An experimental and theoretical study of the inhibition of Escherichia coli lac operon gene expression by antigene oligonucleotides

Double duplex invasion of DNA induced by ultrafast photo-cross-linking using 3-cyanovinylcarbazole for antigene methods

New photoresponsive antigene probes containing^CNVK and^CNU have a high double-duplex invasion capability upon photoirradiation because of the inhibition of photo-cross-linking between the probes.

The sensitivity and significance analysis of parameters in the model of pH regulation on lactic acid production by Lactobacillus bulgaricus

Background

The excessive production of lactic acid by L. bulgaricus during yogurt storage is a phenomenon we are always tried to prevent. The methods used in industry either control the post-acidification inefficiently or kill the probiotics in yogurt. Genetic methods of changing the activity of one enzyme related to lactic acid metabolism make the bacteria short of energy to growth, although they are efficient ways in controlling lactic acid production.

Results

A model of pH-induced promoter regulation on the production of lactic acid by L. bulgaricus was built. The modelled lactic acid metabolism without pH-induced promoter regulation fitted well with wild type L. bulgaricus (R²_LAC = 0.943, R²_LA = 0.942). Both the local sensitivity analysis and Sobol sensitivity analysis indicated parameters T_max, GR, K_LR, S, V₀, V₁ and d_LR were sensitive. In order to guide the future biology experiments, three adjustable parameters, K_LR, V₀ and V₁, were chosen for further simulations. V₀ had little effect on lactic acid production if the pH-induced promoter could be well induced when pH decreased to its threshold. K_LR and V₁ both exhibited great influence on the producing of lactic acid.

Conclusions

The proposed method of introducing a pH-induced promoter to regulate a repressor gene could restrain the synthesis of lactic acid if an appropriate strength of promoter and/or an appropriate strength of ribosome binding sequence (RBS) in lacR gene has been designed.

Nonlinear fitness landscape of a molecular pathway

Genes are regulated because their expression involves a fitness cost to the organism. The production of proteins by transcription and translation is a well-known cost factor, but the enzymatic activity of the proteins produced can also reduce fitness, depending on the internal state and the environment of the cell. Here, we map the fitness costs of a key metabolic network, the lactose utilization pathway in Escherichia coli. We measure the growth of several regulatory lac operon mutants in different environments inducing expression of the lac genes. We find a strikingly nonlinear fitness landscape, which depends on the production rate and on the activity rate of the lac proteins. A simple fitness model of the lac pathway, based on elementary biophysical processes, predicts the growth rate of all observed strains. The nonlinearity of fitness is explained by a feedback loop: production and activity of the lac proteins reduce growth, but growth also affects the density of these molecules. This nonlinearity has important consequences for molecular function and evolution. It generates a cliff in the fitness landscape, beyond which populations cannot maintain growth. In viable populations, there is an expression barrier of the lac genes, which cannot be exceeded in any stationary growth process. Furthermore, the nonlinearity determines how the fitness of operon mutants depends on the inducer environment. We argue that fitness nonlinearities, expression barriers, and gene–environment interactions are generic features of fitness landscapes for metabolic pathways, and we discuss their implications for the evolution of regulation.

The levels of protein produced by an organism are likely to change its fitness, potentially driving the evolution of genetic regulation. Importantly, protein expression generates costs as well as benefits. Here, we use a model genetic system, the lac operon of Escherichia coli, to investigate different sources of fitness costs. We find that fitness depends not only on the production rate of proteins but also on their enzymatic activity. A simple quantitative model, which is based on the biophysics of protein production and activity, accurately reproduces the experimental results and provides testable predictions. The model describes a feedback cycle between a molecular pathway and the growth rate of cells: pathway activity impedes growth, but growth itself affects the pathway. This feedback can generate dramatic effects, such as gene expression barriers, fitness cliffs, and population extinctions, which can be triggered by small environmental or genetic changes. Our results disentangle the complex interplay of protein production and activity, and they show how these processes shape the evolution of simple organisms.

Anti-gene padlocks eliminate Escherichia coli based on their genotype

OBJECTIVES

Several therapeutic strategies that target nucleic acids exist; however, most approaches target messenger RNA, rather than genomic DNA. We describe a novel oligonucleotide-based strategy, called anti-gene padlocks (AGPs), which eliminate Escherichia coli based on their genotype.

METHODS

The strategy employs an oligonucleotide with a double hairpin structure where both strands of the AGP are complementary to both strands of a target gene. We tested AGPs for in vitro binding and inhibition of DNA polymerization. AGPs were electroporated into bacterial cells with and without gene targets along with an ampicillin resistance plasmid, and cell survival was measured.

