Sequence-specific DNA Recognition Research Articles

A mismatch bubble in double-stranded DNA suffices to direct precise transcription initiation by Escherichia coli RNA polymerase.

Formation of a transcription-competent "open" complex between Escherichia coli RNA polymerase and a promoter, where base pairing is disrupted over a region of 12 base pairs including the start site of transcription, is a complex process involving at least three steps: recognition of specific DNA sequences, a conformational change in RNA polymerase, and DNA melting. By using synthetic constructs devoid of promoter-specific sequences, we show here that a mismatch bubble of 12 base pairs suffices to direct transcription initiation in divergent directions from its edges, reflecting the absence of polarity determinants for RNA polymerase binding. Bubble transcription is obtained with both core polymerase and holoenzyme, but efficient formation of heparin-resistant initiation complexes requires the sigma (specificity) factor. Based on these results it is likely that the sigma factor blocks access of the heparin to a site on the holoenzyme.

A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.

Understanding the general mechanisms of sequence specific DNA recognition by proteins is a major challenge in structural biology. The existence of a 'DNA recognition code' for proteins, by which certain amino acid residues on a protein surface confer specificity for certain DNA bases, has been the subject of much discussion. However, no simple code has yet been established. The principles of DNA recognition can be described at two levels. The 'chemical' rules describe the partnerships between amino acid side chains and DNA bases making favourable interactions in the major groove of DNA. Here I analyze the occurrence of nucleotide-amino acid contacts in previously determined crystal structures of DNA-protein complexes and find that simple rules pertain. I also describe 'stereochemical' rules for the probe helix type of DNA-binding motif found in certain transcription factors including leucine zipper and homeodomain proteins. These are a consequence of the binding geometry, and specify the amino acid and base positions used for the contacts, and the sizes of residues in the contact interface. The chemical rules can be generalized for any DNA-binding motif, while the stereochemical rules are specific to a particular DNA-binding motif. The recognition code for a particular binding motif can be described by combining the two sets of rules.

Steroid hormone receptors: activators of gene transcription.

Over the past three decades, a great deal of evidence has accumulated in favor of the hypothesis that steroid hormones act via regulation of gene expression. The action is mediated by specific nuclear receptor proteins, which belong to a superfamily of ligand-modulated transcription factors that regulate homeostasis, reproduction, development and differentiation. This family includes receptors for steroid hormones, thyroid hormones, hormonal forms of vitamin A and D, peroxisomal activators, and ecdysone. Molecular cloning and structure/function analyses have revealed that all members of the steroid/thyroid hormone/retinoic acid receptor family have a similar functional domain structure: a variable N-terminal region, which is involved in modulation of gene expression; a short well-conserved DNA-binding domain, which is crucial for recognition of specific DNA sequences and for receptor dimerization; and a partially conserved C-terminal ligand-binding domain, which is important for hormone binding and also for receptor dimerization and transactivation. In contrast to other members of the receptor superfamily steroid hormone receptors form transient complexes with several heat shock proteins. This interaction promotes proper folding and stability of the receptor molecule. Hormone binding induces a conformational change in the receptor molecule and simultaneously a dissociation of all heat shock proteins, which results in DNA-binding of the hormone-receptor complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Sequence-specific DNA recognition by the thyroid transcription factor-1 homeodomain.

The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivatives of TTF-1HD indicate a precise correspondence of some of its amino acid residues with specific bases in its binding site, allowing a crude orientation of the TTF-1HD within the protein-DNA complex. TTF-1HD shows an overall geometry of interaction with DNA similar to that previously observed for Antennapedia class HDs, even though the binding specificities of these two types of HDs are distinct. We demonstrate that the crucial difference between the binding sites of Antennapedia class and TTF-1 HDs is in the motifs 5'-TAAT-3', recognized by Antennapedia, and 5'-CAAG-3', preferentially bound by TTF-1. Furthermore, the binding of wild type and mutants TTF-1 HD to oligonucleotides containing either 5'-TAAT-3' or 5'-CAAG-3' indicate that only in the presence of the latter motif the Gln50 in TTF-1 HD is utilized for DNA recognition. Since the Gln at position 50 is an essential determinant for DNA binding specificity for several other HDs that bind to 5'-TAAT-3' containing sequences, we suggest that utilization by different HDs of key residues may depend on the sequence context and probably follows a precise hierarchy of contacts.

