DNA-binding regulates site-specific ubiquitination of IRF-1

2013 ◽  
Vol 449 (3) ◽  
pp. 707-717 ◽  
Author(s):  
Vivien Landré ◽  
Emmanuelle Pion ◽  
Vikram Narayan ◽  
Dimitris P. Xirodimas ◽  
Kathryn L. Ball
Keyword(s):  
Dna Binding ◽  
E3 Ligase ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Docking Site ◽  
Interacting Protein ◽  
Site Specific ◽  
E3 Ligases ◽  
Intrinsically Disordered ◽  
C Terminus

Understanding the determinants for site-specific ubiquitination by E3 ligase components of the ubiquitin machinery is proving to be a challenge. In the present study we investigate the role of an E3 ligase docking site (Mf2 domain) in an intrinsically disordered domain of IRF-1 [IFN (interferon) regulatory factor-1], a short-lived IFNγ-regulated transcription factor, in ubiquitination of the protein. Ubiquitin modification of full-length IRF-1 by E3 ligases such as CHIP [C-terminus of the Hsc (heat-shock cognate) 70-interacting protein] and MDM2 (murine double minute 2), which dock to the Mf2 domain, was specific for lysine residues found predominantly in loop structures that extend from the DNA-binding domain, whereas no modification was detected in the more conformationally flexible C-terminal half of the protein. The E3 docking site was not available when IRF-1 was in its DNA-bound conformation and cognate DNA-binding sequences strongly suppressed ubiquitination, highlighting a strict relationship between ligase binding and site-specific modification at residues in the DNA-binding domain. Hyperubiquitination of a non-DNA-binding mutant supports a mechanism where an active DNA-bound pool of IRF-1 is protected from polyubiquitination and degradation.

scholarly journals The p53 C Terminus Controls Site-Specific DNA Binding and Promotes Structural Changes within the Central DNA Binding Domain

2015 ◽  
Vol 57 (6) ◽  
pp. 1034-1046 ◽  
Author(s):  
Oleg Laptenko ◽  
Idit Shiff ◽  
Will Freed-Pastor ◽  
Andrew Zupnick ◽  
Melissa Mattia ◽  
...  
Keyword(s):  
Dna Binding ◽  
Structural Changes ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Site Specific ◽  
C Terminus

scholarly journals Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping

2020 ◽  
Vol 432 (19) ◽  
pp. 5411-5429 ◽  
Author(s):  
Exequiel Medina ◽  
Pablo Villalobos ◽  
George L. Hamilton ◽  
Elizabeth A. Komives ◽  
Hugo Sanabria ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Domain Swapping ◽  
Dna Binding Domain ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Disordered Regions

scholarly journals Regulation of Cell Cycle Transcription Factor Swi4 through Auto-Inhibition of DNA Binding

1999 ◽  
Vol 19 (10) ◽  
pp. 6729-6741 ◽  
Author(s):  
Kristin Baetz ◽  
Brenda Andrews
Keyword(s):  
Cell Cycle ◽  
Transcription Factors ◽  
Dna Binding ◽  
Binding Domain ◽  
Terminal Region ◽  
Full Length ◽  
Intramolecular Interactions ◽  
Dna Binding Domain ◽  
C Terminus ◽  
Binding Factor

