Alternative Splicing of Wilms' Tumor Suppressor Protein Modulates DNA Binding Activity through Isoform-Specific DNA-Induced Conformational Changes†

Biochemistry ◽  
2000 ◽  
Vol 39 (18) ◽  
pp. 5341-5348 ◽  
Author(s):  
John H. Laity ◽  
John Chung ◽  
H. Jane Dyson ◽  
Peter E. Wright
Keyword(s):  
Alternative Splicing ◽  
Tumor Suppressor ◽  
Dna Binding ◽  
Conformational Changes ◽  
Wilms Tumor ◽  
Binding Activity ◽  
Tumor Suppressor Protein ◽  
Dna Binding Activity

Effects of Denys−Drash Syndrome Point Mutations on the DNA Binding Activity of the Wilms' Tumor Suppressor Protein WT1†

Biochemistry ◽  
1996 ◽  
Vol 35 (37) ◽  
pp. 12070-12076 ◽  
Author(s):  
Franck Borel ◽  
Kathleen C. Barilla ◽  
Tatyana B. Hamilton ◽  
May Iskandar ◽  
Paul J. Romaniuk
Keyword(s):  
Tumor Suppressor ◽  
Dna Binding ◽  
Wilms Tumor ◽  
Point Mutations ◽  
Binding Activity ◽  
Tumor Suppressor Protein ◽  
Dna Binding Activity ◽  
Drash Syndrome

scholarly journals Structure of the p53/RNA polymerase II assembly

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shu-Hao Liou ◽  
Sameer K. Singh ◽  
Robert H. Singer ◽  
Robert A. Coleman ◽  
Wei-Li Liu
Keyword(s):  
Dna Binding ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Conformational Changes ◽  
P53 Protein ◽  
Binding Activity ◽  
Transactivation Domain ◽  
Pol Ii ◽  
Dna Binding Activity ◽  
Regulated Gene Expression

AbstractThe tumor suppressor p53 protein activates expression of a vast gene network in response to stress stimuli for cellular integrity. The molecular mechanism underlying how p53 targets RNA polymerase II (Pol II) to regulate transcription remains unclear. To elucidate the p53/Pol II interaction, we have determined a 4.6 Å resolution structure of the human p53/Pol II assembly via single particle cryo-electron microscopy. Our structure reveals that p53’s DNA binding domain targets the upstream DNA binding site within Pol II. This association introduces conformational changes of the Pol II clamp into a further-closed state. A cavity was identified between p53 and Pol II that could possibly host DNA. The transactivation domain of p53 binds the surface of Pol II’s jaw that contacts downstream DNA. These findings suggest that p53’s functional domains directly regulate DNA binding activity of Pol II to mediate transcription, thereby providing insights into p53-regulated gene expression.

The complex interactions of p53 with target DNA: we learn as we go

2003 ◽  
Vol 81 (3) ◽  
pp. 141-150 ◽  
Author(s):  
Ella Kim ◽  
Wolfgang Deppert
Keyword(s):  
Tumor Suppressor ◽  
Dna Binding ◽  
Target Genes ◽  
Dna Structure ◽  
Structural Features ◽  
Binding Activity ◽  
Tumor Suppressor P53 ◽  
Dna Binding Activity ◽  
Complex Interactions ◽  
Target Dna

The most import biological function of the tumor suppressor p53 is that of a sequence-specific transactivator. In response to a variety of cellular stress stimuli, p53 induces the transcription of an ever-increasing number of target genes, leading to growth arrest and repair, or to apoptosis. Long considered as a "latent" DNA binder that requires prior activation by C-terminal modification, recent data provide strong evidence that the DNA binding activity of p53 is strongly dependent on structural features within the target DNA and is latent only if the target DNA lacks a certain structural signal code. In this review we discuss evidence for complex interactions of p53 with DNA, which are strongly dependent on the dynamics of DNA structure, especially in the context of chromatin. We provide a model of how this complexity may serve to achieve selectivity of target gene regulation by p53 and how DNA structure in the context of chromatin may serve to modulate p53 functions.Key words: tumor suppressor p53, sequence-specific DNA binding, DNA conformation, chromatin, chromatin remodeling.

