Specific DNA Recognition Site Research Articles

Macromolecular Hydration Changes Associated with BamHI Binding and Catalysis

In this report, the effects of osmotic pressure on BamHI cognate binding and catalysis were investigated and compared with a previous study on EcoRI (Robinson, C. R. and Sligar, S. G. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 2186-2191). Our observation of the dependence of binding and catalytic parameters on osmotic pressure has allowed for the comparison of hydration changes associated with site-specific DNA recognition for both endonucleases. Over a large range of osmotic pressures (pi), the dependence of BamHI on osmotic stress during cognate binding and catalysis was very different from that of the related endonuclease EcoRI. The binding of EcoRI to cognate DNA was dominated by a dehydration of the endonuclease-DNA complex, whereas binding by BamHI to its cognate sequence was accompanied by a solvent release corresponding to some 125 fewer waters. Catalytic analysis at elevated osmotic pressures indicated that both endonucleases had undergone a net hydration of the complex with BamHI displaying a much greater dependence on osmotic stress than EcoRI. Although the enzymes shared core structural motifs, comparisons of high resolution x-ray structures revealed many different secondary structural features of the complexed endonucleases. The large difference in hydration changes by both BamHI and EcoRI could be attributed to these dissimilar secondary structural features, as well as the functional differences of the two endonucleases during site-specific DNA recognition.

Molecular Dynamics Simulation in Solvent of the Bacteriophage 434 cI Repressor Protein DNA Binding Domain Amino Acids (R1–69) in Complex with its Cognate Operator (OR1) DNA Sequence

We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of the 434 cl Repressor protein DNA binding domain (DBD) amino acids (R1–69) and DNA of operator (OR1) and its flanks consisting of 28 nucleotide base pairs. Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic interaction energies were calculated. Amino acids of the 434 cl repressor DNA recognition helix 3 formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the ORl DNA major groove halfsites and flanking regions. In addition, hydrophilic amino acids within the loop between helix 3 and helix 4 have strong electrostatic attraction to codon-anticodon nucleotides located within the central nucleotides of the minor groove between the ORI major groove halfsites These interactions together induced significant structural changes in the operator DNA manifested by overtwisting of the central nucleotide base pairs and narrowing of the minor groove between the DNA major groove halfsites. Finally, these findings offer a code for site specific DNA recognition by the 434 cl repressor protein.

Two Distinct Isoforms of cDNA Encoding Rainbow Trout Androgen Receptors

Androgens play an important role in male sexual differentiation and development. The activity of androgens is mediated by an androgen receptor (AR), which binds to specific DNA recognition sites and regulates transcription. We describe here the isolation of two distinct rainbow trout cDNA clones, designated rtAR-alpha and rtAR-beta, which contain the entire androgen receptor coding region. Comparison of the predicted amino acid sequence of rtAR-alpha to that of rtAR-beta revealed 85% identity. Interestingly, despite this high homology, rtAR-alpha activated transcription of an androgen-responsive reporter gene in co-transfection assays, but rtAR-beta did not. These results suggest that rainbow trout contains two distinct isoforms of androgen receptors whose functions differ. The region of rtAR-beta responsible for its inactivity was mapped to its ligand binding domain by analyzing chimeras of the rtAR-alpha, rtAR-beta, and rtGR-I (glucocorticoid) receptors. Alteration of any one of three out of four segments within this domain restored activity. Extracts made from COS-1 cells transfected with an rtAR-alpha expression plasmid produced a high level of [3H]mibolerone binding, whereas no binding was observed by extracts of cells transfected with an rtAR-beta expression plasmid. These data demonstrate that the lack of transactivation activity of rtAR-beta is due to its inability to bind hormone.

Induction of cytochrome P4501A1 by ozone-oxidized tryptophan in Hepa lclc7 cells.

The present investigation was undertaken to determine whether administration of O3-oxidized amino acids to mouse hepatoma cells, Hepa lclc7 (Hepa-1), in culture would effect Cyp1a1 gene expression. The results demonstrate that, of all the amino acids tested, only O3-oxidized tryptophan caused a significant induction of CYP1A1-dependent 7-ethoxyresorufin O-deethylase (EROD) activity compared to the controls (p < 0.01). CYP1A1 mRNA and protein were markedly induced in the O3-oxidized tryptophan administered group compared to the controls. Gel mobility shift assays using nuclear extracts of Hepa-1 cells revealed that oxidized products of tryptophan can induce both aryl hydrocarbon receptor (AhR) transformation and binding of the liganded AhR complex to its specific DNA recognition site, thereby initiating transcription of the Cyp1a1 gene with concomitant increase of CYP1A1 protein and EROD activity in Hepa-1 cells.

