scholarly journals Core Promoter Binding by Histone-Like TAF Complexes

2005 ◽  
Vol 25 (1) ◽  
pp. 206-219 ◽  
Author(s):  
Hanshuang Shao ◽  
Merav Revach ◽  
Sandra Moshonov ◽  
Yael Tzuman ◽  
Kfir Gazit ◽  
...  
Keyword(s):  
Dna Binding ◽  
Specific Binding ◽  
Core Promoter ◽  
Binding Activity ◽  
Major Function ◽  
Dna Binding Domains ◽  
Histone Fold ◽  
Binding Domains ◽  
Dna Binding Activity ◽  
Promoter Recognition

ABSTRACT A major function of TFIID is core promoter recognition. TFIID consists of TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). Most of them contain a histone fold domain (HFD) that lacks the DNA-contacting residues of histones. Whether and how TAF HFDs contribute to core promoter DNA binding are yet unresolved. Here we examined the DNA binding activity of TAF9, TAF6, TAF4b, and TAF12, which are related to histones H3, H4, H2A, and H2B, respectively. Each of these TAFs has intrinsic DNA binding activity adjacent to or within the HFD. The DNA binding domains were mapped to evolutionarily conserved and essential regions. Remarkably, HFD-mediated interaction enhanced the DNA binding activity of each of the TAF6-TAF9 and TAF4b-TAF12 pairs and of a histone-like octamer complex composed of the four TAFs. Furthermore, HFD-mediated interaction stimulated sequence-specific binding by TAF6 and TAF9. These results suggest that TAF HFDs merge with other conserved domains for efficient and specific core promoter binding.

scholarly journals The DNA Binding Domains of P1 ParB and the Architecture of the P1 Plasmid Partition Complex

2001 ◽  
Vol 276 (15) ◽  
pp. 12385-12394 ◽  
Author(s):  
Jennifer A. Surtees ◽  
Barbara E. Funnell
Keyword(s):  
Dna Binding ◽  
Binding Activity ◽  
Integration Host Factor ◽  
Mobility Shift ◽  
Dna Binding Domains ◽  
High Affinity ◽  
Binding Domains ◽  
Dna Binding Activity ◽  
C Terminus ◽  
Gel Mobility Shift

Stable maintenance of P1 plasmids inEscherichia coliis mediated by a high affinity nucleoprotein complex called the partition complex, which consists of ParB and theE. coliintegration host factor (IHF) bound specifically to the P1parSsite. IHF strongly stimulates ParB binding toparS, and the minimal partition complex contains a single dimer of ParB. To examine the architecture of the partition complex, we have investigated the DNA binding activity of various ParB fragments. Gel mobility shift and DNase I protection assays showed that the first 141 residues of ParB are dispensable for the formation of the minimal, high affinity partition complex. A fragment missing only the last 16 amino acids of ParB bound specifically toparS, but binding was weak and was no longer stimulated by IHF. The ability of IHF to stimulate ParB binding toparScorrelated with the ability of ParB to dimerize via its C terminus. Using full and partialparSsites, we show that two regions of ParB, one in the center and the other near the C terminus of the protein, interact with distinct sequences withinparS. Based on these data, we have proposed a model of how the ParB dimer bindsparSto form the minimal partition complex.

scholarly journals On exploring effects of coevolving residues on DNA binding specificity of transcription factors

2021 ◽  
Author(s):  
Yizhao Luan ◽  
Zhi Xie
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Specificity ◽  
Binding Activity ◽  
Dna Interactions ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Activity ◽  
Dna Binding Specificity ◽  
The Stability

Transcription factors (TFs) regulate gene expression by specifically binding to DNA targets. Many factors have been revealed to influence TF-DNA binding specificity. Coevolution of residues in proteins occurs due to a common evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically analyzed TF-DNA interactions from high-throughput experiments for seven TF families, including Homeobox, HLH, bZIP_1, Ets, HMG_box, zf-C4 and Zn_clus TFs. Based on TF-DNA interactions, we detected TF subclass determining sites (TSDSs) defining the heterogeneity of DNA binding preference for each TF family. We showed that the TSDSs were more likely to be coevolving with TSDSs than with non-TSDSs, particularly for Homeobox, HLH, Ets, bZIP_1 and HMG_box TF families. Mutation of the highly coevolving residues could significantly reduce the stability of TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence of the functional importance of coevolved residues in refining transcriptional regulation and provided clues to the application of engineered DNA-binding domains and protein.

scholarly journals Crystallization of and selenomethionine phasing strategy for a SETMAR–DNA complex