The DNA binding domains of the varicella-zoster virus gene 62 and herpes simplex virus type 1 ICP4 transactivator proteins heterodimerize and bind to DNA.

The product of varicella-zoster virus gene 62 (VZV 140k) is the functional counterpart of the major transcriptional regulatory protein of herpes simplex virus type 1 (HSV-1), ICP4. We have found that the purified bacterially expressed DNA binding domain of VZV 140k (residues 417-647) is a stable dimer in solution. As demonstrated by the appearance of a novel protein--DNA complex of intermediate mobility in gel retardation assays, following in vitro co-translation of a pair of differently sized VZV 140k DNA binding domain peptides, the 140k DNA binding domain peptide binds to DNA as a dimer. In addition, the DNA binding domain peptide of HSV-1 ICP4 readily heterodimerizes with the VZV 140k peptide on co-translation, indicating that HSV-1 ICP4 and VZV 140k possess very similar dimerization interfaces. It appears that only one fully wild type subunit of the dimer is sufficient to mediate sequence specific DNA recognition in certain circumstances. Co-immunoprecipitation analysis of mutant DNA binding domain peptides, co-translated with an epitope-tagged ICP4 DNA binding domain, shows that the sequence requirements for dimerization are lower than those necessary for DNA binding.

Hhal methyltransferase flips its target base out of the DNA helix

The crystal structure has been determined at 2.8 Å resolution for a chemically-trapped covalent reaction intermediate between the Hhal DNA cytosine-5-methyltransferase, S-adenosyl- l-homocysteine, and a duplex 13-mer DNA oligonucleotide containing methylated 5-fluorocytosine at its target. The DNA is located in a cleft between the two domains of the protein and has the characteristic conformation of B-form DNA, except for a disrupted G-C base pair that contains the target cytosine. The cytosine residue has swung completely out of the DNA helix and is positioned in the active site, which itself has undergone a large conformational change. The DNA is contacted from both the major and the minor grooves, but almost all base-specific interactions between the enzyme and the recognition bases occur in the major groove, through two glycine-rich loops from the small domain. The structure suggests how the active nucleophile reaches its target, directly supports the proposed mechanism for cytosine-5 DNA methylation, and illustrates a novel mode of sequence-specific DNA recognition.

POU domains and homeodomains

Transcription factors containing homeodomain and POU domain DNA-binding motifs play central developmental roles in eukaryotes. Over the past year, considerable progress has been made in the structural characterization of these domains and in elucidating the factors that determine sequence-specific DNA recognition. NMR structures have been reported for the Oct-1 POU-specific domain, and NMR and X-ray structures of a variant homeodomain have been described. These structures contain non-canonical helix-turn-helix motifs in which additional amino acids are accommodated in the turn region. New insights into the role of protein-protein interactions in determining functional specificity have been forthcoming.

Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain.

The DNA-binding domain of c-Myb consists of three homologous tandem repeats of 52 amino acids. The structure of the third (C-terminal) repeat obtained by NMR analysis has a conformation related to the helix-turn-helix motif. To identify the role of each repeat in the sequence recognition of DNA, we analyzed specific interactions between c-Myb and DNA by measuring binding affinities for systematic mutants of Myb-binding DNA sites and various truncated c-Myb mutants. We found that specific interactions are localized unevenly in the AACTGAC region in the consensus binding site of c-Myb: The first adenine, third cytosine, and fifth guanine are involved in very specific interactions, in which any base substitutions reduce the binding affinity by > 500-fold. On the other hand, the interaction at the second adenine is less specific, with the affinity reduction in the range of 6- to 15-fold. The seventh cytosine involves a rather peculiar interaction, in which only guanine substitution abolishes the specific binding. The binding analyses, together with the chemical protection analyses, showed that the c-Myb fragment containing the second and third repeats covers the AACTGAC region from the major groove of DNA in such an orientation that the third repeat covers the core AAC sequence. These results suggest that the third repeat recognizes the core AAC sequence very specifically, whereas the second repeat recognizes the GAC sequence in a more redundant manner. The first (N-terminal) repeat, which covers the major groove of DNA only partially, is not significant in the sequence recognition, but it contributes to increase the stability of the Myb-DNA complex. The presence of an N-terminal acidic region upstream of the first repeat, which is important for the activation of c-myb protooncogene, was found to reduce the binding affinity by interfering with the first repeat in binding to DNA.

