Thermodynamics of b-HLH-LZ Protein Binding to DNA:  The Energetic Importance of Protein−DNA Contacts in Site-Specific E-Box Recognition by the Complete Gene Product of the Max p21 Transcription Factor†

Biochemistry ◽  
2007 ◽  
Vol 46 (43) ◽  
pp. 12427-12440 ◽  
Author(s):  
Laura Meier-Andrejszki ◽  
Saša Bjelić ◽  
Jean-François Naud ◽  
Pierre Lavigne ◽  
Ilian Jelesarov
2002 ◽  
Vol 361 (2) ◽  
pp. 391-400 ◽  
Author(s):  
Yutong WANG ◽  
Yanqiao ZHANG ◽  
F. Bradley HILLGARTNER

In chick embryo hepatocytes (CEH), stimulation of malic enzyme transcription by 3,3′,5-tri-iodothyronine (T3) is mediated by a liver-specific and T3-inducible DNase I hypersensitive region (−3910 to −3640bp) in the malic enzyme gene. Previous studies have shown that this region contains a cluster of five T3 response elements (T3REs), referred to as a T3 response unit (T3RU), plus three accessory elements that enhance T3 responsiveness conferred by the T3RU. Here we report the identification of two additional accessory elements within the −3910 to −3640bp region. Each element augments T3 regulation of malic enzyme transcription in CEH. One element, designated region G (−3681/−3666bp), contains a single nuclear-hormone-receptor half-site that binds the orphan receptor chicken ovalbumin upstream-promoter transcription factor. The other element, designated region H (−3655/−3646bp), contains an E-box motif that binds proteins of unknown identity. Stimulation of T3RE function by region G or region H does not require the presence of additional malic enzyme sequences. In contrast with the stimulatory effects of regions G and H on T3 responsiveness in CEH, neither of these elements is effective in modulating T3 responsiveness in chick embryo fibroblasts (CEF). Instead, region H functions as a T3-insensitive repressor of transcription in CEF. These results indicate that chicken ovalbumin upstream-promoter transcription factor and E-box-binding proteins interact with nuclear T3 receptors to enhance T3 regulation of malic enzyme transcription in CEH and that alterations in region G and region H activities contribute to diminished T3 regulation of malic enzyme transcription in CEF relative to CEH. As the pattern of protein binding to regions G and H varies substantially between CEH and CEF, the mechanism for cell-type-dependent differences in region G and region H activity may involve alterations in protein binding to these T3 accessory elements.


Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 15
Author(s):  
Aishat Motolani ◽  
Matthew Martin ◽  
Mengyao Sun ◽  
Tao Lu

The nuclear factor kappa B (NF-κB) is a ubiquitous transcription factor central to inflammation and various malignant diseases in humans. The regulation of NF-κB can be influenced by a myriad of post-translational modifications (PTMs), including phosphorylation, one of the most popular PTM formats in NF-κB signaling. The regulation by phosphorylation modification is not limited to NF-κB subunits, but it also encompasses the diverse regulators of NF-κB signaling. The differential site-specific phosphorylation of NF-κB itself or some NF-κB regulators can result in dysregulated NF-κB signaling, often culminating in events that induce cancer progression and other hyper NF-κB related diseases, such as inflammation, cardiovascular diseases, diabetes, as well as neurodegenerative diseases, etc. In this review, we discuss the regulatory role of phosphorylation in NF-κB signaling and the mechanisms through which they aid cancer progression. Additionally, we highlight some of the known and novel NF-κB regulators that are frequently subjected to phosphorylation. Finally, we provide some future perspectives in terms of drug development to target kinases that regulate NF-κB signaling for cancer therapeutic purposes.


Nature ◽  
1992 ◽  
Vol 358 (6384) ◽  
pp. 331-334 ◽  
Author(s):  
Seong-Jin Kim ◽  
Susanne Wagner ◽  
Fang Liu ◽  
Michael A. O'Reilly ◽  
Paul D. Robbins ◽  
...  

