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.

Single crystals of long DNA molecules

We have grown single crystals of long DNA molecules, 54 and 65 base pairs in length which encompass the binding site of the Xenopus protein transcription factor IIIA (TFIIIA). These molecules are considerably longer than those previously crystallised. X-ray diffraction shows that the crystals are ordered to a resolution of 9 A. The DNA molecules are arranged side to side in layers which are orientated at 120 degrees with respect to adjacent layers. The phosphate backbones of molecules in adjacent layers are interdigitated in both the major and minor grooves. The intensity distribution indicates that the average structure is B-like, although CD spectra in solution are more consistent with the structure, intermediate between A- and B-, found in crystals of a nonamer fragment of the binding site. The B-character in our crystals may therefore be impressed by the tight packing between layers.

A novel method for the purification of the Xenopus transcription factor IIIA

We have developed a quick and simple purification method that yields large quantities of the Xenopus zinc finger protein transcription factor IIIA (TFIIIA). The protein is purified in the form of the 7S storage particle (TFIIIA/5S RNA complex) found in the ovaries of immature Xenopus. Our method yields 0.5 to 1 mg of pure 7S particle per ovary. It involves a high speed centrifugation step, fractionation on a gel filtration column and a precipitation step using calcium chloride. TFIIIA purified using this protocol retains full DNA binding activity and has the expected zinc ion content.

The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure

On the basis of nuclease digestion studies we proposed that the DNA binding site of transcription factor IIIA (TFIIIA) may have an overall structure with A-type rather than B-type characteristics. This proposal was substantiated by the crystal structure of a part of the TFIIIA binding site. Recently, however, it has been reported that the binding site for TFIIIA is B-form in solution, thus implying that the conformation present in crystals is not the structure in solution. We have carried out a study using comparative circular dichroism (CD) spectroscopy of a number of double stranded deoxyoligonucleotides of different sequence, and known crystal structure. The correlation we have found between CD characteristics and certain structural parameters indicates that the solution and crystal structures of the TFIIIA binding site are closely related. This structure may be classed as an intermediate type, between A-form and B-form DNA.

EXAFS study of the zinc-binding sites in the protein transcription factor IIIA

The protein transcription factor IIIA (TFIIIA) is involved in the synthesis of 5S RNA in vitro by RNA polymerase III. It can be isolated from Xenopus laevis oocytes as a 7S particle in which the protein is associated with 5S RNA. Recently it has been shown that the native particle contains 7-11 zinc atoms. Analysis of the amino-acid sequence of TFIIIA revealed nine similar domains of approximately 30 amino acids, each containing two invariant pairs of histidines and cysteines, which have been implicated as possible binding sites for the zinc atoms. Other regulatory proteins with sequence homology to the zinc-binding domains of TFIIIA have now been reported. Here, we report the results of an EXAFS (extended X-ray absorption fine structure) study of TFIIIA which shows that the coordination sphere of the zinc sites consists of two cysteine and two histidine residues.

Mapping of the sites of protection on a 5 S RNA gene by the Xenopus transcription factor IIIA. A model for the interaction

The contact points of transcription factor IIIA with the internal control region of the 5 S RNA gene of Xenopus have been investigated by probing the accessibility of the DNA in the protein-DNA complex to dimethylsulphate and to micrococcal nuclease. The results of quantitative measurements, combined with those from earlier DNase I and DNase II protection studies, are consistent with a series of multiple contacts about five base-pairs apart, or half a double-helical turn, along the whole length of the internal control region. The nine patches of contact we have mapped could correspond to nine DNA-binding fingers in the protein. A model for the overall geometry of the interaction is presented in which the protein lies on one face of the DNA double helix.

Oligonucleotide binding to the coat protein disk of tobacco mosaic virus. Possible steps in the mechanism of assembly

Binding of the oligoribonucleotides AAG, AAGAAG and AAGAAGUUG to the disk aggregate of tobacco mosaic virus coat protein has been studied in solution under conditions favourable for virus assembly. The two longer oligomers bind strongly with Kd around 1 microM, approach complete saturation of binding sites and cause the formation of long, nicked helical rods resembling the virus. It is suggested that the binding of these oligomers, with sequences chosen from the assembly origin of the viral RNA, simulates the tobacco mosaic virus assembly process. No binding could be detected for AAG, indicating that chain length is a crucial determinant in the interaction. The binding of AAGAAG to coat protein crystals is very much weaker than that observed in solution, and the crystals crack at high oligomer concentrations. The corresponding oligodeoxyribonucleotide, d(AAGAAG), shows no binding to the protein in solution; the interaction is extremely specific for RNA.

Studies of tobacco mosaic virus reassembly with an RNA tail blocked by a hybridised and cross-linked probe

Segments of cloned cDNA to tobacco mosaic virus RNA, 150--300-bases long, have been hybridised and cross-linked to the RNA, which has then been used for reassembly experiments. This enables the elongation reaction, which does not encapsidate the double-stranded region generated, to be stopped at specific regions along the RNA and the resulting particles to be characterised, by measuring the lengths of the rods in the electron microscope. With hybridisation to the 3'-tail the entire RNA contiguous to the nucleation region is encapsidated, from the 5'-terminus up to the modified region. When the double-stranded region is on the 5'-side of the nucleation region, the mean length of the particles corresponds to a situation in which the double-stranded region is unable to enter the central hole of the growing rod, but the 3'-tail of the RNA is completely encapsidated. The longest particles hybridised on the 5'-tail (i.e. in a class longer than the mean length) show an effect complementary to those with a 3'-block, and have lengths which correspond to encapsidation from the modified region to the 3'-terminus, despite the continued presence of the 5'-tail up the rod. In all cases where there is a remaining 5'-tail the lengths observed can only be explained if elongation has occurred substantially, or probably completely, along the 3'-tail. Hence elongation must have occurred simultaneously along both the 5' and 3'-tails of the tobacco mosaic virus RNA after initiation on the internal nucleation region.