The Function of Individual Zinc Fingers in Sequence-specific DNA Recognition by Transcription Factor IIIA

Mutations in Zn2+-coordinating histidine residues have been used to generate forms of transcription factor IIIA containing structural disruptions in single zinc fingers. These mutant proteins have been analyzed with respect to the structural and functional independence of individual zinc fingers in TFIIIA. They have also been used to assess the energetic contributions to binding and the sites of interaction of each of the nine zinc fingers of TFIIIA with the 5 S rRNA gene. The results are surprising and suggest a complex mode of binding in which the interactions of structurally independent zinc fingers with the DNA substrate are non-uniform and functionally interdependent in a way that may help to explain some of the unusual properties of TFIIIA.

Alteration of DNA Binding Specificity by Nickel (II) Substitution in Three Zinc (II) Fingers of Transcription Factor Sp1

Transcription factor Sp1, which has a DNA binding domain composed of three zinc fingers, binds to GC box (consensus sequence, G/T-GGGCGG-G/A-G/A-C/T) and activates the transcription by RNA polymerase II. Metal substitution of nickel(II) for zinc(II) in Sp1 causes no differences in the mode of protein-DNA interaction. However, sequence preference of Ni(II)Sp1 changes from 5′-GGGGCGGGGC to 5′-GGGGCGTGGC, and is distinct from that of Zn(II)Sp1. The result indicates an important effect of metal-induced folding on sequence-specific recognition of DNA by zinc-finger proteins.

Common features in DNA recognition helices of eukaryotic transcription factors.

Eukaryotic transcription factors which use an alpha-helix for DNA recognition, including the leucine zipper and homoeo domain proteins, have common features in the amino acid sequence of the DNA recognition helix, and also in the way this helix interacts with DNA. These factors all share a similar 12 residue segment in the DNA recognition helix, which is named the probe helix, since it covers all the pertinent interactions. Moreover, in all cases the interactions can be divided into two parts: the Arg/Lys residues at positions 7, 9, 11 and 12 in the C-terminal half of the segment contact phosphate groups, whereas the N-terminal half interacts with the DNA bases by using residues at positions 1, 4, 5 and 8. The residue occupying position 1 is the most important for sequence specific DNA recognition. Similar 12 residue sequences are found in the DNA binding domain of many transcription factors including those of the TEA family, the Myc type of bHLH family, the MADS family, the Ets family and the OmpR family. These generalities show that it might be possible to find a stereochemical code which explains three-dimensional interactions between DNA and an alpha-helix of this type.

NUCLEAR HORMONE RECEPTORS: REGULATORS OF GENE EXPRESSION

Over the past three decades, a great deal of evidence has accumulated in favor of the hypothesis that steroid hormones act via regulation of gene expression. The action is mediated by specific nuclear receptor proteins, which belong to a superfamily of ligand-modulated transcription factors that regulate homeostasis, reproduction, development and differentiation. This family includes receptors for steroid hormones, thyroid hormones and hormonal forms of vitamin A and D. All members of this superfamily have a similar functional domain structure: a variable N-terminal region, which is involved in modulation of gene expression. A short well conserved DNA-binding domain, which is crucial for recognition of specific DNA sequences and for receptor dimerization; and a partially conserved C-terminal hormone-binding domain. Hormone-receptor complexes regulate gene expression by binding to hormone-response elements which are located in the 5′-flanking sequences of hormone-responsive genes. Binding of nuclear hormone receptors to their cognate hormone response elements occurs as dimers. Receptors enhance transcription by stabilizing general transcription factors either directly at the TATA-box or through interactions with proteins bound to upstream promoter sequences or via interaction with transcription intermediairy factors which can be considered as coupling proteins between the receptor and other protein components in the transcription initiation complex. Receptor gene defects are frequently the cause of several forms of hormone resistance.