Mechanistic studies on the DNA linking activity of Epstein-Barr nuclear antigen 1.

The DNA replication, plasmid segregation and transactivation functions of Epstein-Barr nuclear antigen 1 (EBNA1) require the binding of EBNA1 to specific DNA recognition sites in the two non-contiguous functional elements of the Epstein-Barr virus latent origin of replication, oriP . EBNA1 molecules bound to these elements interact with each other resulting in the formation of looped individual DNA molecules and multiply linked DNA molecules. We have developed a glycerol gradient sedimentation assay suitable for quantitative analysis of the DNA linking activity of EBNA1 and used it to investigate the contribution of EBNA1 residues to the linking interaction and the mechanism of the interaction. Using overlapping internal deletion mutants, we found that two regions of EBNA1 can cause DNA linking, amino acids 40-100 and 327-377, but that the stabilities of the linked complexes formed by the two regions differ dramatically; only complexes formed through the latter region are stable to glycerol gradient sedimentation analysis. Mechanistic studies using EBNA1 in combination with GAL4-EBNA1 fusion proteins showed that linking interactions mediated by residues 327-377 are homotypic. Our results also suggest that only the DNA-bound form of EBNA1 participates in the protein-protein interactions seen in DNA linking.

Effects of estradiol and progesterone on cytochrome P4501A1 expression in Hepa 1c1c7 cells.

The effects of estradiol and progesterone on the expression of cytochrome P4501A1 were investigated in Hepa 1c1c7 cells. Both steroids, at 10 microM concentration, increased P4501A1-mediated 7-ethoxyresorufin O-deethyalase activity and amounts of its immunoreactive protein and CYP1A1 mRNA. Gel shift assay revealed that the steroids could induce both AhR transformation and binding of the ligand-AhR complex to its specific DNA recognition site. Transient transfection demonstrated that 5'flanking region of CYP1A1 could respond to the steroid action. The competitive binding assay showed that the steroids bound to AhR with moderate affinity. These results suggested that steroidal structure can be AhR ligands and induce CYP1A1 expression in AhR-dependent manner.

A basic motif in the N-terminal region of RAG1 enhances V(D)J recombination activity.

The variable portions of antigen receptor genes are assembled from component gene segments by a site-specific recombination reaction known as V(D)J recombination. The RAG1 and RAG2 proteins are the critical lymphoid cell-specific components of the recombination enzymatic machinery and are responsible for site-specific DNA recognition and cleavage. Previous studies had defined a minimal, recombinationally active core region of murine RAG1 consisting of amino acids 384 to 1008 of the 1,040-residue RAG1 protein. No recombination function has heretofore been ascribed to any portion of the 383-amino-acid N-terminal region that is missing from the core, but it seems likely to be of functional significance, based on its evolutionary conservation. Using extrachromosomal recombination substrates, we demonstrate here that the N-terminal region enhances the recombination activity of RAG1 by up to an order of magnitude in a variety of cell lines. Deletion analysis localized a region of the N terminus critical for this effect to amino acids 216 to 238, and further mutagenesis demonstrated that a small basic amino acid motif (BIIa) in this region is essential for enhancing the activity of RAG1. Despite the fact that BIIa is important for the interaction of RAG1 with the nuclear localization factor Srp-1, it does not appear to enhance recombination by facilitating nuclear transport of RAG1. A variety of models for how this region stimulates the recombination activity of RAG1 are considered.

POU Domain Factors of the Brn-3 Class Recognize Functional DNA Elements Which Are Distinctive, Symmetrical, and Highly Conserved in Evolution

To better understand the diversity of function within the POU domain class of transcriptional regulators, we have determined the optimal DNA recognition site of several proteins of the POU-IV (Brn-3) subclass by random oligonucleotide selection. The consensus recognition element derived in this study, ATAATTAAT, is clearly distinct from octamer sites described for the POU factor Oct-1. The optimal POU-IV site determined here also binds Brn-3.0 with significantly higher affinity than consensus recognition sites previously proposed for this POU subclass. The binding affinity of Brn-3.0 on its optimal site, several variants of this site, and several naturally occurring POU recognition elements is highly correlated with the activation of reporter gene expression by Brn-3.0 in transfection assays. The preferred DNA recognition site of Brn-3.0 resembles strongly the optimal sites of another mammalian POU-IV class protein, Brn-3.2, and of the Caenorhabditis elegans Brn-3.0 homolog Unc-86, demonstrating that the site-specific DNA recognition properties of these factors are highly conserved between widely divergent species.