2016 ◽  
Vol 72 (9) ◽  
pp. 713-719 ◽  
Author(s):  
Qiujia Chen ◽  
Millie Georgiadis
Keyword(s):  
Dna Binding ◽  
Catalytic Domain ◽  
Specific Binding ◽  
Critical Role ◽  
Binding Activity ◽  
Structural Basis ◽  
Unexpected Finding ◽  
Terminal Inverted Repeat ◽  
Dna Binding Activity ◽  
New Genes

Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of theHsmar1transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestralHsmar1terminal inverted repeat (TIR) sequence. Thus, the DNA-binding activity of SETMAR is likely to have an important biological function. To determine the structural basis for the recognition of TIR DNA by SETMAR, the design of TIR-containing oligonucleotides and SETMAR DBD variants, crystallization of DBD–DNA complexes, phasing strategies and initial phasing experiments are reported here. An unexpected finding was that oligonucleotides containing two BrdUs in place of thymidines produced better quality crystals in complex with SETMAR than their natural counterparts.

scholarly journals Secondary interaction between MDMX and p53 core domain inhibits p53 DNA binding

2016 ◽  
Vol 113 (19) ◽  
pp. E2558-E2563 ◽  
Author(s):  
Xi Wei ◽  
Shaofang Wu ◽  
Tanjing Song ◽  
Lihong Chen ◽  
Ming Gao ◽  
...  
Keyword(s):  
Dna Binding ◽  
Specific Binding ◽  
Binding Activity ◽  
Proteolytic Fragment ◽  
Core Domain ◽  
Acidic Domain ◽  
Dna Binding Activity ◽  
Ubiquitin E3 Ligase ◽  
Important Regulator ◽  
Release Assay

The MDMX oncoprotein is an important regulator of tumor suppressor p53 activity during embryonic development. Despite sequence homology to the ubiquitin E3 ligase MDM2, MDMX depletion activates p53 without significant increase in p53 level, implicating a degradation-independent mechanism. We present evidence that MDMX inhibits the sequence-specific DNA binding activity of p53. This function requires the cooperation between MDMX and CK1α, and phosphorylation of S289 on MDMX. Depletion of MDMX or CK1α increases p53 DNA binding without stabilization of p53. A proteolytic fragment release assay revealed that in the MDMX–p53 complex, the MDMX acidic domain and RING domain interact stably with the p53 DNA binding domain. These interactions are referred to as secondary interactions because they only occur after the canonical-specific binding between the MDMX and p53 N termini, but exhibit significant binding stability in the mature complex. CK1α cooperates with MDMX to inhibit p53 DNA binding by further stabilizing the MDMX acidic domain and p53 core domain interaction. These results suggest that secondary intermolecular interaction is important in p53 regulation by MDMX, which may represent a common phenomenon in complexes containing multidomain proteins.

scholarly journals RNA polymerase II transcription factors H4TF-1 and H4TF-2 require metal to bind specific DNA sequences.

1987 ◽  
Vol 7 (12) ◽  
pp. 4582-4584 ◽  
Author(s):  
L Dailey ◽  
S B Roberts ◽  
N Heintz
Keyword(s):  
Dna Binding ◽  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Chelating Agents ◽  
In Vitro Transcription ◽  
Binding Activity ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Rna Polymerase Ii Transcription

Specific DNA-binding and in vitro transcription activities of H4TF-1 and H4TF-2 are inactivated by chelating agents. Binding activity is restored by addition of Zn2+, and H4TF-2 is also reactivated by Fe2+. In contrast, preformed factor-DNA complexes are resistant to chelators. Therefore, metal ions are a required component of the H4TF-1 and H4TF-2 DNA-binding domains.

scholarly journals Regulation of the DNA-binding and transcriptional activities of Xenopus laevis NFI-X by a novel C-terminal domain.

1995 ◽  
Vol 15 (10) ◽  
pp. 5552-5562 ◽  
Author(s):  
E Roulet ◽  
M T Armentero ◽  
G Krey ◽  
B Corthésy ◽  
C Dreyer ◽  
...  
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Xenopus Laevis ◽  
Transcriptional Activation ◽  
Binding Activity ◽  
New Members ◽  
Binding Domains ◽  
Dna Binding Activity

The nuclear factor I (NFI) family consists of sequence-specific DNA-binding proteins that activate both transcription and adenovirus DNA replication. We have characterized three new members of the NFI family that belong to the Xenopus laevis NFI-X subtype and differ in their C-termini. We show that these polypeptides can activate transcription in HeLa and Drosophila Schneider line 2 cells, using an activation domain that is subdivided into adjacent variable and subtype-specific domains each having independent activation properties in chimeric proteins. Together, these two domains constitute the full NFI-X transactivation potential. In addition, we find that the X. laevis NFI-X proteins are capable of activating adenovirus DNA replication through their conserved N-terminal DNA-binding domains. Surprisingly, their in vitro DNA-binding activities are specifically inhibited by a novel repressor domain contained within the C-terminal part, while the dimerization and replication functions per se are not affected. However, inhibition of DNA-binding activity in vitro is relieved within the cell, as transcriptional activation occurs irrespective of the presence of the repressor domain. Moreover, the region comprising the repressor domain participates in transactivation. Mechanisms that may allow the relief of DNA-binding inhibition in vivo and trigger transcriptional activation are discussed.

