, that this interaction occurs through the putative DNA-binding domains of both proteins. Sp1 specifically interacted with the amino-terminal region of RelA(p65). Similarly, RelA bound directly to the zinc finger region of Sp1. This interaction was specific and resulted in cooperative DNA binding to the kappa B and Sp1 sites in the HIV-1 long terminal repeat. Furthermore, the amino-terminal region of RelA did not associate with several other transcription factors, including MyoD, E12, or Kox15, another zinc finger protein. These findings suggest that the juxtaposition of DNA-binding sites promotes a specific protein interaction between the DNA-binding regions of these transcription factors. This interaction is required for HIV transcriptional activation and may provide a mechanism to allow for selective activation of kappa B-regulated genes.

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Homing Endonucleases Encoded by Germ Line-Limited Genes in Tetrahymena thermophila Have APETELA2 DNA Binding Domains

Eukaryotic Cell ◽

10.1128/ec.3.3.685-694.2004 ◽

2004 ◽

Vol 3 (3) ◽

pp. 685-694 ◽

Cited By ~ 24

Author(s):

Jeffrey D. Wuitschick ◽

Paul R. Lindstrom ◽

Alison E. Meyer ◽

Kathleen M. Karrer

Keyword(s):

Dna Binding ◽

Germ Line ◽

Homing Endonuclease ◽

Genome Comparison ◽

Homing Endonucleases ◽

Reading Frame ◽

Dna Binding Domains ◽

Amino Terminal ◽

Binding Domains ◽

Insertion Elements

ABSTRACT Three insertion elements were previously found in a family of germ line-limited mobile elements, the Tlr elements, in the ciliate Tetrahymena. Each of the insertions contains an open reading frame (ORF). Sequence analysis of the deduced proteins encoded by the elements suggests that they are homing endonucleases. The genes are designated TIE1-1, TIE2-1, and TIE3-1 for Tetrahymena insertion-homing endonuclease. The endonuclease motif occupies the amino terminal half of each TIE protein. The C-terminal regions of the proteins are similar to the APETELA2 DNA binding domain of plant transcription factors. The TIE1 and TIE3 elements belong to families of repeated sequences in the germ line micronuclear genome. Comparison of the genes and the deduced proteins they encode suggests that there are at least two distinct families of homing endonuclease genes, each of which appears to be preferentially associated with a specific region of the Tlr elements. The TIE1 and TIE3 elements and their cognates undergo programmed elimination from the developing somatic macronucleus of Tetrahymena. The possible role of homing endonuclease-like genes in the DNA breakage step in developmentally programmed DNA elimination in Tetrahymena is discussed.

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An interaction between the DNA-binding domains of RelA(p65) and Sp1 mediates human immunodeficiency virus gene activation.

Molecular and Cellular Biology ◽

10.1128/mcb.14.10.6570 ◽

1994 ◽

Vol 14 (10) ◽

pp. 6570-6583 ◽

Cited By ~ 168

Author(s):

N D Perkins ◽

A B Agranoff ◽

E Pascal ◽

G J Nabel

Keyword(s):

Human Immunodeficiency Virus ◽

Transcription Factors ◽

Dna Binding ◽

Binding Sites ◽

Nf Kappa B ◽

Dna Binding Domains ◽

Amino Terminal ◽

Binding Domains ◽

Immunodeficiency Virus ◽

Hiv 1

Induction of human immunodeficiency virus type 1 (HIV-1) gene expression in stimulated T cells has been attributed to the activation of the transcription factor NF-kappa B. The twice-repeated kappa B sites within the HIV-1 long terminal repeat are in close proximity to three binding sites for Sp1. We have previously shown that a cooperative interaction of NF-kappa B with Sp1 is required for the efficient stimulation of HIV-1 transcription. In this report, we define the domains of each protein responsible for this effect. Although the transactivation domains seemed likely to mediate this interaction, we find, surprisingly, that this interaction occurs through the putative DNA-binding domains of both proteins. Sp1 specifically interacted with the amino-terminal region of RelA(p65). Similarly, RelA bound directly to the zinc finger region of Sp1. This interaction was specific and resulted in cooperative DNA binding to the kappa B and Sp1 sites in the HIV-1 long terminal repeat. Furthermore, the amino-terminal region of RelA did not associate with several other transcription factors, including MyoD, E12, or Kox15, another zinc finger protein. These findings suggest that the juxtaposition of DNA-binding sites promotes a specific protein interaction between the DNA-binding regions of these transcription factors. This interaction is required for HIV transcriptional activation and may provide a mechanism to allow for selective activation of kappa B-regulated genes.

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Domains Required for Transcriptional Activation Show Conservation in the Mga Family of Virulence Gene Regulators

Journal of Bacteriology ◽

10.1128/jb.188.3.863-873.2006 ◽

2006 ◽

Vol 188 (3) ◽

pp. 863-873 ◽

Cited By ~ 11

Author(s):

Cheryl M. Vahling ◽

Kevin S. McIver

Keyword(s):

