The LexA repressor and its isolated amino-terminal domain interact cooperatively with poly[d(A-T)], a contiguous pseudo-operator, but not with random DNA: a circular dichroism study

Biochemical characterization ofMycobacterium tuberculosisLexA and structural studies of its C-terminal segment

LexA is a protein that is involved in the SOS response. The protein fromMycobacterium tuberculosisand its mutants have been biochemically characterized and the structures of their catalytic segments have been determined. The protein is made up of an N-terminal segment, which includes the DNA-binding domain, and a C-terminal segment encompassing much of the catalytic domain. The two segments are defined by a cleavage site. Full-length LexA, the two segments, two point mutants involving changes in the active-site residues (S160A and K197A) and another mutant involving a change at the cleavage site (G126D) were cloned and purified. The wild-type protein autocleaves at basic pH, while the mutants do not. The wild-type and the mutant proteins dimerize and bind DNA with equal facility. The C-terminal segment also dimerizes, and it also shows a tendency to form tetramers. The C-terminal segment readily crystallized. The crystals obtained from attempts involving the full-length protein and its mutants contained only the C-terminal segment including the catalytic core and a few residues preceding it, in a dimeric or tetrameric form, indicating protein cleavage during the long period involved in crystal formation. Modes of tetramerization of the full-length protein similar to those observed for the catalytic core are feasible. A complex ofM. tuberculosisLexA and the cognate SOS box could be modeled in which the mutual orientation of the two N-terminal domains differs from that in theEscherichia coliLexA–DNA complex. These results represent the first thorough characterization ofM. tuberculosisLexA and provide definitive information on its structure and assembly. They also provide leads for further exploration of this important protein.

Dimerisation mutants of Lac repressor. I. A monomeric mutant, L251A, that binds Lac operator DNA as a dimer

Dimer formation between monomers of the Escherichia coli Lac repressor is substantially specificed by the interactions between three alpha-helices in each monomer which form a hydrophobic interface. As a first step in analysing the specificity of this interaction, we examined the mutant L251A. LacR bearing this mutation in a background lacking the C-terminal heptad repeats is completely incapable of forming dimers in solution, with a dimer-monomer equilibrium dissociation constant, or Kd, higher than 10(-5)M. This correlates with a 200-fold decrease in its ability to repress the lac operon in vivo compared to dimeric LacR. Surprisingly, the mutant is still capable of forming dimers upon binding to short operator DNA in vitro. Analysis of the kinetic parameters of binding of the mutant to operator DNA reveals a 2000 to 3000-fold increase in the equilibrium dissociation constant (Kd) of the mutant-DNA complex in comparison to dimeric LacR-operator complexes, with the change almost entirely due to a greater than 1000-fold decrease in association rate. The dissociation rate varies only by a factor of about two, in comparison to dimeric LacR. This change reflects a kinetic pathway in which dimer formation, in solution or on DNA, is the rate-limiting step. These findings have implications for the specificity and stability of the protein-protein interface in question.

Preferential interactions of the Escherichia coli LexA repressor with anions and protons are coupled to binding the recA operator

The binding of Escherichia coli LexA repressor to the recA operator was examined as a function of the concentration of NaCl, KCl, NaF, and MgCl2 at pH 7.5, 21 degrees C. The effects of pH at 100 mM NaCl were also examined. Changes both in the qualitative appearance of the binding isotherms and in the magnitude of the apparent binding affinity with changes in solution conditions suggest that binding of anions and protons by LexA repressor is linked to oligomerization and/or operator binding. Binding of LexA repressor to the recA operator in the presence of NaCl ranging from 25 to 400 mM at picomolar DNA concentration showed a broad, apparently noncooperative, binding isotherm. Binding of LexA repressor in NaF at the same [DNA] yielded binding isotherms with a narrow transition, reflecting an apparently cooperative binding process. Also, the apparent binding affinity was weaker in NaF than in NaCl. Furthermore, the binding affinity and also the apparent binding mode, cooperative vs noncooperative, were pH dependent. The binding affinity of LexA repressor for operator was greatest near neutral pH. The apparent binding mode was noncooperative at pH 7-9 but was cooperative at pH 6 or 9.3. These observations suggest that the specific cation and anion composition and concentrations must be considered in understanding the details of regulation of the SOS system.

