The possible roles of residues 79 and 80 of the Trp repressor from Escherichia coli K-12 in trp operator recognition

Mutational analysis of conserved residues in the putative DNA-binding domain of the response regulator Spo0A of Bacillus subtilis

The Spo0A protein of Bacillus subtilis is a DNA-binding protein that is required for the expression of genes involved in the initiation of sporulation. Spo0A binds directly to and both activates and represses transcription from the promoters of several genes required during the onset of endospore formation. The C-terminal 113 residues are known to contain the DNA-binding activity of Spo0A. Previous studies identified a region of the C-terminal half of Spo0A that is highly conserved among species of endospore-forming Bacillus and Clostridium and which encodes a putative helix-turn-helix DNA-binding domain. To test the functional significance of this region and determine if this motif is involved in DNA binding, we changed three conserved residues, S210, E213, and R214, to Gly and/or Ala by site-directed mutagenesis. We then isolated and analyzed the five substitution-containing Spo0A proteins for DNA binding and sporulation-specific gene activation. The S210A Spo0A mutant exhibited no change from wild-type binding, although it was defective in spoIIA and spoIIE promoter activation. In contrast, both the E213G and E213A Spo0A variants showed decreased binding and completely abolished transcriptional activation of spoIIA and spoIIE, while the R214G and R214A variants completely abolished both DNA binding and transcriptional activation. These data suggest that these conserved residues are important for transcriptional activation and that the E213 residue is involved in DNA binding.

Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites

The interaction of trp repressor with its DNA targets is unusual in that specific recognition in this system does not rely exclusively on direct hydrogen bonds to the DNA bases that are crucial for sequence-specific recognition. It has been suggested that trp operators are mainly recognized by water-mediated interactions and by structural recognition of DNA deformability. Here we study the effect of the central dinucleotide on the mode of interaction of the trp repressor with its binding sites. The study was carried out on two consensus sequences: (1) trpTA, the consensus of naturally occurring trp binding sites, containing a T-A step between the two hexameric half-site sequences, ACTAGT; (2) trpAC, a consensus sequence derived from a functional selection study, containing a central A-C step. We show that the identity of the central dinucleotide does not affect the interaction of the first trp repressor molecule with the primary DNA target site, however, it influences the assembly of additional repressor molecules at adjacent sites. Central A-C steps stabilize tandem binding, whereas T-A steps destabilize it. It has been previously suggested that in vivo regulation of trp operators is due to their differential ability to bind multiple repressor molecules. The observations presented here support this model. We ascribe this ability to two sequence-dependent factors which act together: the identity and number of half-site sequences, recognized by water-mediated hydrogen bonds, and the ability of the intervening dinucleotides to form direct bidentate hydrogen bonds to the repressor. Furthermore, we measured the intrinsic and the induced bending of trp operators by the repressor. We find that the operators are straight in their free form, bent by 23 degrees when bound by a single trp repressor molecule, and bent by 30 degrees when bound by two repressor molecules.

Mutants in position 69 of the Trp repressor of Escherichia coli K12 with altered DNA-binding specificity

Structural analysis by X-ray crystallography has indicated that direct contact occurs between Arg69, the second residue of the first helix of the helix-turnhelix (HTH) motif of the Trp repressor, and guanine in position 9 of the alpha-centred consensus trp operator. We therefore replaced residue 69 of the Trp repressor with Gly, Ile, Leu or Gln and tested the resultant repressor mutants for their binding to synthetic symmetrical alpha- or beta-centred trp operator variants, in vivo and in vitro. We present genetic and biochemical evidence that Ile in position 69 of the Trp repressor interacts specifically with thymine in position 9 of the alpha-centred trp operator. There are also interactions with other bases in positions 8 and 9 of the alpha-centred trp operator. In vitro, the Trp repressor of mutant RI69 binds to the consensus alpha-centred trp operator and a similar trp operator variant that carries a T in position 9. In vivo analysis of the interactions of Trp repressor mutant RI69 with symmetrical variants of the beta-centred trp operator shows a change in the specificity of binding to a beta-centred symmetrical trp operator variant with a gua-nine to thymine substitution in position 5, which corresponds to position 9 of the alpha-centred trp operator.

Co-operative binding of two Trp repressor dimers to alpha- or beta-centred trp operators

The alpha-centred trp operator binds one dimer of the Trp repressor, whereas the beta-centred trp operator binds two dimers of the Trp repressor (Carey et al., 1991; Haran et al., 1992). The Trp repressor with a Tyr-Gly-7 substitution binds almost as well as the wild-type Trp repressor to the alpha-centred trp operator, but it does not bind to the beta-centred trp operator. This confirms that Tyr-7 is involved in the interaction between Trp repressor dimers, as seen in the crystal structure (Lawson and Carey, 1993). Further experiments with alpha-centred trp operator variants showed that positions +/-1 of the alpha-centred trp operators play a crucial role in tetramerisation. The two innermost base pairs of the alpha-centred trp operator are not involved in contacts with the dimer of the Trp repressor binding to it. However, substitutions in these positions (T-A to G-T) effectively transform the alpha-centred trp operator into a beta-centred trp operator, and thus encourage the binding of two Trp repressor dimers to this operator. Finally, we demonstrate, with suitable heterodimers, that one subunit of each dimer suffices to bind to a beta-centred trp operator.