ABSTRACTInSaccharomyces cerevisiae, two transcription factors, SBF (SCB binding factor) and MBF (MCB binding factor), promote the induction of gene expression at the G1/S-phase transition of the mitotic cell cycle. Swi4 and Mbp1 are the DNA binding components of SBF and MBF, respectively. The Swi6 protein is a common subunit of both transcription factors and is presumed to play a regulatory role. SBF binding to its target sequences, the SCBs, is a highly regulated event and requires the association of Swi4 with Swi6 through their C-terminal domains. Swi4 binding to SCBs is restricted to the late M and G1phases, when Swi6 is localized to the nucleus. We show that in contrast to Swi6, Swi4 remains nuclear throughout the cell cycle. This finding suggests that the DNA binding domain of Swi4 is inaccessible in the full-length protein when not complexed with Swi6. To explore this hypothesis, we expressed Swi4 and Swi6 in insect cells by using the baculovirus system. We determined that partially purified Swi4 cannot bind SCBs in the absence of Swi6. However, Swi4 derivatives carrying point mutations or alterations in the extreme C terminus were able to bind DNA or activate transcription in the absence of Swi6, and the C terminus of Swi4 inhibited Swi4 derivatives from binding DNA intrans. Full-length Swi4 was determined to be monomeric in solution, suggesting an intramolecular mechanism for auto-inhibition of binding to DNA by Swi4. We detected a direct in vitro interaction between a C-terminal fragment of Swi4 and the N-terminal 197 amino acids of Swi4, which contain the DNA binding domain. Together, our data suggest that intramolecular interactions involving the C-terminal region of Swi4 physically prevent the DNA binding domain from binding SCBs. The interaction of the carboxy-terminal region of Swi4 with Swi6 alleviates this inhibition, allowing Swi4 to bind DNA.

scholarly journals A DNA binding domain is contained in the C-terminus ofwild typep53 protein

1991 ◽  
Vol 19 (19) ◽  
pp. 5191-5198 ◽  
Author(s):  
Orit Shohat Foord ◽  
Protima Bhattacharya ◽  
Ziv Reich ◽  
Varda Rotter
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
C Terminus

Site-Specific Recognition by an Isolated DNA-Binding Domain of the Sine Oculis Protein†

Biochemistry ◽  
1997 ◽  
Vol 36 (12) ◽  
pp. 3680-3686 ◽  
Author(s):  
Tony R. Hazbun ◽  
Florence L. Stahura ◽  
Michael C. Mossing
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Site Specific ◽  
Sine Oculis ◽  
Specific Recognition

scholarly journals Activation of CREB/ATF Sites by Polyomavirus Large T Antigen

2005 ◽  
Vol 79 (7) ◽  
pp. 4180-4190 ◽  
Author(s):  
Tara M. Love ◽  
Rowena de Jesus ◽  
Jennifer A. Kean ◽  
Qing Sheng ◽  
Andrew Leger ◽  
...  
Keyword(s):  
Dna Binding ◽  
T Antigen ◽  
Binding Domain ◽  
Cell Phenotype ◽  
Dna Binding Domain ◽  
Large T Antigen ◽  
Direct Role ◽  
Site Specific ◽  
Creb Phosphorylation

ABSTRACT Polyomavirus large T antigen (LT) has a direct role in viral replication and a profound effect on cell phenotype. It promotes cell cycle progression, immortalizes primary cells, blocks differentiation, and causes apoptosis. While much of large T function is related to its effects on tumor suppressors of the retinoblastoma susceptibility (Rb) gene family, we have previously shown that activation of the cyclin A promoter can occur through a non-Rb-dependent mechanism. Here we show that activation occurs via an ATF/CREB site. Investigation of the mechanism indicates that large T can synergize with CREB family members to activate transcription. Experiments with Gal4-CREB constructs show that synergy is independent of CREB phosphorylation by protein kinase A. Examination of synergy with Gal4-CREB deletion constructs indicates that large T acts on the constitutive activation domain of CREB. Large T can bind to CREB in vivo. Genetic analysis shows that the DNA-binding domain (residues 264 to 420) is sufficient to activate transcription when it is localized to the nucleus. Further analysis of the DNA-binding domain shows that while site-specific DNA binding is not required, non-site-specific DNA binding is important for the activation. Thus, CREB binding and DNA binding are both important for large T activation of CREB/ATF sites. In contrast to previous models where large T transactivation occurred indirectly, these results also suggest that large T can act directly at promoters to activate transcription.

scholarly journals The monomer-binding orphan receptor Rev-Erb represses transcription as a dimer on a novel direct repeat.