Binding of Escherichia coli LexA repressor to the RecA operator

Equilibrium binding of Escherichia coli LexA repressor to the recA operator was studied by the polyacrylamide gel mobility shift assay as a function of solution conditions. In the presence of NaCl at 20 degrees C, there was a significant salt dependence in binding to the recA operator, typical for protein-nucleic acid interactions with some electrostatic contribution to the binding free energy. In preliminary experiments in which the anion of the Na+ salt was changed from chloride to fluoride, little change was found with anion identity. This indicates that the salt effect on the binding interaction arises solely from the polyelectrolyte effect, not from anion binding or release by the protein upon complex formation. Increasing the temperature to 37 degrees C changed the binding affinity for complex formation at any given salt concentration and resulted in a change in the sensitivity of complex formation to NaCl concentration. Quantitative analysis of the data to obtain equilibrium binding constants is discussed.

Control of the LexA regulon by pH: evidence for a reversible inactivation of the LexA repressor during the growth cycle of Escherichia coli

The LexA repressor controls the expression of several genes, including lexA, recA, and sfiA, which are induced when exponentially growing bacteria are exposed to DNA-damaging agents. Induction of this so-called SOS response takes place while LexA is cleaved in a reaction that requires the RecA protein and damaged DNA. We have shown that large fluctuations in the cellular concentration of the LexA repressor and in the rate of transcription of the sfiA gene also occur spontaneously during bacterial growth in complex medium such as LB. The possibility that changes in external or internal pH may explain these fluctuations has been explored. A consistent pattern was established whereby conditions leading to either increased or decreased pH were associated with altered expression of the lexA and sfiA genes. These data can be explained by a model in which the LexA repressor exists in either of two forms in equilibrium: a form favoured at homeostatic internal pH, which has a low affinity for the operators of LexA-controlled genes; and a form accumulated in response to a transient decrease in internal pH, which has a high affinity for operators.

Isolation and characterization of LexA mutant repressors with enhanced DNA binding affinity

The LexA repressor from Escherichia coli is a sequence-specific DNA binding protein that shows no pronounced sequence homology with any of the known structural motifs involved in DNA binding. Since little is known about how this protein interacts with DNA, we have selected and characterized a great number of intragenic, second-site mutations which restored at least partially the activity of LexA mutant repressors deficient in DNA binding. In 47 cases, the suppressor effect of these mutations was due to an Ind- phenotype leading presumably to a stabilization of the mutant protein. With one exception, these second-site mutations are all found in a small cluster (amino acid residues 80 to 85) including the LexA cleavage site between amino acid residues 84 and 85 and include both already known Ind- mutations as well as new variants like GN80, GS80, VL82 and AV84. The remaining 26 independently isolated second-site suppressor mutations all mapped within the amino-terminal DNA binding domain of LexA, at positions 22 (situated in the turn between helix 1 and helix 2) and positions 57, 59, 62, 71 and 73. These latter amino acid residues are all found beyond helix 3, in a region where we have previously identified a cluster of LexA (Def) mutant repressors. In several cases the parental LexA (Def) mutation has been removed by subcloning or site-directed mutagenesis. With one exception, these LexA variants show tighter in vivo repression than the LexA wild-type repressor. The most strongly improved variant (LexA EK71, i.e. Glu71----Lys) that shows an about threefold increased repression rate in vivo, was purified and its binding to a short consensus operator DNA fragment studied using a modified nitrocellulose filter binding assay. As expected from the in vivo data, LexA EK71 interacts more tightly with both operator and (more dramatically) with non-operator DNA. A determination of the equilibrium association constants of LexA EK71 and LexA wild-type as a function of monovalent salt concentration suggests that LexA EK71 might form an additional ionic interaction with operator DNA as compared to the LexA wild-type repressor. A comparison of the binding of LexA to a non-operator DNA fragment further shows that LexA interacts with the consensus operator very selectively with a specificity factor of Ks/Kns of 1.4 x 10(6) under near-physiological salt conditions.

Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice. Effects on ligand-lattice association

A method using binding site "neighbor-effect" parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be extended to more complex situations. The general equation for the isotherm is v/LF = SFKF, where v is the ratio of bound ligands to lattice residues, LF is the free ligand concentration, SF is the fraction of binding sites that are free, and KF is the average association constant of a free site. Solutions are derived for three cases: symmetric ligands, and asymmetric ligands on isotropic or anisotropic lattices. For symmetric ligands there is one NEP, E, which is the ratio of the average binding affinity of a free site if the status of the lattice residue neighboring one end of the site is unspecified (left to chance) to the affinity when this residue is free (holding the other neighbor constant). Thus KF is KE2, where K is the affinity of an isolated site. If a site is n residues long, SF is f ffn-1, where f = 1 - nv is the fraction of residues that are free and ff is the conditional probability that a free residue is bordered on a given side by another free residue. The expression for ff is 1/(1 + x/E), where x is v/f, E is (1 - x + [(1 - x)2 + 4x omega]1/2)/2, and omega is the co-operativity parameter. The binding of asymmetric ligands to an isotropic lattice is described by two NEPs; the last case involves four NEPs and a bound ligand orientation parameter. For each case, the expected length distribution of clusters of bound ligands can be calculated as a function of v. When Scatchard plots with the same intercepts and initial slope are compared, it is found that ligand asymmetry lowers the isotherm (relative to the corresponding symmetric ligand isotherm), whereas lattice anisotrophy raises it.

1H-NMR investigation of the interaction of the amino terminal domain of the LexA repressor with a synthetic half-operator

A synthetic half-operator DNA-duplex, d(GCTACTGTATGT), containing a portion of the proposed recognition sequence (CTGT) of several "SOS" genes, has been synthesized. The dodecamer has been characterized through 1H-NMR spectroscopy. Complete assignment of exchangeable hydrogen bonded imino protons has been achieved by applying 1D NOE techniques and an analysis of the temperature dependence of the chemical shifts. In order to determine the specific role of the CTGT consensus sequence in the overall recognition process, the oligonucleotide duplex has been titrated with the amino terminal DNA binding domain of the LexA repressor. The observation of substantial changes of 1H-NMR chemical shifts in the imino proton region upon interaction with the protein strongly suggests that the protein binds specifically to the operator DNA. The largest deviations of 1H-NMR chemical shifts upon protein binding have been observed for protons assigned to the CTGT segment, thus strongly suggesting a direct involvement of this sequence in the binding process. At high potassium chloride concentrations the 1H-NMR chemical shift deviations are reverted which is consistent with the known drop in the affinity constant of LexA for operator DNA at high salt concentrations.

DNA binding properties of the LexA repressor

The LexA repressor from Escherichia coli negatively regulates the transcription of about 20 different genes upon binding with variable affinity to single-, double- or even triple-operators as in the case of the recN gene. Binding of LexA to multiple operators is cooperative if the spacing between these operators is favorable. LexA recognizes DNA via its amino-terminal domain. The three-dimensional structure of this domain has been determined by NMR measurements. It contains three alpha-helices spanning residues 8-20, 28-35 and 41-54. In view of this structure, but also according to homology considerations and the unusual contact pattern with the DNA backbone, the LexA repressor is not a normal helix-turn-helix DNA binding protein like for example phage lambda repressor. LexA is at best a distant relative of this class of transcription factors and should probably be considered as a protein that contains a new DNA binding motif. A cluster of LexA mutant repressors deficient in DNA binding falling into the third helix (residues 41-54 bp) suggests that this helix is involved in DNA recognition.