Article

The structure of GABPα/β: An ETS domain-ankyrin repeat heterodimer bound to DNA. Science 279, 1037-1041

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, United States
Science (Impact Factor: 33.61). 03/1998; 279(5353):1037-41. DOI: 10.1126/science.279.5353.1037
Source: PubMed

ABSTRACT

GA-binding protein (GABP) is a transcriptional regulator composed of two structurally dissimilar subunits. The α subunit contains
a DNA-binding domain that is a member of the ETS family, whereas the β subunit contains a series of ankyrin repeats. The crystal
structure of a ternary complex containing a GABPα/β ETS domain–ankyrin repeat heterodimer bound to DNA was determined at 2.15
angstrom resolution. The structure shows how an ETS domain protein can recruit a partner protein using both the ETS domain
and a carboxyl-terminal extension and provides a view of an extensive protein-protein interface formed by a set of ankyrin
repeats. The structure also reveals how the GABPα ETS domain binds to its core GGA DNA-recognition motif.

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    • "ETS TFs interact with TFs from several families to bind sequences containing chimeric aspects of each binding site (Wunderlich and Mirny 2009; Hollenhorst et al. 2011b). GABPa initially was observed interacting with GABPb (another ETS protein) to bind a composite element (Batchelor et al. 1998). Forkhead proteins interact at the 59 end of the ETS motif (De Val et al. 2008) while SRF, PAX, and CREB1 interact at the 39 end of the ETS motif (Hollenhorst et al. 2011b). "
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    ABSTRACT: To achieve proper spatiotemporal control of gene expression, transcription factors cooperatively assemble onto specific DNA sequences. The ETS domain protein monomer of GABPα and the B-ZIP domain protein dimer of CREB1 cooperatively bind DNA only when the ETS ((C)/GCGGAA GT: ) and CRE ( GT: GACGTCAC) motifs overlap precisely, producing the ETS⇔CRE motif ((C)/GCGGAA GT: GACGTCAC). We designed a Protein Binding Microarray (PBM) with 60-bp DNAs containing four identical sectors, each with 177,440 features that explore the cooperative interactions between GABPα and CREB1 upon binding the ETS⇔CRE motif. The DNA sequences include all 15-mers of the form (C)/GCGGA-----CG---, the ETS⇔CRE motif and all single nucleotide polymorphisms (SNPs), and occurrences in the human and mouse genomes. CREB1 enhanced GABPα binding to the canonical ETS⇔CRE motif CCGGAAGT 2-fold, and up to 23-fold for several SNPs at the beginning and end of the ETS motif, which is suggestive of two separate and distinct allosteric mechanisms of cooperative binding. We show that the ETS-CRE array data can be used to identify regions likely cooperatively bound by GABPα and CREB1 in vivo, and demonstrate their ability to identify human genetic variants that might inhibit cooperative binding. Copyright © 2015 Author et al.
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    • "We tested experimentally whether NRF-2 regulates SIRT3 and PSMD13 gene expression using human 293T cells. NRF-2 functions as a heterodimer, with the a subunit binding DNA and the b subunit facilitating binding between heterodimers (Batchelor et al., 1998). When NRF-2a and NRF-2b1 were transiently overexpressed together (Fig. 3A, B), SIRT3 mRNA levels were significantly induced (P = 0.046 for HAtagged NRF-2, P = 0.003 for untagged NRF-2, Fig. 3C) to a greater degree than known NRF-2 target DNA polymerase subunit c-2 (POLG2) (P = 0.26 for HA-tagged NRF-2, P = 0.44 for untagged NRF-2, Fig. 3D). "
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    ABSTRACT: The mitochondrial deacetylase SIRT3 regulates several important metabolic processes. SIRT3 is transcriptionally upregulated in multiple tissues during nutrient stresses such as dietary restriction and fasting, but the molecular mechanism of this induction is unclear. We conducted a bioinformatic study to identify transcription factor(s) involved in SIRT3 induction. Our analysis identified an enrichment of binding sites for nuclear respiratory factor 2 (NRF-2), a transcription factor known to play a role in the expression of mitochondrial genes, in the DNA sequences of SIRT3 and genes with closely correlated expression patterns. In vitro, knockdown or overexpression of NRF-2 modulated SIRT3 levels, and the NRF-2α subunit directly bound to the SIRT3 promoter. Our results suggest that NRF-2 is a regulator of SIRT3 expression and may shed light on how SIRT3 is upregulated during nutrient stress. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.
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    • "It contains the transactivation (TAD) and nuclear localization signal (NLS) domains, whereas it does not physically interact with DNA [12] [13] [14]. Thus, both heteromer-forming subunits share an obligate codependence , a unique phenomenon among the ETS transcription factor family [11] [14]. GABP was described to influence the development and lineage commitment in lymphoid as well as myeloid compartments [15] [16] [17] [18]. "
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    ABSTRACT: In Philadelphia-positive chronic myeloid leukemia (CML), imatinib resistance frequently emerges due to point mutations in the ABL1 kinase domain, but may also be the consequence of uncontrolled upstream signaling. Recently, the heteromeric transcription factor GA-binding protein (GABP) was shown to promote CML-like myeloproliferative disease in mice. In a cohort of 70 CML patients, we demonstrate that expression of the GABP alpha subunit (GABPα) is positively correlated to the BCR-ABL1/ABL1 ratio. Moreover, significantly higher GABPα expression was detected in blast crisis than in chronic phase CML after performing data mining on 91 CML patients. In functional studies, imatinib sensitivity is enhanced after GABPα knockdown in TKI-sensitive K-562 as well as by overexpression of a deletion mutant in TKI-resistant NALM-1 cells. Moreover, in K-562 cells GABP-dependent expression variations of PRKD2 and RAC2, relevant signaling mediators in CML, were observed. Notably, Prkd2 was reported to be a GABP target gene in mice. In line with this, we detected a positive correlation of GABPA and PRKD2 expression in primary human CML, indicating that the effects of GABP are mediated by PRKD2. These findings illustrate an important role of GABP for disease development and imatinib sensitivity in human CML. Copyright © 2015 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.
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