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A A Travers

Publications and source records attributed to A A Travers.

At least 19 recordsLinked to original sources
PubMed1992

Sequence-specific DNA binding by a two zinc-finger peptide from the Drosophila melanogaster Tramtrack protein.

We show that the DNA-binding domain of the Drosophila melanogaster regulatory protein Tramtrack consists of a 66 amino acid sequence containing two zinc-finger motifs and a short sequence N-terminal to the first finger motif. This short N-terminal sequence is essential for DNA binding and we suggest it is involved in maintaining the three-dimensional structure of the first finger domain, as has been seen in the nuclear magnetic resonance structure of one of the zinc-finger domains of the yeast transcription factor SW15. The characterization of the DNA-binding activity of this 66 residue peptide (delta 911zf) shows that it binds in a sequence-specific manner, as a monomer, to a natural target site with an apparent KD approximately 4 x 10(-7) M. The shortest delta 911zf binding site, which retains full affinity, consists of an 11 base-pair sequence with a one nucleotide overhang at each 5' end. DNase I, hydroxyl radical and methylation protection footprinting studies show that, in common with other zinc-finger proteins, delta 911zf binds in the major groove of DNA. The data presented are consistent with the zinc-fingers of Tramtrack contacting both strands of the DNA, and thus the binding differs in detail to that observed in the crystal structure of the three zinc-fingers of Zif268 complexed to their target DNA.

Amino Acid Sequence↗
PubMed1992

DNA curvature does not require bifurcated hydrogen bonds or pyrimidine methyl groups.

Short tracts of the homopolymer dA.dT confer intrinsic curvature on the axis of the DNA double helix. This phenomenon is assumed to be a consequence of such tracts adopting a stable B'-DNA conformation that is distinct from B-form structure normally assumed by other DNA sequences. The more stable B' structure of dA.dT tracts has been attributed to several possible stabilizing factors: (1) optimal base stacking interactions consequent upon the high propeller twist, (2) bifurcated hydrogen bonds between adjacent dA.dT base-pairs, (3) stacking interactions involving the dT methyl groups, and finally (4) a putative spine of ordered water molecules in the minor groove. DNA oligodeoxynucleotides have been synthesized that enable these hypotheses to be tested; of particular interest is the combination of effects due to bifurcation (2) and methylation of the pyrimidines nucleotides (3). The data indicate that neither bifurcated hydrogen bonds nor pyrimidine methyl groups nor both are essential for DNA curvature. The data further suggest that the influence of the minor groove spine of hydration on the B'-formation is small. The experiments favor the hypothesis that base stacking interactions are the dominant force in stabilizing the B'-form structure.

Base Sequence↗
PubMed1992

DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen.

Singlet oxygen (1O2), generated by exciting an eosin-Tris complex with a high intensity beam of radiation at 532 nm, was used to chemically modify bases in fragments of DNA containing the lac UV5 promoter in the presence of the DNA binding proteins, RNA polymerase and CRP (cAMP receptor protein). Subsequent treatment with piperidine selectively cleaved the DNA at specific modified bases in the sequence. Using this technique we show first that the reactivity of DNA bound by CRP differs in the presence and absence of RNA polymerase. Hence the local conformation of CRP-bound DNA must change during the transition to the open complex. However, no reactivity is observed at the sites of the 40 degrees kinks described in the cocrystal structure (Steitz, 1990). Secondly we show that there is unique CRP-dependent reactivity at a specific site (position -46 on the upper strand) in the open complex. Finally, in the open complex, 1O2 also reacts with sites 90 bp upstream from the transcription start point. This reactivity is qualitatively CRP-independent. We infer that 1O2 reacts at sites where the promoter DNA is significantly distorted, and suggest that the pattern observed reflects the functional orientation of an active transcriptional complex in which the DNA is bent to form an extended loop.

Cyclic AMP Receptor Protein↗
PubMed1991

Protein motifs that recognize structural features of DNA.

Many proteins have the ability to bind to a variety of DNA sequences, the recognition of which depends on some general rather than specific feature of the DNA. Some of the protein motifs that are responsible for this type of recognition have been identified in transcription factors and chromosomal proteins. These motifs consist of sequences capable of forming a structural framework in which positively charged residues can be arranged so that binding to a particular DNA structure is preferred.

Amino Acid Sequence↗
PubMed1990

Why bend DNA?

Explore the source record for details and available documents.

DNA↗
PubMed1990

The tramtrack gene encodes a Drosophila finger protein that interacts with the ftz transcriptional regulatory region and shows a novel embryonic expression pattern.

We have identified a Drosophila zinc-finger protein, which binds to a number of sites in the transcriptional control regions of the pair-rule gene fushi-tarazu (ftz). The expression pattern of the mRNA that encodes this protein is essentially complementary to that of ftz both prior to blastoderm formation and during germband extension. We propose that the protein may function by repressing inappropriate segmentation gene transcription during embryogenesis. The gene encoding this ftz promoter-binding protein has been named tramtrack (ttk).