RESULTS

In vitro, AGPs bound the DNA target in a sequence-dependent fashion and inhibited DNA synthesis. When transformed into bacterial cells containing 10, 20 or 30 bp lacZ or 20 bp proA DNA targets in their genomes, AGPs selectively killed or otherwise inhibited growth of these cells, while those lacking the target demonstrated little, if any, toxicity. A single transformation resulted in approximately 30% to 40% loss of target-bearing cells. Structure-function experiments were performed to define essential AGP requirements.

CONCLUSIONS

These results suggest that AGPs may be a useful tool to eliminate specific cell populations.

The effect of stochasticity on the lac operon: an evolutionary perspective

The role of stochasticity on gene expression is widely discussed. Both potential advantages and disadvantages have been revealed. In some systems, noise in gene expression has been quantified, in among others the lac operon of Escherichia coli. Whether stochastic gene expression in this system is detrimental or beneficial for the cells is, however, still unclear. We are interested in the effects of stochasticity from an evolutionary point of view. We study this question in the lac operon, taking a computational approach: using a detailed, quantitative, spatial model, we evolve through a mutation–selection process the shape of the promoter function and therewith the effective amount of stochasticity. We find that noise values for lactose, the natural inducer, are much lower than for artificial, nonmetabolizable inducers, because these artificial inducers experience a stronger positive feedback. In the evolved promoter functions, noise due to stochasticity in gene expression, when induced by lactose, only plays a very minor role in short-term physiological adaptation, because other sources of population heterogeneity dominate. Finally, promoter functions evolved in the stochastic model evolve to higher repressed transcription rates than those evolved in a deterministic version of the model. This causes these promoter functions to experience less stochasticity in gene expression. We show that a high repression rate and hence high stochasticity increases the delay in lactose uptake in a variable environment. We conclude that the lac operon evolved such that the impact of stochastic gene expression is minor in its natural environment, but happens to respond with much stronger stochasticity when confronted with artificial inducers. In this particular system, we have shown that stochasticity is detrimental. Moreover, we demonstrate that in silico evolution in a quantitative model, by mutating the parameters of interest, is a promising way to unravel the functional properties of biological systems.

Gene expression is a process that is inherently stochastic because of the low number of molecules that are involved. In recent years it has become possible to measure the amount of stochasticity in gene expression, which has inspired a debate about the importance of stochasticity in gene expression. Little attention, however, has been paid to stochasticity in gene expression from an evolutionary perspective. We studied the evolutionary consequences of stochastic gene expression in one of the best-known systems of genetic regulation, the lac operon of E. coli, which regulates lactose uptake and metabolism. We used a computational approach, in which we let cells evolve their lac operon promoter function in a fluctuating, spatially explicit, environment. Cells can in this way adapt to the environment, but also change the amount of stochasticity in gene expression. We find that cells evolve their repressed transcription rates to higher values in a stochastic model than in a deterministic model. Higher repressed transcription rates means less stochasticity, and, hence, these cells appear to avoid stochastic gene expression in this particular system. We find that this can be explained by the fact that stochastic gene expression causes a larger delay in lactose uptake, compared with deterministic gene expression.

Hitting bacteria at the heart of the central dogma: sequence-specific inhibition

An important objective in developing new drugs is the achievement of high specificity to maximize curing effect and minimize side-effects, and high specificity is an integral part of the antisense approach. The antisense techniques have been extensively developed from the application of simple long, regular antisense RNA (asRNA) molecules to highly modified versions conferring resistance to nucleases, stability of hybrid formation and other beneficial characteristics, though still preserving the specificity of the original nucleic acids. These new and improved second- and third-generation antisense molecules have shown promising results. The first antisense drug has been approved and more are in clinical trials. However, these antisense drugs are mainly designed for the treatment of different human cancers and other human diseases. Applying antisense gene silencing and exploiting RNA interference (RNAi) are highly developed approaches in many eukaryotic systems. But in bacteria RNAi is absent, and gene silencing by antisense compounds is not nearly as well developed, despite its great potential and the intriguing possibility of applying antisense molecules in the fight against multiresistant bacteria. Recent breakthrough and current status on the development of antisense gene silencing in bacteria including especially phosphorothioate oligonucleotides (PS-ODNs), peptide nucleic acids (PNAs) and phosphorodiamidate morpholino oligomers (PMOs) will be presented in this review.