Conformational changes in bacteriophage Ø 29 connector prevents DNA-binding activity

1990 ◽  
Vol 213 (2) ◽  
pp. 263-273 ◽  
Author(s):  
Lucía Herranz ◽  
Joan Bordas ◽  
Elisabeth Towns-Andrews ◽  
Enrique Mendez ◽  
Pilar Usobiaga ◽  
...  
Keyword(s):  
Dna Binding ◽  
Conformational Changes ◽  
Binding Activity ◽  
O 29 ◽  
Dna Binding Activity

scholarly journals Diverse Flavonoids Stimulate NodD1 Binding to nod Gene Promoters in Sinorhizobium meliloti

2006 ◽  
Vol 188 (15) ◽  
pp. 5417-5427 ◽  
Author(s):  
Melicent C. Peck ◽  
Robert F. Fisher ◽  
Sharon R. Long
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Host Specificity ◽  
Conformational Changes ◽  
Sinorhizobium Meliloti ◽  
Binding Activity ◽  
Gene Promoters ◽  
Dna Binding Activity ◽  
Competition Assays

ABSTRACT NodD1 is a member of the NodD family of LysR-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacterium Sinorhizobium meliloti. Each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. This host specificity results in part from a NodD-dependent upregulation of nod genes in response to a cocktail of flavonoids in the host plant's root exudates. To demonstrate that NodD is a key determinant of host specificity, we expressed nodD genes from different species of rhizobia in a strain of S. meliloti lacking endogenous NodD activity. We observed that nod gene expression was initiated in response to distinct sets of flavonoid inducers depending on the source of NodD. To better understand the effects of flavonoids on NodD, we assayed the DNA binding activity of S. meliloti NodD1 treated with the flavonoid inducer luteolin. In the presence of luteolin, NodD1 exhibited increased binding to nod gene promoters compared to binding in the absence of luteolin. Surprisingly, although they do not stimulate nod gene expression in S. meliloti, the flavonoids naringenin, eriodictyol, and daidzein also stimulated an increase in the DNA binding affinity of NodD1 to nod gene promoters. In vivo competition assays demonstrate that noninducing flavonoids act as competitive inhibitors of luteolin, suggesting that both inducing and noninducing flavonoids are able to directly bind to NodD1 and mediate conformational changes at nod gene promoters but that only luteolin is capable of promoting the downstream changes necessary for nod gene induction.

Nuclear accumulation of the E2F heterodimer regulated by subunit composition and alternative splicing of a nuclear localization signal

1996 ◽  
Vol 109 (10) ◽  
pp. 2443-2452 ◽  
Author(s):  
S. de la Luna ◽  
M.J. Burden ◽  
C.W. Lee ◽  
N.B. La Thangue
Keyword(s):  
Cell Cycle ◽  
Transcription Factor ◽  
Alternative Splicing ◽  
Dna Binding ◽  
Nuclear Localization ◽  
Nuclear Localization Signal ◽  
Binding Activity ◽  
Nuclear Accumulation ◽  
Dna Binding Activity ◽  
Localization Signal

The cellular transcription factor E2F plays a critical role in integrating cell cycle progression with the transcription apparatus by virtue of a physical interaction and control by key regulators of the cell cycle, such as pRb, cyclins and cyclin-dependent kinases. Generic E2F DNA binding activity arises when a member of two families of proteins, E2F and DP, form heterodimeric complexes, an interaction which results in co-operative transcriptional and DNA binding activity. Here, we characterise a new and hitherto unexpected mechanism of control influencing the activity of E2F which is mediated at the level of intracellular location through a dependence on heterodimer formation for nuclear translocation. Nuclear accumulation is dramatically influenced by two distinct processes: alternative splicing of a nuclear localization signal and subunit composition of the E2F heterodimer. These data define a new level of control in the E2F transcription factor whereby interplay between subunits dictates the levels of nuclear DNA binding activity.

scholarly journals Functional interaction between DP-1 and p53.

1996 ◽  
Vol 16 (10) ◽  
pp. 5888-5895 ◽  
Author(s):  
T S Sørensen ◽  
R Girling ◽  
C W Lee ◽  
J Gannon ◽  
L R Bandara ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Tumor Suppressor ◽  
Dna Binding ◽  
Cellular Proliferation ◽  
Binding Activity ◽  
Terminal Region ◽  
Alternative Mechanism ◽  
Chromosomal Dna ◽  
Dna Binding Activity ◽  
Cell Extracts

The cellular transcription factor DRTF1/E2F and the tumor suppressor protein p53 play important roles in controlling early cell cycle events. DRTF1/E2F is believed to coordinate and integrate the transcription of cell cycle-regulating genes, for example, those involved in DNA synthesis, with the activity of regulatory proteins, such as the retinoblastoma tumor suppressor gene product (pRb), which modulate its transcriptional activity. In contrast, p53 is thought to monitor the integrity of chromosomal DNA and when appropriate interfere with cell cycle progression, for example, in response to DNA damage. Generic DRTF1/E2F DNA binding activity and transcriptional activation arise when members of two distinct families of proteins, such as DP-1 and E2F-1, interact as DP/E2F heterodimers. In many cell types, DP-1 is a widespread component of DRTF1/E2F DNA binding activity which when expressed at high levels oncogenically transforms embryonic fibroblasts. Here, we document an association between DP-1 and p53 and demonstrate its presence in mammalian cell extracts. In vitro p53 interacts with an immunochemically distinct form of DP-1 and in vivo can regulate transcription driven by the DP-1/E2F-1 heterodimer. At the biochemical level, p53 competes with E2F-1 for DP-1, with a consequent reduction in DNA binding activity. Mutational analysis defines within DP-1 a C-terminal region required for the interaction with p53 and within p53 an N-terminal region distinct from that required to bind to MDM2. Our results establish DRTF1/E2F as a common cellular target in growth control mediated through the activities of pRb and p53 and suggest an alternative mechanism through which p53 may regulate cellular proliferation.