Sequence-specific recognition and cleavage of DNA by anti-tumour antibiotics

Abstract DNA cleavage by a bleomycin—iron complex occurs preferentially at guanine-pyrimidine (5′ → 3′) sequences, in particular at G-C sites. Metallobleomycin binds in the minor groove of B-DNA and the bithiazole moiety probably plays an important role as an anchor on DNA duplex. The 2-amino group of guanine adjacent to the 5′-side of the cleaved pyrimidine base is one key element of the specific 5′-GC recognition by the bleomycin-metal complex. Endiyne anti-tumour antibiotics such as esperamicin A1 and dynemicin A also interact with the minor groove of DNA, and their strong DNA splitting activity is due to phenylene diradical formation from the enediyne core. A possible binding mode between these antibiotics and B-DNA has been proposed by computer-constructed model building.

T7 RNA polymerase mutants with altered promoter specificities.

The amino acid at position 748 in T7 RNA polymerase (RNAP) functions to discriminate base pairs at positions -10 and -11 in the promoter. We have constructed a series of T7 RNAP mutants having all possible amino acid substitutions at this position. Surprisingly, most (13/19) substitutions result in active RNAPs, and many of these exhibit altered promoter specificities. Identification of mutant RNAPs with altered specificities expands the repertoire of highly specific phage RNAPs that are available for use in phage RNAP-based transcription systems and highlights the complexity of sequence-specific DNA recognition.

Specific recognition of CG base pairs by 2-deoxynebularine within the purine.purine.pyrimidine triple-helix motif.

The sequence-specific recognition of double-helical DNA by oligodeoxyribonucleotide-directed triple-helix formation is limited mostly to purine tracts. Within the geometric constraints of the phosphate-deoxyribose position of a purine-purine-pyrimidine triple-helical structure, model building studies suggested that the deoxyribonucleoside 2'-deoxynebularine (dN) might form one specific hydrogen bond with cytosine (C) or adenine (A) of Watson-Crick cytosine-guanine (CG) or adenine-thymine (AT) base pairs. 2-Deoxynebularine (dN) was incorporated by automated methods into purine-rich oligodeoxyribonucleotides. From affinity cleavage analysis, the stabilities of base triplets within a purine.purine.pyrimidine (Pu.Pu.Py) triple helix were found to decrease in the order N.CG approximately N.AT >> N.GC approximately N.TA (pH 7.4, 37 degrees C). Oligodeoxyribonucleotides containing two N residues were shown to bind specifically within plasmid DNA a single 15 base pair site of the human immunodeficiency virus genome containing two CG base pairs within a purine tract. This binding event occurs under physiologically relevant pH and temperature (pH 7.4, 37 degrees C) and demonstrates the utility of the new base. Quantitative affinity cleavage titration reveals that, in the particular sequence studied, an N.CG base triplet interaction results in a stabilization of the local triple-helical structure by 1 kcal.mol-1 (10 mM NaCl, 1 mM spermine tetrahydrochloride, 50 mM Tris-acetate, pH 7.4, 4 degrees C) compared to an A.CG base triplet mismatch.

Energetics of cooperative binding of oligonucleotides with discrete dimerization domains to DNA by triple helix formation.

Cooperativity in oligonucleotide-directed sequence-specific recognition of DNA by triple helix formation can be enhanced by the addition of discrete dimerization domains. The equilibrium association constants for cooperative binding of oligonucleotides that dimerize by Watson-Crick hydrogen bonds and occupy adjacent sites on double helical DNA by triple helix formation have been measured by quantitative affinity cleavage titration. For two oligonucleotides that bind unique neighboring 11-bp and 15-bp sites on double helical DNA, and dimerize by formation of an 8-bp Watson-Crick mini-helix, the free energy of binding is -8.0 and -9.7 kcal.mol-1, respectively, and the cooperative energy of interaction is -2.3 kcal.mol-1 (1 kcal = 4.18 kJ). The energetics of this artificial nucleic acid cooperative intermolecular assembly can mimic naturally occurring cooperative protein-DNA systems, such as the phage lambda repressor.