Dna Binding ◽

Transcriptional Activation ◽

Group A Streptococcus ◽

Gene Activation ◽

Random Mutagenesis ◽

Virulence Gene ◽

Common Mechanism ◽

Dna Binding Domains ◽

Amino Terminal ◽

Binding Domains

ABSTRACT Mga, or the multigene regulator of the group A streptococcus (GAS) (Streptococcus pyogenes), is a transcriptional regulator of virulence genes important for colonization and immune evasion. All serotypes of the GAS possess one of two divergent mga alleles (mga-1 or mga-2), and orthologues of Mga have also been identified in other pathogenic streptococci. To date, the only functional motifs established within Mga are two amino-terminal DNA-binding domains (HTH-3 and HTH-4). To uncover novel domains, a random mutagenesis screen using an M6 Mga (mga-1) was undertaken to find mutations leading to a defect in transcriptional activation of the Mga-regulated emm gene. In addition to mutations in the established DNA-binding domains, the screen also revealed mutations in a region conserved among several Mga orthologues. Alanine scanning helped resolve the boundaries of this conserved Mga domain (CMD-1) spanning from residues 10 to 15 of the protein, with the two flanking amino acid residues likely involved in protein stability. Transcriptional reporter analyses demonstrated the importance of CMD-1 for activation of Pemm and autoactivation of Pmga in the serotype M6 Mga. Mutational analyses showed that both CMD-1 and HTH-4 are also necessary for activation of the promoter target Pmrp in a divergent serotype M4 Mga (mga-2), suggesting a conserved functionality. However, in contrast to M6, the M4 Mga mutants did not show a defect in autoregulation. Mutation of similar conserved residues in the Mga-like regulator DmgB from S. dysgalactiae subsp. dysgalactiae showed that CMD-1 and HTH-4 are critical for transcriptional activation in this orthologue, implying that a common mechanism of virulence gene activation may exist for members of the Mga family of regulators.

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N-terminal DNA-binding domains contribute to differential DNA-binding specificities of NF-kappa B p50 and p65.

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.852 ◽

1993 ◽

Vol 13 (2) ◽

pp. 852-860 ◽

Cited By ~ 87

Author(s):

M B Toledano ◽

D Ghosh ◽

F Trinh ◽

W J Leonard

Keyword(s):

Dna Binding ◽

Point Mutations ◽

Terminal Region ◽

Sequence Motif ◽

Structural Determinants ◽

Nf Kappa B ◽

Dna Binding Domains ◽

Binding Domains ◽

Dna Binding Specificity

We previously reported that either oxidation or alkylation of NF-kappa B in vitro abrogates DNA binding. We used this phenomenon to help elucidate structural determinants of NF-kappa B binding. We now demonstrate that Cys-62 of NF-kappa B p50 mediates the redox effect and lies within an N-terminal region required for DNA binding but not for dimerization. Several point mutations in this region confer a transdominant negative binding phenotype to p50. The region is highly conserved in all Rel family proteins, and we have determined that it is also critical for DNA binding of NF-kappa B p65. Replacement of the N-terminal region of p65 with the corresponding region from p50 changes its DNA-binding specificity towards that of p50. These data suggest that the N-terminal regions of p50 and p65 are critical for DNA binding and help determine the DNA-binding specificities of p50 and p65. We have defined within the N-terminal region a sequence motif, R(F/G)(R/K)YXCE, which is present in Rel family proteins and also in zinc finger proteins capable of binding to kappa B sites. The potential significance of this finding is discussed.

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Faculty Opinions recommendation of Excess non-synonymous substitutions suggest that positive selection episodes occurred during the evolution of DNA-binding domains in the Arabidopsis R2R3-MYB gene family.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1015386.196756 ◽

2003 ◽

Author(s):

Elena Alvarez-Buylla

Keyword(s):

Dna Binding ◽

Positive Selection ◽

Gene Family ◽

Synonymous Substitutions ◽

Dna Binding Domains ◽

Binding Domains ◽

Myb Gene ◽

R2r3 Myb

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Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1

Journal of Biological Chemistry ◽

10.1074/jbc.m114.575340 ◽

2014 ◽

Vol 289 (31) ◽

pp. 21605-21616 ◽

Cited By ~ 18

Author(s):

Shuo Wang ◽

Miles H. Linde ◽

Manoj Munde ◽

Victor D. Carvalho ◽

W. David Wilson ◽

...

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Binding Domains ◽

Binding Domains ◽

Ets Family ◽

Site Recognition

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Intra-domain communication between the N-terminal and DNA-binding domains of the androgen receptor: modulation of androgen response element DNA binding

Journal of Molecular Endocrinology ◽

10.1677/jme.1.01723 ◽

2005 ◽

Vol 34 (3) ◽

pp. 603-615 ◽

Cited By ~ 45

Author(s):

Jacqueline Brodie ◽

Iain J McEwan

Keyword(s):

Androgen Receptor ◽

Dna Binding ◽

Fluorescence Emission ◽

Progesterone Receptors ◽

Fluorescence Emission Spectrum ◽

Response Element ◽

Amino Terminal ◽

Binding Domains ◽

Receptor Modulation

The androgen receptor (AR) is a ligand-activated transcription factor that recognises and binds to specific DNA response elements upon activation by the steroids testosterone or dihydrotestosterone. In vitro, two types of response element have been characterised - non-selective elements that bind the androgen, glucocorticoid and progesterone receptors, and androgen receptor-selective sequences. In the present study, the allosteric effects of DNA binding on the receptor amino-terminal domain (NTD) were studied. Binding to both types of DNA response element resulted in changes in the intrinsic fluorescence emission spectrum for four tryptophan residues within the AR-NTD and resulted in a more protease-resistant conformation. In binding experiments, it was observed that the presence of the AR-NTD reduced the affinity of receptor polypeptides for binding to both selective and non-selective DNA elements derived from the probasin, PEM and prostatin C3 genes respectively, without significantly altering the protein–base pair contacts. Taken together, these results highlight the role of intra-domain communications between the AR-NTD and the DNA binding domain in receptor structure and function.

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