scholarly journals Specific Binding of Integrase to the Origin of Transfer (oriT) of the Conjugative Transposon Tn916

2001 ◽  
Vol 183 (9) ◽  
pp. 2947-2951 ◽  
Author(s):  
Douglas Hinerfeld ◽  
Gordon Churchward
Keyword(s):  
Dna Binding ◽  
Specific Binding ◽  
Binding Domain ◽  
Conjugal Transfer ◽  
Dna Binding Domain ◽  
Conjugative Transposon ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
A Site ◽  
Integrase Protein

ABSTRACT Purified integrase protein (Int) of the conjugative transposon Tn916 was shown, using nuclease protection experiments, to bind specifically to a site within the origin of conjugal transfer of the transposon, oriT. A sequence similar to the ends of the transposon that are bound by the C-terminal DNA-binding domain of Int was present in the protected region. However, Int binding tooriT required both the N- and C-terminal DNA-binding domains of Int, and the pattern of nuclease protection differed from that observed when Int binds to the transposon ends and flanking DNA. Binding of Int to oriT may be part of a mechanism to prevent premature conjugal transfer of Tn916 prior to excision from the donor DNA.

scholarly journals Inhibition of DNA Binding by Differential Sumoylation of Heat Shock Factors

2006 ◽  
Vol 26 (3) ◽  
pp. 955-964 ◽  
Author(s):  
Julius Anckar ◽  
Ville Hietakangas ◽  
Konstantin Denessiouk ◽  
Dennis J. Thiele ◽  
Mark S. Johnson ◽  
...  
Keyword(s):  
Heat Shock ◽  
Dna Binding ◽  
Regulation Of Gene Expression ◽  
Binding Activity ◽  
Covalent Modification ◽  
Heat Shock Factors ◽  
Substrate Selection ◽  
Binding Domains ◽  
Dna Binding Activity ◽  
Specific Regulation

ABSTRACT Covalent modification of proteins by the small ubiquitin-related modifier SUMO regulates diverse biological functions. Sumoylation usually requires a consensus tetrapeptide, through which the binding of the SUMO-conjugating enzyme Ubc9 to the target protein is directed. However, additional specificity determinants are in many cases required. To gain insights into SUMO substrate selection, we have utilized the differential sumoylation of highly similar loop structures within the DNA-binding domains of heat shock transcription factor 1 (HSF1) and HSF2. Site-specific mutagenesis in combination with molecular modeling revealed that the sumoylation specificity is determined by several amino acids near the consensus site, which are likely to present the SUMO consensus motif to Ubc9. Importantly, we also demonstrate that sumoylation of the HSF2 loop impedes HSF2 DNA-binding activity, without affecting its oligomerization. Hence, SUMO modification of the HSF2 loop contributes to HSF-specific regulation of DNA binding and broadens the concept of sumoylation in the negative regulation of gene expression.

scholarly journals Dependence on androgens of the specific DNA-binding activity of rat ventral-prostate non-histone chromosomal proteins

1981 ◽  
Vol 194 (1) ◽  
pp. 91-98
Author(s):  
B H Lesser ◽  
N L Elliot
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Specific Binding ◽  
Binding Activity ◽  
Male Rats ◽  
Ventral Prostate ◽  
Trace Quantity ◽  
Chromosomal Proteins ◽  
Dna Binding Activity ◽  
Rat Prostate

Interactions between rat prostate non-histone chromosomal proteins and DNA were studied by using a nitrocellulose-filter-binding technique to monitor the formation of DNA–protein complexes. The total binding activity of the non-histones, as measured by binding of proteins to a trace quantity of labelled DNA, displays no preference for rat DNA relative to Escherichia coli DNA. Sequestration of non-specific binding proteins by preincubation with unlabelled bacterial DNA enables detection of a fraction of rat prostate non-histones that binds preferentially to labelled rat DNA relative to labelled E. coli DNA. After castration of adult male rats, both total and specific binding activities decrease. Administration of 5 alpha-dihydrotestosterone to castrated rats stimulates both total and specific DNA-binding activities of prostate non-histones; specific binding is stimulated to a greater extent than total DNA, indicating that the specific binding proteins constitute a larger fraction of the non-histone proteins in the presence of androgens. The specific DNa-binding activity is dependent on the dose of steroid administered.

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