The HsdS polypeptide of the type IC restriction enzyme EcoR124 is a sequence-specific DNA-binding protein.

The HsdS and HsdM polypeptides of the type IC restriction enzyme EcoR124 have been purified independently and used in a set of gel retardation experiments to determine the minimum requirements for sequence-specific recognition of DNA by this enzyme. The HsdS polypeptide alone is able to bind to DNA in a sequence-specific manner. In addition, whilst the presence of the HsdM polypeptide gives rise to a stimulation of DNA binding by the HsdS subunit it is not clear whether, under the conditions of the experiments reported here, the HsdS subunit maintains the same interactions with the HsdM subunits observed in the absence of DNA.

Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1.

We have overexpressed and purified two peptide fragments of Sp1 that contain the three "zinc-finger" domains necessary for specific Sp1 DNA binding. These peptides assume a stable, folded conformation in solution in the presence of Zn2+ as shown by DNA binding assays and NMR spectroscopy. Mobility-shift assays demonstrate that the Sp1 peptides recognize a number of different Sp1 DNA binding sites (GC boxes, with the core sequence GGGCGG). The dissociation constant for a 92-amino acid peptide binding to the GGGGCGGGGC sequence (Kd approximately 10 nM) and the relative affinities for several other DNA sequences definitively demonstrate Sp1-like binding properties. The thermodynamic binding site for Sp1-Zn92 has been mapped using the primer-extension/mobility-shift assay revealing that the 5' portion of the GC box DNA sequence (GGG GCG) contributes more strongly to the total binding energy than the 3' portion (GGGC). These findings are interpreted in the context of the Sp1 amino acid sequence in comparison with the structurally characterized Zif-268/DNA complex. A model is proposed that offers a structural explanation for the ability of Sp1 to recognize a diverse array of DNA sequences in terms of the individual (and different) DNA binding properties of each of the three zinc-finger domains.

Recognition of all four base pairs of double-helical DNA by triple-helix formation: design of nonnatural deoxyribonucleosides for pyrimidine.cntdot.purine base pair binding

The sequence-specific recognition of double-helical DNA by oligonucleotide-directed triple-helix formation is limited mostly to purine tracts. Design leads that could expand the recognition code to all four Watson-Crick base pairs would provide one step toward a general solution targeting single sites in megabase size DNA. The nonnatural deoxyribonucleoside 1-(2-deoxy-beta-D-ribofuranosyl)-4-(3-benzamidophenyl)imidazole (D3) was synthesized in four steps and incorporated by automated methods into pyrimidine oligodeoxyribonucleotides. Within a pyrimidine oligonucleotide, D3 binds pyrimidine.purine base pairs with higher affinity than it binds purine.pyrimidine base pairs. From affinity-cleaving analysis, the stabilities of base triplets decrease in the order D3.TA is similar to D3.CG > D3.AT > D3.GC. Such specificity allows binding by triple-helix formation at an 18 base pair site in SV40 DNA containing all four base pairs at physiologically relevant pH and temperature. The stabilities of these novel triplets may be an example of shape-selective recognition of CG and TA Watson-Crick base pairs in the major groove.

Polypeptides containing highly conserved regions of transcription initiation factor σ70 exhibit specificity of binding to promoter DNA

The σ 70 subunit of E. coli RNA polymerase is required for sequence-specific recognition of promoter DNA. Genetic studies and sequence analysis have indicated that σ 70 contains two specific DNA-binding domains that recognize the two conserved portions of the prokaryotic promoter. However, intact σ 70 does not bind to DNA. Using C-terminal and internal polypeptides of σ 70, carrying one or both putative DNA-binding domains, we demonstrate that σ 70 does contain two DNA-binding domains, but that N-terminal sequences inhibit the ability of intact σ 70 to bind to DNA. Thus, we propose that σ 70 is a sequence-specific DNA-binding protein that normally functions through an allosteric interaction with the core subunits of RNA polymerase.