Binding of an inducer to the lac repressor

LacI-DNA-IPTG loops: equilibria among conformations by single-molecule FRET

The E. coli Lac repressor (LacI) tetramer binds simultaneously to a promoter-proximal DNA binding site (operator) and an auxiliary operator, resulting in a DNA loop, which increases repression efficiency. Induction of the lac operon by allolactose reduces the affinity of LacI for DNA, but induction does not completely prevent looping in vivo. Our previous work on the conformations of LacI loops used a hyperstable model DNA construct, 9C14, that contains a sequence directed bend flanked by operators. Single-molecule fluorescence resonance energy transfer (SM-FRET) on a dual fluorophore-labeled LacI-9C14 loop showed that it adopts a single, stable, high-FRET V-shaped LacI conformation. Ligand-induced changes in loop geometry can affect loop stability, and the current work assesses loop population distributions for LacI-9C14 complexes containing the synthetic inducer IPTG. SM-FRET confirms that the high-FRET LacI-9C14 loop is only partially destabilized by saturating IPTG. LacI titration experiments and FRET fluctuation analysis suggest that the addition of IPTG induces loop conformational dynamics and re-equilibration between loop population distributions that include a mixture of looped states that do not exhibit high-efficiency FRET. The results show that repression by looping even at saturating IPTG should be considered in models for regulation of the operon. We propose that persistent DNA loops near the operator function biologically to accelerate rerepression upon exhaustion of inducer.

Regulatory consequences of gene translocation in bacteria

Gene translocations play an important role in the plasticity and evolution of bacterial genomes. In this study, we investigated the impact on gene regulation of three genome organizational features that can be altered by translocations: (i) chromosome position; (ii) gene orientation; and (iii) the distance between a target gene and its transcription factor gene (‘target-TF distance’). Specifically, we quantified the effect of these features on constitutive expression, transcription factor binding and/or gene expression noise using a synthetic network in Escherichia coli composed of a transcription factor (LacI repressor) and its target gene (yfp). Here we show that gene regulation is generally robust to changes in chromosome position, gene orientation and target-TF distance. The only demonstrable effect was that chromosome position alters constitutive expression, due to changes in gene copy number and local sequence effects, and that this determines maximum and minimum expression levels. The results were incorporated into a mathematical model which was used to quantitatively predict the responses of a simple gene network to gene translocations; the predictions were confirmed experimentally. In summary, gene translocation can modulate constitutive gene expression levels due to changes in chromosome position but it has minimal impact on other facets of gene regulation.

Noise contributions in an inducible genetic switch: a whole-cell simulation study

Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently published in vivo single-molecule fluorescence experiments along with in vitro rate constants. For the well-stirred system, investigation of the intrinsic noise in the circuit as a function of the inducer concentration and in the presence/absence of the feedback mechanism reveals that the noise peaks near the switching threshold. Applying maximum likelihood estimation, we show that the analytic two-state model of gene expression can be used to extract stochastic rates from the simulation data. The simulations also provide mRNA–protein probability landscapes, which demonstrate that switching is the result of crossing both mRNA and protein thresholds. Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due to cell structure and crowding in the cytoplasm. Compared to systems without spatial heterogeneity, the model for the fast-growth cells predicts a slight decrease in the overall noise and an increase in the repressors rebinding rate due to anomalous subdiffusion. The tomograms for E. coli grown under slow-growth conditions identify the positions of the ribosomes and the condensed nucleoid. The smaller slow-growth cells have increased mRNA localization and a larger internal inducer concentration, leading to a significant decrease in the lifetime of the repressor–operator complex and an increase in the frequency of transcriptional bursts.

Expressing genes in a bacterial cell is noisy and random. A colony of bacteria grown from a single cell can show remarkable differences in the copy number per cell of a given protein after only a few generations. In this work we use computer simulations to study the variation in how individual cells in a population express a set of genes in response to an environmental signal. The modeled system is the lac genetic switch that Escherichia coli uses to find, collect, and process lactose sugar from the environment. The noise inherent in the genetic circuit controlling the cell's response determines how similar the cells are to each other and we study how the different components of the circuit affect this noise. Furthermore, an estimated 30–50% of the cell volume is taken up by a wide variety of large biomolecules. To study the response of the circuit caused by crowding, we simulate the circuit inside a three-dimensional model of an E. coli cell built using data from cryoelectron tomography reconstructions of a single cell and proteomics data. Correctly including random effects of molecular crowding will be critical to developing fully dynamic models of living cells.

Comparison of deterministic and stochastic models of the lac operon genetic network

The lac operon has been a paradigm for genetic regulation with positive feedback, and several modeling studies have described its dynamics at various levels of detail. However, it has not yet been analyzed how stochasticity can enrich the system's behavior, creating effects that are not observed in the deterministic case. To address this problem we use a comparative approach. We develop a reaction network for the dynamics of the lac operon genetic switch and derive corresponding deterministic and stochastic models that incorporate biological details. We then analyze the effects of key biomolecular mechanisms, such as promoter strength and binding affinities, on the behavior of the models. No assumptions or approximations are made when building the models other than those utilized in the reaction network. Thus, we are able to carry out a meaningful comparison between the predictions of the two models to demonstrate genuine effects of stochasticity. Such a comparison reveals that in the presence of stochasticity, certain biomolecular mechanisms can profoundly influence the region where the system exhibits bistability, a key characteristic of the lac operon dynamics. For these cases, the temporal asymptotic behavior of the deterministic model remains unchanged, indicating a role of stochasticity in modulating the behavior of the system.

Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction

In vivo induction of the Escherichia coli lactose operon as a function of inducer concentration generates a sigmoidal curve, indicating a non-linear response. Suggested explanations for this dependence include a 2:1 inducer–repressor stoichiometry of induction, which is the currently accepted view. It is, however, known for decades that, in vitro, operator binding as a function of inducer concentration is not sigmoidal. This discrepancy between in vivo and in vitro data has so far not been resolved. We demonstrate that the in vivo non-linearity of induction is due to cooperative repression of the wild-type lac operon through DNA loop formation. In the absence of DNA loops, in vivo induction curves are hyperbolic. In the light of this result, we re-address the question of functional molecular inducer–repressor stoichiometry in induction of the lac operon.

Substitutions at histidine 74 and aspartate 278 alter ligand binding and allostery in lactose repressor protein

In the inducer-bound structure of the lac repressor protein, the side chains of H74 and D278 are positioned to form an ion pair between monomers that appears to be disrupted upon operator binding (Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G., and Lu, P. (1996) Science 271, 1247-1254). A series of single substitutions at H74 and D278 and a double mutant, H74D-D278H, were generated to determine the influence of this interaction on ligand binding and allostery in lac repressor. Introduction of apolar amino acids at H74 resulted in distinct effects on ligand binding. Alanine and leucine substitutions decreased operator binding, while tryptophan and phenylalanine increased affinity for operator DNA. Introduction of a negatively charged residue at position 74 in H74D had minimal effects, and "inverting" the side chains in H74D/D278H did not significantly alter inducer or operator binding at neutral pH. In contrast, all substitutions of D278 increased affinity for operator DNA and diminished inducer binding. These observations can be interpreted in the context of the Monod-Wyman-Changeux model. If a salt bridge were essential for stabilizing or destabilizing the inducer-bound conformation, a mutation at either residue that interrupts this interaction should have a similar effect on allostery. Because the type and degree of alteration in ligand binding properties depended on the nature of the substitution at these residues, the individual roles played by H74 and D278 in lac repressor allostery appear more important than their direct contact across the monomer-monomer interface.

Lactose repressor protein: functional properties and structure

The lactose repressor protein (LacI), the prototype for genetic regulatory proteins, controls expression of lactose metabolic genes by binding to its cognate operator sequences in E. coli DNA. Inducer binding elicits a conformational change that diminishes affinity for operator sequences with no effect on nonspecific binding. The release of operator is followed by synthesis of mRNA encoding the enzymes for lactose utilization. Genetic, chemical and physical studies provided detailed insight into the function of this protein prior to the recent completion of X-ray crystallographic structures. The structural information can now be correlated with the phenotypic data for numerous mutants. These structures also provide the opportunity for physical and chemical studies on mutants designed to examine various aspects of lac repressor structure and function. In addition to providing insight into protein structure-function correlations, LacI has been utilized in a wide variety of applications both in prokaryotic gene expression and in eukaryotic gene regulation and studies of mutagenesis.

Concentration-affinity equivalence in gene regulation: convergence of genetic and environmental effects

It is proposed that equivalent phenotypic effects can be obtained by either structural changes in macromolecules involved in gene regulation or changes in activity of the structurally unaltered macromolecules. This equivalence between changes in activity (concentration) and changes in structure can come into play within physiologically plausible limits and seems to represent an important interface between environment and genome--namely, between environmentally determined and genetically determined gene expression. The equivalence principle helps explain the appearance of phenocopies. It also points to a general pathway favorable to the occurrence, during evolution, of frequent episodes corresponding to Waddington's genetic assimilation and is likely to represent one component of the system responsible for the high frequency of recurrence of parallel evolution.

Chemical modification of arginine residues in the lactose repressor

The lactose repressor protein was chemically modified with 2,3-butanedione and phenylglyoxal. Arginine reaction was quantitated by either amino acid analysis or incorporation of 14C-labeled phenylglyoxal. Inducer binding activity was unaffected by the modification of arginine residues, while both operator and nonspecific DNA binding activities were diminished, although to differing degrees. The correlation of the decrease in DNA binding activities with the modification of approximately 1-2 equiv of arginine per monomer suggests increased reactivity of a functionally essential residue(s). For both reagents, operator DNA binding activity was protected by the presence of calf thymus DNA, and the extent of reaction with phenylglyoxal was simultaneously diminished. This protection presumably results from steric restriction of reagent access to an arginine(s) that is (are) essential for DNA binding interactions. These experiments suggest that there is (are) an essential reactive arginine(s) critical for repressor binding to DNA.

Association of Escherichia coli lac repressor with poly[d(A-T)] monitored with 8-anilino-1-napthalenesulfonate

The association of lac repressor with poly[d(A-T)] was monitored with the fluorescent prob 8-anilino-1-naphthalenesulfonate (Ans). Excess poly[d(A-T)] decreased the emission intensity of the repressor--Ans complex by 30%. Fluorescence titrations indicated that 33 +/- 4 base pairs were required to bind all of the repressor. Sedimentation studies indicated, however, that all of the repressor sedimented as a protein--DNA complex with as few as 10 to 15 base pairs per tetramer, even in the presence of Ans. These data are interpreted with two models: one where repressors bind to both sides of the DNA (Butler, A. P., et al. (1977) Biochemistry 16, 4757: Zingsheim, H.P., et al. (1977) J. Mol. Biol. 115, 565), the other where a double layer of repressors bind to a single side of the DNA. Removal of the amino-terminal regions from the repressor decreased the fluorescence from bound Ans by 77%. The amino-terminal fragments alone did not enhance Ans fluorescence.