In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose

Bistability in the lac operon of Escherichia coli has been widely studied, both experimentally and theoretically. Experimentally, bistability has been observed when E. coli is induced by an artificial, nonmetabolizable, inducer. However, if the lac operon is induced with lactose, the natural inducer, bistability has not been demonstrated. We derive an analytical expression that can predict the occurrence of bistability both for artificial inducers and lactose. We find very different conditions for bistability in the two cases. Indeed, for artificial inducers bistability is predicted, but for lactose the condition for bistability is much more difficult to satisfy. Moreover, we demonstrate that in silico evolution of the lac operon generates an operon that avoids bistability with respect to lactose, but does exhibit bistability with respect to artificial inducers. The activity of this evolved operon strikingly resembles the experimentally observed activity of the operon. Thus our computational experiments suggest that the wild-type lac operon, which regulates lactose metabolism, is not a bistable switch. Nevertheless, for engineering purposes, this operon can be used as a bistable switch with artificial inducers.

The chemical and biochemical properties of methylphosphotriester DNA

Methylphosphotriester DNA shows a number of interesting bio-organic properties. Its behavior is quite different from selected modified DNAs as the related methylphosphonate oligonucleotides.

DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics

In this paper, a discrete event based mechanistic simulation platform DEMSIM is developed for testing and validating putative regulatory interactions. The proposed framework models the main processes in gene expression, which are transcription, translation and decay processes, as stand-alone modules while superimposing the regulatory circuitry to obtain an accurate time evolution of the system. The stochasticity inherent to gene expression and regulation processes is captured using Monte Carlo based sampling. The proposed framework is applied to the extensively studied lac operon system, the SOS response system and the araBAD operon system of Escherichia coli. The results for the lac gene system demonstrate the simulation framework's ability to capture the dynamics of gene regulation, whereas the results for the SOS response system indicate that the framework is able to make accurate predictions about system behavior in response to perturbations. Finally, simulation studies for the araBAD system suggest that the developed framework is able to distinguish between different plausible regulatory mechanisms postulated to explain observed gene expression profiles. Overall, the obtained results highlight the effectiveness of DEMSIM at describing the underlying biological processes involved in gene regulation for querying alternative regulatory hypotheses.

Dynamics and bistability in a reduced model of the lac operon

It is known that the lac operon regulatory pathway is capable of showing bistable behavior. This is an important complex feature, arising from the nonlinearity of the involved mechanisms, which is essential to understand the dynamic behavior of this molecular regulatory system. To find which of the mechanisms involved in the regulation of the lac operon is the origin of bistability, we take a previously published model which accounts for the dynamics of mRNA, lactose, allolactose, permease and beta-galactosidase involvement and simplify it by ignoring permease dynamics (assuming a constant permease concentration). To test the behavior of the reduced model, three existing sets of data on beta-galactosidase levels as a function of time are simulated and we obtain a reasonable agreement between the data and the model predictions. The steady states of the reduced model were numerically and analytically analyzed and it was shown that it may indeed display bistability, depending on the extracellular lactose concentration and growth rate.

Genomic data for alternate production strategies. I. Identification of major contaminating species for Cobalt+2 immobilized metal affinity chromatography

Recent advances in technology have allowed for the identification of complex protein mixtures in a rapid fashion. This report highlights the use of 2D gel electrophoresis, mass spectrometry, and database analysis to determine contaminating species of the Escherichia coli genome that are present during immobilized metal affinity chromatography (IMAC), highlighting Co(2+) as the affinity ligand. Four proteins (triosephosphate isomerase, alpha galactosidase, Hsp90, and glucosamine 6-phosphate synthase) constitute the majority of E. coli proteins that bind and potentially may coelute during chromatography. Results are discussed within the context of changes that when implemented could lead to an increase in IMAC efficiency, not by altering column conditions, but rather by changing the nature of the nuisance proteins that principally reduce column capacity and extend processing times. Such a study illustrates the use of proteome data to aid in bioprocess design.

Triplex-forming oligonucleotides as modulators of gene expression

Triplex-forming oligonucleotides (TFOs) have gained prominence in the recent years because of their potential applications in antigene therapy. In particular they have been used as (i) inducers of site-specific mutations, (ii) reagents that selectively and specifically cleave target DNA, and (iii) as modulators of gene expression. In this mini-review, we have made an attempt to highlight the characteristics of these TFOs and the effects of various modifications in the phosphate backbone as well as in the purine and pyrimidine moieties, which contribute to the stability and efficiency of triplex formation. Studies to explore the mechanism of down-regulation of transcription of various genes suggest that at least some TFOs exert their effect by inhibiting binding of specific transcription factors to their cognate cis-acting elements. Recent reports indicate the presence of these potential triplex-forming DNA structures in the genomes of prokaryotes and eukaryotes that may play a major role in target site selection and chromosome segregation as well as in the cause of heritable diseases. Finally, some potential problems in the development of these TFOs as antigene therapeutic agents have also been discussed.