Amino Acid Sequence↗
PubMed1989

Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin.

Nucleosome dimers containing, on average, a single molecule of histone H5 have been isolated from chicken erythrocyte nuclei and the associated DNA fragments cloned and sequenced. The average sequence organization of at least one of the two nucleosomes in the dimers is highly asymmetric and suggests that the torsional, as well as the axial, flexibility of DNA is a determinant of nucleosome positioning. On average the nucleosome dimer is a polar structure containing linker DNA of variable lengths. The sequences associated with H5 containing nucleosomes and core particles are sufficiently different to indicate that removal of histone H5 (or H1) from chromatin may result in the migration of the histone octamer and a consequent exposure of sites for regulatory proteins.

Animals↗
PubMed1988

Identification of the binding sites for potential regulatory proteins in the upstream enhancer element of the Drosophila fushi tarazu gene.

With a view to identifying proteins that regulate the expression of the Drosophila ftz gene we have sequenced its enhancer-like upstream element (USE) and determined the binding sites for embryonic nuclear proteins within this region by in vitro DNAaseI footprinting. We find that greater than 50% of this element is bound by nuclear protein. By footprinting and gel-retardation studies in embryonic extracts from different developmental stages, we have characterised a number of USE/protein complexes whose nature alters in concert with changes in the ftz expression pattern, suggesting that these USE-binding proteins may be involved in the regulation of gene activity. In some cases this suggestion is substantiated by the observation that the protected DNA sequences show homology to the binding sites for ftz regulating DNA-binding proteins such as the pair-rule gene product even-skipped.

Animals↗
PubMed1987

The bending of DNA in nucleosomes and its wider implications.

The DNA of a nucleosome core particle is wrapped tightly around a histone octamer with approximately 80 base pairs per superhelical turn. Studies of both naturally occurring and reconstituted systems have shown that DNA sequences very often adopt well-defined locations with respect to the octamer. Recent work in this laboratory has provided a structural explanation for this sequence-dependent positioning in terms of the differential flexibility of different sequences and of departures from smooth bending. The 'rules' that are emerging for DNA bendability and, from the results of other workers, on intrinsically bent DNA, are likely to be useful in considering looping and bending of DNA in other processes in which it is thought to be wrapped around a protein core.

DNA↗
PubMed1987

Structure and function of E. coli promoter DNA.

The process of transcription initiation requires both the recognition of a promoter site by RNA polymerase and the melting of a short stretch of DNA. In this review I discuss the properties of promoters that are relevant to sequence recognition and to the ability of the polymerase to act as a melting protein. The regulation of promoter activity is thus dependent on both factors interacting with RNA polymerase and so altering its affinity for promoter sites and also modulations of DNA structure.

Base Sequence↗
PubMed1986

Sequence periodicities in chicken nucleosome core DNA.

The rotational positioning of DNA about the histone octamer appears to be determined by certain sequence-dependent modulations of DNA structure. To establish the detailed nature of these interactions, we have analysed the sequences of 177 different DNA molecules from chicken erythrocyte core particles. All variations in the sequence content of these molecules, which may be attributed to sequence-dependent preferences for DNA bending, correlate well with the detailed path of the DNA as it wraps around the histone octamer in the crystal structure of the nucleosome core. The sequence-dependent preferences that correlate most closely with the rotational orientation of the DNA, relative to the surface of the protein, are of two kinds: ApApA/TpTpT and ApApT/ApTpT, the minor grooves of which face predominantly in towards the protein; and also GpGpC/GpCpC and ApGpC/GpCpT, whose minor grooves face outward. Fourier analysis has been used to obtain fractional variations in occurrence for all ten dinucleotide and all 32 trinucleotide arrangements. These sequence preferences should apply generally to many other cases of protein-DNA recognition, where the DNA wraps around a protein. In addition, it is observed that long runs of homopolymer (dA) X (dT) prefer to occupy the ends of core DNA, five to six turns away from the dyad. These same sequences are apparently excluded from the near-centre of core DNA, two to three turns from the dyad. Hence, the translational positioning of any single histone octamer along a DNA molecule of defined sequence may be strongly influenced by the placement of (dA) X (dT) sequences. It may also be influenced by any aversion of the protein for sequences in the "linker" region, the sequence content of which remains to be determined.

Animals↗
PubMed1986

Alteration of the growth-rate-dependent regulation of Escherichia coli tyrT expression by promoter mutations.

The growth-rate regulation of transcription of the Escherichia coli tyrT gene depends on sequences in at least two distinct regions of the promoter, the upstream element required for optimal activity and the discriminator adjacent to the transcription start-point. Since mutations in the discriminator also alter the response of the promoter to amino acid starvation, we conclude that growth rate and amino acid control mechanisms share a common target molecule, probably RNA polymerase.

Base Sequence↗