Induction of cytochrome P4501A1 by photooxidized tryptophan in Hepa lclc7 cells

Mouse hepatoma Hepa-lclc? (Hepa-1) cells were cultivated in the presence of UV-irradiated amino acids. The results demonstrated that all of the amino acids tested, UV-oxidized tryptophan caused the highest induction of 7-ethoxyresorufin O-deethylase (EROD) activity compared with the controls (P < 0.01). The induction of EROD activity by oxidized tryptophan was dose dependent, and maximal induction was obtained at 12 hr after administration. Studies with various Hepa-1 mutants, which are defective in either the aryl hydrocarbon (Ah) receptor or Ah receptor nuclear translocator protein, indicated that the induction of EROD activity by oxidized tryptophan occurs through the Ah receptor. Gel mobility shift assays using nuclear extracts of Hepa-1 cells revealed that oxidized products of tryptophan can induce both Ah receptor transformation and binding of the liganded Ah receptor complex to its specific DNA recognition site. CYP1A1 mRNA, quantified by reverse transcription-polymerase chain reaction, and CYP1A1 protein were induced markedly in the oxidized tryptophan group compared with the controls. Injection of isolated oxidized tryptophan products into adult male rats caused significant induction of EROD activity in the pulmonary and hepatic microsomes compared with the controls (P < 0.01). These results demonstrated that oxidized tryptophan induces Ah receptor activation and binding of the liganded Ah receptor complex to its specific DNA recognition site, thereby initiating transcription and translation of the CYP1A1 gene with concomitant increase of EROD activity in Hepa-1 cells. Induction of EROD activity in the liver and lungs after injection of isolated oxidized tryptophan products into rats suggests that a similar mechanism may be operative in vivo.

A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis.

Two DNA binding proteins, Cro and the amino-terminal domain of the repressor of bacteriophage 434 (434 Cro and 434 repressor) that regulate gene expression and contain a helix-turn-helix (HTH) motif responsible for their site-specific DNA recognition adopt very similar three-dimensional structures when compared to each other. To reveal structural differences between these two similar proteins, their dynamic structures, as examined by normal mode analysis, are compared in this paper. Two kinds of structural data, one for the monomer and the other for a complex with DNA, for each protein, are used in the analyses. From a comparison between the monomers it is found that the interactions of Ala-24 in 434 Cro or Val-24 in 434 repressor, both located in the HTH motif, with residues 44, 47, 48, and 51 located in the domain facing the motif, and the interactions between residues 17, 18, 28, and 32, located in the HTH motif, cause significant differences in the correlative motions of these residues. From the comparison between the monomer and the complex with DNA for each protein, it was found that the first helix in the HTH motif is distorted in the complex form. While the residues in the HTH motif in 434 Cro have relatively larger positive correlation coefficients of motions with other residues within the HTH motif, such correlations are not large in the HTH motif of 434 repressor. It is suggestive to their specificity because the 434 repressor is less specific than 434 Cro. Although a structural comparison of proteins has been performed mainly from a static or geometrical point of view, this study demonstrates that the comparison from a dynamic point of view, using the normal mode analysis, is useful and convenient to explore a difference that is difficult to find only from a geometrical point of view, especially for proteins very similar in structure.

Recognition of DNA by octahedral coordination complexes

Strategies for the site-specific recognition of DNA are described through the design of a family of octahedral metallointercalating complexes. Coordination complexes, which mimic DNA-binding proteins with regard to their affinity and specificity for DNA sites, may be prepared by the specific functionalization of chiral metal complexes so as to achieve the ensemble of non-covalent contacts in the DNA major groove anchored through intercalation.

Solution Structure of the Head-to-Head Dimer of Calicheamicin Oligosaccharide Domain and d(CGTAGGATATCCTACG)2