scholarly journals p53 regulates cyclophosphamide teratogenesis by controlling caspases 3, 8, 9 activation and NF-κB DNA binding

Reproduction ◽  
2007 ◽  
Vol 134 (2) ◽  
pp. 379-388 ◽  
Author(s):  
Olga Pekar ◽  
Nataly Molotski ◽  
Shoshana Savion ◽  
Amos Fein ◽  
Vladimir Toder ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Dna Binding ◽  
Molecular Mechanisms ◽  
Binding Activity ◽  
Tumor Suppressor Protein ◽  
Dna Binding Activity ◽  
Organ Level ◽  
Induced Apoptosis ◽  
The Brain ◽  
Transcription Factor Nuclear Factor

The tumor suppressor protein p53 regulates the sensitivity of embryos to such human teratogens as ionizing radiation, diabetes, and cytostatics. Yet, the molecular mechanisms whereby it fulfills this function remain undefined. We used p53 heterozygous (p53+/−) female mice mated with p53+/− males and then exposed to cyclophosphamide (CP) to test whether caspases 3, 8, and 9 and the transcription factor nuclear factor (NF)-κB may serve as p53 targets. Mice were exposed to CP on day 12 of pregnancy and killed on days 15 and 18 of pregnancy to evaluate CP-induced teratogenic effect. The brain and limbs of embryos harvested 24 h after CP treatment were used to evaluate NF-κB (p65) DNA-binding activity by an ELISA-based method, the activity of the caspases by appropriate colorimetric kits, apoptosis, and cell proliferation by TUNEL, and 5′-bromo-2′-deoxyuridine incorporation respectively. We observed that the activation of caspases 3, 8, and 9 and the suppression of NF-κB DNA binding following CP-induced teratogenic insult took place only in teratologically sensitive organs of p53+/+ but not p53−/− embryos. CP-induced apoptosis and suppression of cell proliferation were also more intensive in the former, and they exhibited a higher incidence of structural anomalies, such as open eyes, digit, limb, and tail anomalies. The analysis of the correlations between the p53 embryonic genotype, the activity of the tested molecules, and the CP-induced dysmorphic events at the cellular and organ level suggests caspases 3, 8, and 9 and NF-κB as components of p53-targeting mechanisms in embryos exposed to the teratogen.

scholarly journals Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR

2013 ◽  
Vol 42 (4) ◽  
pp. 2774-2788 ◽  
Author(s):  
Ivan Birukou ◽  
Susan M. Seo ◽  
Bryan D. Schindler ◽  
Glenn W. Kaatz ◽  
Richard G. Brennan
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Conformational Changes ◽  
Efflux Pump ◽  
Binding Activity ◽  
Multidrug Efflux ◽  
Multidrug Efflux Pump ◽  
Structural Mechanism ◽  
Dna Binding Activity ◽  
Complex Structural

Abstract The multidrug efflux pump MepA is a major contributor to multidrug resistance in Staphylococcus aureus. MepR, a member of the multiple antibiotic resistance regulator (MarR) family, represses mepA and its own gene. Here, we report the structure of a MepR–mepR operator complex. Structural comparison of DNA-bound MepR with ‘induced’ apoMepR reveals the large conformational changes needed to allow the DNA-binding winged helix-turn-helix motifs to interact with the consecutive major and minor grooves of the GTTAG signature sequence. Intriguingly, MepR makes no hydrogen bonds to major groove nucleobases. Rather, recognition-helix residues Thr60, Gly61, Pro62 and Thr63 make sequence-specifying van der Waals contacts with the TTAG bases. Removing these contacts dramatically affects MepR–DNA binding activity. The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp85, interacts with the O2 of T4 and O4′ ribosyl oxygens of A23 and T4. Mutating Asp85 and Arg87, both conserved throughout the MarR family, markedly affects MepR repressor activity. The His14′:Arg59 and Arg10′:His35:Phe108 interaction networks stabilize the DNA-binding conformation of MepR thereby contributing significantly to its high affinity binding. A structure-guided model of the MepR–mepA operator complex suggests that MepR dimers do not interact directly and cooperative binding is likely achieved by DNA-mediated allosteric effects.

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