1995 ◽  
Vol 15 (9) ◽  
pp. 4791-4802 ◽  
Author(s):  
H P Harding ◽  
M A Lazar
Keyword(s):  
Retinoic Acid ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Domain ◽  
Luciferase Reporter ◽  
Dna Binding Domain ◽  
Transactivation Domain ◽  
Direct Repeats ◽  
Basal Transcription ◽  
C Terminus

Rev-Erb is an orphan nuclear receptor which binds as a monomer to the thyroid/retinoic acid receptor half-site AGGTCA flanked 5' by an A/T-rich sequence, referred to here as a Rev monomer site. Fusion of Rev-Erb to the DNA binding domain of yeast GAL4 strongly repressed basal transcription of a GAL4-luciferase reporter gene as a result of the presence of a C-terminal domain containing both the hinge and heptad repeat regions. Nevertheless, wild-type Rev-Erb did not repress basal transcription from the Rev monomer binding site. Therefore, a DNA binding site selection strategy was devised to test the hypothesis that Rev-Erb may function on a different site as a dimer. This approach identified sequences containing two Rev monomer sites arranged as direct repeats with the AGGTCA motifs separated by 2 bp (Rev-DR2). Remarkably, Rev-Erb bound as a homodimer to Rev-DR2 but not to other direct repeats or to a standard DR2 sequence. The DNA binding domain contained all of the determinants for Rev-DR2-specific homodimerization. Rev-Erb bound cooperatively as a homodimer to Rev-DR2, and this interaction was 5 to 10 times more stable than Rev-Erb monomer binding to the Rev monomer site. Functionally, Rev-Erb markedly repressed the basal activity of a variety of promoters with a strong Rev-DR2 specificity. The C terminus was required for this repression, consistent with the GAL4 results. However, the Rev-DR2 specificity did not require the C terminus in vivo, since fusion of C-terminally truncated Rev-Erb to a heterologous transactivation domain created a transcriptional activator specific for Rev-DR2. In addition to idealized Rev-DR2 sites, Rev-Erb also repressed basal as well as retinoic acid-induced transcription from a naturally occurring Rev-DR2 in the CRBPI gene. Thus, although Rev-Erb is distinguished from other thyroid/steroid receptor superfamily members by its ability to bind DNA as a monomer, it functions as a homodimer to repress transcription of genes containing a novel DR2 element.

scholarly journals Functional Dissection of Human and Mouse POT1 Proteins

2008 ◽  
Vol 29 (2) ◽  
pp. 471-482 ◽  
Author(s):  
Wilhelm Palm ◽  
Dirk Hockemeyer ◽  
Tatsuya Kibe ◽  
Titia de Lange
Keyword(s):  
Dna Damage ◽  
Dna Binding ◽  
Dna Damage Response ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Telomeric Dna ◽  
C Terminus ◽  
Damage Response ◽  
End Resection

ABSTRACT The single-stranded telomeric DNA binding protein POT1 protects mammalian chromosome ends from the ATR-dependent DNA damage response, regulates telomerase-mediated telomere extension, and limits 5′-end resection at telomere termini. Whereas most mammals have a single POT1 gene, mice have two POT1 proteins that are functionally distinct. POT1a represses the DNA damage response, and POT1b controls 5′-end resection. In contrast, as we report here, POT1a and POT1b do not differ in their ability to repress telomere recombination. By swapping domains, we show that the DNA binding domain of POT1a specifies its ability to repress the DNA damage response. However, no differences were detected in the in vitro DNA binding features of POT1a and POT1b. In contrast to the repression of ATR signaling by POT1a, the ability of POT1b to control 5′-end resection was found to require two regions in the C terminus, one corresponding to the TPP1 binding domain and a second representing a new domain located between amino acids (aa) 300 and 350. Interestingly, the DNA binding domain of human POT1 can replace that of POT1a to repress ATR signaling, and the POT1b region from aa 300 to 350 required for the regulation of the telomere terminus is functionally conserved in human POT1. Thus, human POT1 combines the features of POT1a and POT1b.

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