Swapping of the beta-hairpin region between Sp1 and GLI zinc fingers: significant role of the beta-hairpin region in DNA binding properties of C2H2-type zinc finger peptides

The recent design strategy of zinc finger peptides has mainly focused on the alpha-helix region, which plays a direct role in DNA recognition. On the other hand, the study of non-DNA-contacting regions is extremely scarce. By swapping the beta-hairpin regions between the Sp1 and GLI zinc fingers, in this study, we investigated how the beta-hairpin region of the C(2)H(2)-type zinc finger peptides contributes to the DNA binding properties. Surprisingly, the Sp1 mutant with the GLI-type beta-hairpin had a higher DNA binding affinity than that of the wild-type Sp1. The result of the DNase I footprinting analyses also showed the change in the DNA binding pattern. In contrast, the GLI zinc finger completely lost DNA binding ability as a result of exchanging the beta-hairpin region. These results strongly indicate that the beta-hairpin region appears to function as a scaffold and has an important effect on the DNA binding properties of the C(2)H(2)-type zinc finger peptides.     

Zinc fingers: DNA binding and protein-protein interactions

The zinc finger domain is a very ubiquitous structural element whose hallmark is the coordination of a zinc atom by several amino acid residues (cysteines and histidines, and occasionally aspartate and glutamate). These structural elements are associated with protein-nucleic acid recognition as well as protein-protein interactions. The purpose of this review is to examine recent data on the DNA and protein binding properties of a few zinc fingers whose three dimensional structure is known.     

Metal binding and DNA recognition in transcription factor Sp1.

DNA binding domain of Sp1 encompassing three Cys2His2-type Zn-finger motifs is cloned and expressed in E.coli. The Sp1 fragment shows metal-dependent folding and DNA binding. The Zn(II)-induced folding of the three fingers is probably cooperative. Release of one equivalent of Zn decreases but does not abolish DNA binding activity of Sp1.     

Recognition and structural perturbation of GC box DNA by Sp1 zinc finger.

Interaction of Sp1 with GC box DNA was investigated by several footprinting experiments. Methylation of four guanine bases is strongly protected by Sp1 binding, while one guanine base in GC box is extremely hypermethylated. Sp1 binding also induces new cleavage at 5'-GA-3' site within GC box by bleomycin-iron complex.     

The Arabidopsis TAG1 transposase has an N-terminal zinc finger DNA binding domain that recognizes distinct subterminal motifs

The in vitro DNA binding activity of the Arabidopsis Tag1 transposase (TAG1) was characterized to determine the mechanism of DNA recognition. In addition to terminal inverted repeats, the Tag1 element contains four different subterminal repeats that flank a transcribed region encoding a 729-amino acid protein. A single site-specific DNA binding domain is located near the N terminus of TAG1, between residues 21 and 133. This domain binds specifically to the AAACCC and TGACCC subterminal repeats, found near the 5' and 3' ends of the element, respectively. The ACCC sequence within these repeats is critical for recognition because mutations at positions 3, 5, and 6 abolished binding, yet the first two bases also are important because substitutions at these positions decreased binding by up to 90%. Weak interaction also occurs with the terminal inverted repeats, but no binding was observed to the other two 3' subterminal repeat regions. Sequence analysis of the TAG1 DNA binding domain revealed a C(2)HC zinc finger motif. Tests for metal dependence showed that DNA binding activity was inhibited by divalent metal chelators and greatly enhanced by zinc. Furthermore, mutation of each cysteine residue predicted to be a metal ligand in the C(2)HC motif abolished DNA binding. Together, these data show that the DNA binding domain of TAG1 specifically binds to distinct subterminal repeats and contains a zinc finger.     

Increased spacing between Sp1 and TATAA renders human immunodeficiency virus type 1 replication defective: implication for Tat function.

Expression of the human immunodeficiency virus type 1 (HIV-1) is strongly activated by Tat. The proper action of Tat requires three elements: TATAA, TAR, and upstream motifs in the HIV-1 long terminal repeat. We show here that the correct spatial arrangement among Tat, Sp1, and TATAA crucially influences HIV expression. Under conditions in which basal promoter activity is unperturbed, distancing Sp1 from TATAA markedly affected Tat trans activation. An increase in the Sp1-TATAA distance from 18 to 101 nucleotides (depending on the inserted sequence) rendered HIV-1 either partially or wholly replication defective. This critical dependence on spacing suggests that Tat-, Sp1-, and TATAA-binding factors must correctly contact each other for optimal expression and replication of HIV-1.     

DNA binding properties of the vitamin D3 receptor zinc finger region.

The DNA binding domains of the nuclear receptor superfamily are highly conserved and consist of residues that fold into two zinc finger-like motifs, suggesting that the structures of this region among the members of the superfamily are likely to be very similar. Furthermore, the response elements that these receptors bind to are similar in sequence and organization. Nevertheless, these receptors selectively recognize target response elements and differentially regulate linked genes. In order to study the details of receptor:DNA binding, we have overexpressed and purified the vitamin D3 receptor DNA binding domain (VDRF) and have begun characterizing its DNA binding properties. We find that the VDRF protein binds strongly and specifically to direct repeats constituting a vitamin D response element from the mouse osteopontin (Spp-1) promoter region but weakly to the human osteocalcin vitamin D response element. Unlike receptors that recognize hormone response elements oriented as inverted repeats, such as the glucocorticoid receptor (GR) and estrogen receptor, VDRF appears to bind half-sites noncooperatively, without the free energy contribution of dimerization seen when the glucocorticoid receptor DNA binding domain associates with a glucocorticoid response element. By comparing and contrasting the DNA binding properties of the vitamin D and glucocorticoid receptors, we suggest a model for how receptors that prefer direct repeats differ in their binding strategy from those that recognize inverted repeats.     

Functional characterization of iron-substituted neural zinc finger factor 1: metal and DNA binding

Neural zinc finger factor 1 (NZF-1) is a nonclassical zinc finger protein involved in neuronal development. NZF-1 contains multiple copies of a unique CCHHC zinc-binding domain that recognize a promoter element in the β-retinoic acid receptor gene termed β-retinoic acid receptor element (β-RARE). Previous studies have established that a two-domain fragment of NZF-1 bound with zinc is sufficient for specific DNA binding. Proper functioning of the nervous system relies heavily on iron and misregulation of this highly redox active metal has serious consequences. Several classes of zinc finger proteins have been shown to bind other metal ions, including iron. To determine if ferrous iron can coordinate to the metal-binding sites of NZF-1 and assess the functional consequences of such coordination, a fragment of NZF-1 that contains two zinc-binding domains, NZF-1 double finger (NZF-1-DF), was prepared. UV–vis spectroscopy experiments demonstrated that Fe(II) is capable of binding to NZF-1-DF. Upon reconstitution with either Fe(II) or Zn(II), NZF-1-DF binds selectively and tightly (nanomolar affinity) to its target β-RARE DNA sequence, whereas apo-NZF-1-DF does not bind to DNA and instead aggregates.