1992 ◽  
Vol 12 (5) ◽  
pp. 2302-2314
Author(s):  
J D Trawick ◽  
N Kraut ◽  
F R Simon ◽  
R O Poyton

Transcription of the Saccharomyces cerevisiae COX6 gene is regulated by heme and carbon source. It is also affected by the HAP2/3/4 transcription factor complex and by SNF1 and SSN6. Previously, we have shown that most of this regulation is mediated through UAS6, an 84-bp upstream activation segment of the COX6 promoter. In this study, by using linker scanning mutagenesis and protein binding assays, we have identified three elements within UAS6 and one element downstream of it that are important. Two of these, HDS1 (heme-dependent site 1; between -269 and -251 bp) and HDS2 (between -228 and -220 bp), mediate regulation of COX6 by heme. Both act negatively. The other two elements, domain 2 (between -279 and -269 bp) and domain 1 (between -302 and -281 bp), act positively. Domain 2 is required for optimal transcription in cells grown in repressing but not derepressing carbon sources. Domain 1 is essential for transcription per se in cells grown on repressing carbon sources, is required for optimal transcription in cells grown on a derepressing carbon source, is sufficient for glucose repression-derepression, and is the element of UAS6 at which HAP2 affects COX6 transcription. This element contains the major protein binding sites within UAS6. It has consensus binding sequences for ABF1 and HAP2. Gel mobility shift experiments show that domain 1 binds ABF1 and forms different numbers of DNA-protein complexes in extracts from cells grown in repressing or derepressing carbon sources. In contrast, gel mobility shift experiments have failed to reveal that HAP2 or HAP3 binds to domain 1 or that hap3 mutations affect the complexes bound to it. Together, these findings permit the following conclusions: COX6 transcription is regulated both positively and negatively; heme and carbon source exert their effects through different sites; domain 1 is absolutely essential for transcription on repressing carbon sources; ABF1 is a major component in the regulation of COX6 transcription; and the HAP2/3/4 complex most likely affects COX6 transcription indirectly.


1995 ◽  
Vol 15 (1) ◽  
pp. 476-487 ◽  
Author(s):  
X Guo ◽  
Y P Zhang ◽  
D A Mitchell ◽  
D T Denhardt ◽  
A F Chambers

The role of RAS in transducing signals from an activated receptor into altered gene expression is becoming clear, though some links in the chain are still missing. Cells possessing activated RAS express higher levels of osteopontin (OPN), an alpha v beta 3 integrin-binding secreted phosphoprotein implicated in a number of developmental, physiological, and pathological processes. We report that in T24 H-ras-transformed NIH 3T3 cells enhanced transcription contributes to the increased expression of OPN. Transient transfection studies, DNA-protein binding assays, and methylation protection experiments have identified a novel ras-activated enhancer, distinct from known ras response elements, that appears responsible for part of the increase in OPN transcription in cells with an activated RAS. In electrophoretic mobility shift assays, the protein-binding motif GGAGGCAGG was found to be essential for the formation of several complexes, one of which (complex A) was generated at elevated levels by cell lines that are metastatic. Southwestern blotting and UV light cross-linking studies indicated the presence of several proteins able to interact with this sequence. The proteins that form these complexes have molecular masses estimated at approximately 16, 28, 32, 45, 80, and 100 kDa. Because the approximately 16-kDa protein was responsible for complex A formation, we have designated it MATF for metastasis-associated transcription factor. The GGANNNAGG motif is also found in some other promoters, suggesting that they may be similarly controlled by MATF.


2001 ◽  
Vol 21 (4) ◽  
pp. 1207-1217 ◽  
Author(s):  
Michael J. McDonald ◽  
Michael Rosbash ◽  
Patrick Emery

ABSTRACT Transcriptional regulation plays an important role inDrosophila melanogaster circadian rhythms. The period promoter has been well studied, but the timeless promoter has not been analyzed in detail. Mutagenesis of the canonical E box in the timelesspromoter reduces but does not eliminate timeless mRNA cycling or locomotor activity rhythms. This is because there are at least two other cis-acting elements close to the canonical E box, which can also be transactivated by the circadian transcription factor dCLOCK. These E-box-like sequences cooperate with the canonical E-box element to promote high-amplitude transcription, which is necessary for wild-type rhythmicity.


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