The head-to-head dimer of the calicheamicin oligosaccharide domain exhibits an impressive nanomolar affinity for its specific DNA recognition sites and a substantially higher degree of sequence selectivity relative to the oligosaccharide monomer. In an effort to determine the structural basis for these binding properties, the solution structure of the 1:1 complex between the head-to-head dimer and the self-complementary oligonucleotide d(CGTAGGATATCCTACG) 2 has been solved using 1 H NMR-derived distance and torsion angle constraints and molecular dynamics calculations. Complete sequence specific proton assignments of both the DNA duplex and the carbohydrate have been obtained by 2D-NMR. A total of 607 experimentally derived constraints were identified including 452 proton-proton distance constraints derived from NOESY cross peaks intensities and assigned hydrogen bonds, along with 155 dihedral angle constraints obtained from a detailed analysis of the multiplet structure of cross-peaks for the sugar rings and from qualitative analysis of nuclear Overhauser effects for the DNA backbone. The final conformation of the complex is represented by an ensemble of seven structures (the average all-atom root mean square deviation from the mean is 1.07 A in the well-defined region) obtained by refining 14 initial conformations with widely different nonstandard DNA geometries. A number of favorable interactions are found to stabilize the structure of the complex and account for binding sequence preferences. Overall, the binding mode of each oligosaccharide unit of the head-to-head dimer in the DNA minor groove seems to be very close to that observed in the case of the monomeric calicheamicin oligosaccharide bound to its corresponding TCCT recognition site. Variable temperature NMR studies have shown that this dimer binds to d(CGTAGGATATCCTACG) 2 in two subtly different conformations, probably differing in the positioning of rings E and E', interconverting with a rate constant of0.35 s -1 . The solution structure of this carbohydrate-DNA complex provides confirmation of design principles for new calicheamicin-based DNA-binding agents and confirms insights obtained previously into the molecular basis for oligosaccharide recognition within the DNA minor groove.

A new approach to enhancing the efficiency and specificity of interaction in duplexes by the use of tandem structure

Abstract

DNA Binding of the Transformed Guinea Pig Hepatic Ah Receptor Complex: Identification and Partial Characterization of 2 High-Affinity DNA-Binding Forms

We have examined and characterized the binding of transformed guinea pig hepatic Ah receptor to its specific DNA recognition site, the dioxin-responsive element (DRE), using gel retardation analysis. Saturation binding analysis of transformed TCDD:AhR complexes were indicative of a single high-affinity binding site (Kd = 2.5 ± 0.8 nM); however, DNA-binding analysis revealed the presence of two distinct TCDD-inducible protein-DRE complexes. Sucrose gradient centrifugation and subsequent gel retardation analysis of the fractions demonstrated a similarity in the distribution of [3H]TCDD-specific binding and TCDD-inducible protein-DNA complex formation, supporting the presence of the AhR in both complexes. In addition, the formation of both DNA-binding complexes exhibited the same nucleotide specificity previously determined for the AhR complex. Since labeling studies using a radioiodinated photoaffinity dioxin agonist demonstrated that guinea pig cytosol contains a single ligand binding subunit of 105 kDa, the difference in migration of the complexes is due to other proteins associated with each complex. Overall, our results demonstrate the presence of two distinct high affinity DNA-binding forms of transformed guinea pig AhR complex which exhibit similar DNA-binding affinity and nucleotide specificity

Getting a grip on DNA recognition: structures of the basic region leucine zipper, and the basic region helix-loop-helix DNA-binding domains

The basic region leucine zipper and basic region helix-loop-helix proteins constitute two large families of eukaryotic transcription factors. Recent crystal structures of basic region leucine zipper-DNA and basic region helix-loop-helix-DNA complexes provide the details of these protein-DNA interactions and offer insights into the details of the site-specific recognition of DNA.

Conservation of genetic information: a code for site-specific DNA recognition.

We present findings of genetic information conservation between the glucocorticoid response element (GRE) DNA and the cDNA encoding the glucocorticoid receptor (GR) DNA-binding domain (DBD). The regions of nucleotide sub-sequence similarity to the GRE in the GR DBD occur specifically at nucleotide sequences on the ends of exons 3,4, and 5 at their splice junction sites. These sequences encode the DNA recognition helix on exon 3, a beta-strand on exon 4, and a putative alpha-helix on exon 5, respectively. The nucleotide sequence of exon 5 that encodes the putative alpha-helix located on the carboxyl terminus of the GR DBD shares sequence similarity with the flanking nucleotide regions of the GRE. We generated a computer model of the GR DBD using atomic coordinates derived from nuclear magnetic resonance spectroscopy to which we attached the exon 5-encoded putative alpha-helix. We docked this GR DBD structure at the 39-base-pair nucleotide sequence containing the GRE binding site and flanking nucleotides, which contained conserved genetic information. We observed that amino acids of the DNA recognition helix, the beta-strand, and the putative alpha-helix are spatially aligned with trinucleotides identical to their cognate codons within the GRE and its flanking nucleotides.

Defining a minimal estrogen receptor DNA binding domain.

