Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor

Force and the α-C-terminal domains bias RNA polymerase recycling

After an RNA polymerase reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA and recommence RNA synthesis from the previous or a different promoter. Magnetic tweezers were used to monitor such secondary transcription and determine the effects of low forces assisting or opposing translocation, protein roadblocks, and transcription factors. Remarkably, up to 50% of Escherichia coli (E. coli) RNA polymerases diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained associated with the DNA promoting sliding and enabling re-initiation from promoters in either orientation. However, deletions of the α-C-terminal domains severely limited the ability of RNAP to turn around between successive rounds of transcription. The addition of elongation factor NusG, which competes with σ70 for binding to RNAP, limited additional rounds of transcription. Surprisingly, sliding RNA polymerases blocked by a DNA-bound lac repressor could slowly re-initiate transcription and were not affected by NusG, suggesting a σ-independent pathway. Low forces effectively biased promoter selection suggesting a prominent role for topological entanglements that affect RNA polymerase translocation.

Reciprocating RNA Polymerase batters through roadblocks

RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo.

Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor

Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map allosteric effects in a paradigm ligand-responsive transcription factor, the lac repressor (LacI), in different functional states (apo, or bound to inducer, anti-inducer, and/or DNA). Although X-ray crystal structures of the LacI core domain in these states are nearly indistinguishable, HDX/MS experiments reveal widespread differences in flexibility. We integrate these results with modeling of protein-ligand-solvent interactions to propose a revised model for allostery in LacI, where ligand binding allosterically shifts the conformational ensemble as a result of distinct changes in the rigidity of secondary structures in the different states. Our model provides a mechanistic basis for the altered function of distal mutations. More generally, our approach provides a platform for characterizing and engineering protein allostery.

Determining the Transcription Rates Yielding Steady-State Production of mRNA in the Lac Genetic Switch of Escherichia coli

To elucidate the regulatory dynamics of the gene expression activation and inactivation, an in silico biochemical model of the lac circuit in Escherichia coli was used to evaluate the transcription rates that yield the steady-state mRNA production in active and inactive states of the lac circuit. This result can be used in synthetic biology applications to understand the limits of the genetic synthesis. Since most genetic networks involve many interconnected components with positive and negative feedback control, intuitive understanding of their dynamics is often difficult to obtain. Although the kinetic model of the lac circuit considered involves only a single positive feedback, the developed computational framework can be used to evaluate supported ranges of other reaction rates in genetic circuits with more complex regulatory networks. More specifically, the inducible lac gene switch in E. coli is regulated by unbinding and binding of the inducer-repressor complexes to or from the DNA operator to switch the gene expression on and off. The dependency of mRNA production at steady state on different transcription rates and the repressor complexes has been studied by computer simulations in the Lattice Microbe software. Provided that the lac circuit is in active state, the transcription rate is independent of the inducer-repressor complexes present in the cell. In inactive state, the transcription rate is dependent on the specific inducer-repressor complex bound to the operator that inactivates the gene expression. We found that the repressor complex with the largest affinity to the operator yields the smallest range of the feasible transcription rates to yield the steady state while the lac circuit is in inactive state. In contrast, the steady state in active state can be obtained for any value of the transcription rate.

Lactose repressor hinge domain independently binds DNA

The short 8-10 amino acid "hinge" sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer-binding domains. Structural studies of full-length or truncated LacI-operator DNA complexes demonstrate insertion of the dimeric helical "hinge" structure at the center of the operator sequence. This association bends the DNA ∼40° and aligns flanking semi-symmetric DNA sites for optimal contact by the N-terminal helix-turn-helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences. To determine ability of the hinge helix alone to mediate DNA binding, we examined (i) binding of LacI variants with deletion of residues 1-50 to remove the HtH DNA binding domain or residues 1-58 to remove both HtH and hinge domains and (ii) binding of a synthetic peptide corresponding to the hinge sequence with a Val52Cys substitution that allows reversible dimer formation via a disulfide linkage. Binding affinity for DNA is orders of magnitude lower in the absence of the helix-turn-helix domain with its highly positive charge. LacI missing residues 1-50 binds to DNA with ∼4-fold greater affinity for operator than for nonspecific sequences with minimal impact of inducer presence; in contrast, LacI missing residues 1-58 exhibits no detectable affinity for DNA. In oxidized form, the dimeric hinge peptide alone binds to O1 and nonspecific DNA with similarly small difference in affinity; reduction to monomer diminished binding to both O1 and nonspecific targets. These results comport with recent reports regarding LacI hinge interaction with DNA sequences.

Data on publications, structural analyses, and queries used to build and utilize the AlloRep database

The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, “AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators” (Sousa et al., 2016) [1].

Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores

As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for coevolution between pairs of positions. Coevolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of coevolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded coevolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; "central" positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise coevolution scores: instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints-detectable by divergent algorithms--that occur at key protein locations. Finally, we discuss the fact that multiple patterns coexist in evolutionary data that, together, give rise to emergent protein functions.

Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins

To modulate transcription, a variety of input signals must be sensed by genetic regulatory proteins. In these proteins, flexibility and disorder are emerging as common themes. Prokaryotic regulators generally have short, flexible segments, whereas eukaryotic regulators have extended regions that lack predicted secondary structure (intrinsic disorder). Two examples illustrate the impact of flexibility and disorder on gene regulation: the prokaryotic LacI/GalR family, with detailed information from studies on LacI, and the eukaryotic family of Hox proteins, with specific insights from investigations of Ultrabithorax (Ubx). The widespread importance of structural disorder in gene regulatory proteins may derive from the need for flexibility in signal response and, particularly in eukaryotes, in protein partner selection.

Case study on temperature-accelerated molecular dynamics simulation of ligand dissociation: inducer dissociation from the Lac repressor protein

We studied ligand dissociation from the inducer-binding domain of the Lac repressor protein using temperature-accelerated molecular dynamics (TAMD) simulations. With TAMD, ligand dissociation could be observed within relatively short simulation time. This allowed many dissociation trajectories to be sampled. Under the adiabatic approximation of TAMD, all but one degree of freedom of the system were sampled from usual canonical ensembles at room temperature. Thus, meaningful statistical analyses could be carried out on the trajectories. A systematic approach was proposed to analyze possible correlations between ligand dissociation and fluctuations of various protein conformational coordinates. These analyses employed relative entropies, allowing both linear and nonlinear correlations to be considered. Applying the simulation and analysis methods to the inducer binding domain of the Lac repressor protein, we found that ligand dissociation from this protein correlated mainly with fluctuations of side-chain conformations of a few residues that surround the binding pocket. In addition, the two binding sites of the dimeric protein were dynamically coupled: occupation of one site by an inducer molecule could significantly reduce or slow down conformational dynamics around the other binding pocket.

A single mutation in the core domain of the lac repressor reduces leakiness

BACKGROUND

The lac operon provides cells with the ability to switch from glucose to lactose metabolism precisely when necessary. This metabolic switch is mediated by the lac repressor (LacI), which in the absence of lactose binds to the operator DNA sequence to inhibit transcription. Allosteric rearrangements triggered by binding of the lactose isomer allolactose to the core domain of the repressor impede DNA binding and lift repression. In Nature, the ability to detect and respond to environmental conditions comes at the cost of the encoded enzymes being constitutively expressed at low levels. The readily-switched regulation provided by LacI has resulted in its widespread use for protein overexpression, and its applications in molecular biology represent early examples of synthetic biology. However, the leakiness of LacI that is essential for the natural function of the lac operon leads to an increased energetic burden, and potentially toxicity, in heterologous protein production.

RESULTS

Analysis of the features that confer promiscuity to the inducer-binding site of LacI identified tryptophan 220 as a target for saturation mutagenesis. We found that phenylalanine (similarly to tryptophan) affords a functional repressor that is still responsive to IPTG. Characterisation of the W220F mutant, LacIWF, by measuring the time dependence of GFP production at different IPTG concentrations and at various incubation temperatures showed a 10-fold reduction in leakiness and no decrease in GFP production. Cells harbouring a cytotoxic protein under regulatory control of LacIWF showed no decrease in viability in the early phases of cell growth. Changes in responsiveness to IPTG observed in vivo are supported by the thermal shift assay behaviour of purified LacIWF with IPTG and operator DNA.

CONCLUSIONS

In LacI, long-range communications are responsible for the transmission of the signal from the inducer binding site to the DNA binding domain and our results are consistent with the involvement of position 220 in modulating these. The mutation of this single tryptophan residue to phenylalanine generated an enhanced repressor with a 10-fold decrease in leakiness. By minimising the energetic burden and cytotoxicity caused by leakiness, LacIWF constitutes a useful switch for protein overproduction and synthetic biology.

Allostery and the lac Operon

The ability to regulate gene expression is essential for controlling metabolic events in a cell. Proteins that function like molecular switches respond to fluctuations in the environment to maintain homeostasis. The operon model, proposed by Jacob and Monod, provides a cogent depiction for how gene expression is regulated. A molecular mechanism for the regulation followed shortly with the theory for allosteric transition. Over the past half-century, the details of the lac operon and the allosteric model have been tested using genetic, biochemical, and structural techniques. Remarkably, the principles originally put forward 50 years ago remain essentially unchanged. Models for the operon and the theory of allosteric transitions are two of the most profound discoveries of molecular biology.