The estrogen receptor (ER) is a transcriptional regulator which binds to cognate palindromic DNA sequences known as estrogen response elements (EREs). A 66 amino acid core region which contains two zinc fingers and is highly conserved among the nuclear receptors is essential for site specific DNA recognition. However, it remains unclear how many flanking amino acids in addition to the zinc finger core are required for DNA binding. Here, we have characterized the minimal DNA binding region of the human ER by analysing the DNA binding properties of a series of deletion mutants expressed in bacteria. We find that the 66 amino acid zinc finger core of the DBD fails to bind DNA, and that the C-terminal end of the minimal ER DBD required for binding to perfectly palindromic EREs corresponds to the limit of 100% amino acid homology between the chicken and human receptors, which represents the boundary between regions C and D in the ER. Moreover, amino acids of region D up to 30 residues C-terminal to the zinc fingers greatly stabilize DNA binding by the DBD to perfectly palindromic EREs and are absolutely required for formation of gel retardation complexes by the DBD on certain physiological imperfectly palindromic EREs. These results indicate that in addition to the zinc finger core, amino acids C-terminal to the core in regions C and D play a key role in DNA binding by the ER, particularly to imperfectly palindromic response elements. The ER DBD expressed in E. coli binds as a dimer to ERE palindromes in a highly cooperative manner and forms only low levels of monomeric protein-DNA complexes on either palindromic or half-palindromic response elements. Conversion of ER amino acids 222 to 226, which lie within region C, to the corresponding residues of the human RAR alpha abolishes formation of dimeric protein-DNA complexes. Conversely, replacement of the same region of RAR alpha with ER residues 222 to 226 creates a derivative that, unlike the RAR alpha DBD, binds cooperatively to an ERE, indicating that this region is important for dimerization in the ER.

DNA sequence-specific binding of transformed ah receptor to a dioxin responsive enhancer: Looks aren't everything

Gel retardation analysis has been utilized to examine the ability of transformed hepatic cytosolic TCDD:AhR complex to bind to its specific DNA recognition site, the dioxin responsive element (DRE). Although DRE sequence alignment has identified a conserved DNA recognition sequence of C/GNNNC/GTNGCGTGNC/GT/ANNNC/G, site-directed mutagenesis has demonstrated that not all of these bases are important for DNA binding. A putative TCDD:AhR DRE-binding consensus of GCGTGNNA/TNNNG/C has been derived from our studies and it is highly conserved among species. In addition, we present a model for the DNA-binding of transformed TCDD:AhR complex.

Heterogeneity of rat hepatic Ah receptor: identification of two receptor forms which differ in their biochemical properties.

In cytosol, the rat hepatic Ah receptor (AhR) appears to exist in two distinct forms (AhR alpha, AhR beta) in similar concentration. The binding of ligand (2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)) to AhR alpha requires the receptor be in its oligomeric 8-10 to S conformation (bound to other protein subunits), while ligand binding to AhR beta can occur with the dissociated 5-6 S form. Occupancy of AhR alpha by ligand (TCDD) protects it from salt-dependent inactivation; AhR beta is not inactivated by high salt conditions. The addition of molybdate to cytosol during tissue homogenization stabilized AhR alpha against salt-dependent inactivation and subunit dissociation but did not prevent dissociation of AhR beta by high salt. Although the presence of molybdate appears to stabilize AhR alpha in its oligomeric 8-10 S, it had no significant effect on the overall amount of TCDD:AhR complex which bound to its specific DNA recognition site, the dioxin responsive element (DRE). These results suggest that AhR alpha, unlike AhR beta, is either unable to transform or bind to the DRE with high affinity.

The DNA binding arm of lambda repressor: critical contacts from a flexible region

Segments of protein that do not adopt a well-ordered conformation in the absence of DNA can still contribute to site-specific recognition of DNA. The first six residues (NH2-Ser1-Thr2-Lys3-Lys4-Lys5-Pro6-) of phage lambda repressor are flexible but are important for site-specific binding. Low-temperature x-ray crystallography and codondirected saturation mutagenesis were used to study the role of this segment. All of the functional sequences have the form [X]1-[X]2-[Lys or Arg]3-[Lys]4-[Lys or Arg]5-[X]6. A high-resolution (1.8 angstrom) crystal structure shows that Lys3 and Lys4 each make multiple hydrogen bonds with guanines and that Lys5 interacts with the phosphate backbone. The symmetry of the complex breaks down near the center of the site, and these results suggest a revision in the traditional alignment of the six lambda operator sites.