-
Journal of the Royal Society, Interface Aug 2008In this paper, the history and importance of the lac operon in the development of molecular and systems biology are briefly reviewed. We start by presenting a... (Review)
Review
In this paper, the history and importance of the lac operon in the development of molecular and systems biology are briefly reviewed. We start by presenting a description of the regulatory mechanisms in this operon, taking into account the most recent discoveries. Then we offer a survey of the history of the lac operon, including the discovery of its main elements and the subsequent influence on the development of molecular and systems biology. Next the bistable behaviour of the operon is discussed, both with respect to its discovery and its molecular origin. A review of the literature in which this bistable phenomenon has been studied from a mathematical modelling viewpoint is then given. We conclude with some brief remarks.
Topics: Escherichia coli; Genomic Instability; Lac Operon; Mathematics; Membrane Transport Proteins; Models, Genetic; Molecular Biology; Systems Biology
PubMed: 18426771
DOI: 10.1098/rsif.2008.0086.focus -
ACS Synthetic Biology Feb 2023Reverse genetics (RG) systems have been instrumental for determining the molecular aspects of viral replication, pathogenesis, and for the development of therapeutics....
Reverse genetics (RG) systems have been instrumental for determining the molecular aspects of viral replication, pathogenesis, and for the development of therapeutics. Here, we demonstrate that genes encoding the influenza surface antigens hemagglutinin and neuraminidase have varying stability when cloned into a common RG plasmid and transformed into . Using GFP as a reporter, we demonstrate that expresses the target genes in the RG plasmid at low levels. Incorporating operators or a transcriptional terminator into the plasmid reduced expression and stabilized the viral genes to varying degrees. Sandwiching the viral gene between two operators provided the largest contribution to stability and we confirmed the stabilization is Lac repressor-dependent and crucial for subsequent plasmid propagations in . Viruses rescued from the operator-stabilized plasmid displayed similar kinetics and titers to the original plasmid in two different viral backbones. Together, these results indicate that silencing transcription from the plasmid in helps to maintain the correct influenza gene sequence and that the operator addition does not impair virus production. It is envisaged that sandwiching DNA segments between operators can be used for reducing DNA segment instability in any plasmid that is propagated in which express the Lac repressor.
Topics: Humans; Escherichia coli; Lac Repressors; Influenza, Human; Reverse Genetics; Plasmids; Lac Operon
PubMed: 36716395
DOI: 10.1021/acssynbio.2c00358 -
Biophysical Journal Jan 2022The lactose uptake pathway of E. coli is a paradigmatic example of multistability in gene regulatory circuits. In the induced state of the lac pathway, the genes...
The lactose uptake pathway of E. coli is a paradigmatic example of multistability in gene regulatory circuits. In the induced state of the lac pathway, the genes comprising the lac operon are transcribed, leading to the production of proteins that import and metabolize lactose. In the uninduced state, a stable repressor-DNA loop frequently blocks the transcription of the lac genes. Transitions from one phenotypic state to the other are driven by fluctuations, which arise from the random timing of the binding of ligands and proteins. This stochasticity affects transcription and translation, and ultimately molecular copy numbers. Our aim is to understand the transition from the induced to the uninduced state of the lac operon. We use a detailed computational model to show that repressor-operator binding and unbinding, fluctuations in the total number of repressors, and inducer-repressor binding and unbinding all play a role in this transition. Based on the timescales on which these processes operate, we construct a minimal model of the transition to the uninduced state and compare the results with simulations and experimental observations. The induced state turns out to be very stable, with a transition rate to the uninduced state lower than 2×10 per minute. In contrast to the transition to the induced state, the transition to the uninduced state is well described in terms of a 2D diffusive system crossing a barrier, with the diffusion rates emerging from a model of repressor unbinding.
Topics: Escherichia coli; Escherichia coli Proteins; Lac Operon; Lac Repressors; Lactose
PubMed: 34953812
DOI: 10.1016/j.bpj.2021.12.027 -
PloS One 2013The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop....
The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.
Topics: DNA, Bacterial; Lac Operon; Lac Repressors; Models, Molecular; Monte Carlo Method; Nucleic Acid Conformation; Protein Conformation
PubMed: 23457581
DOI: 10.1371/journal.pone.0056548 -
MBio Nov 2019Transcription of bacterial genes is controlled by the coordinated action of and -acting regulators. The activity and mode of action of these regulators can reflect...
Transcription of bacterial genes is controlled by the coordinated action of and -acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in different environments. A well-studied example is the regulatory function that integrates the environmental availability of glucose and lactose to control the operon. Most studies of operon regulation have focused on a few closely related strains. To determine the range of natural variation in regulatory function, we introduced a reporter construct into 23 diverse strains and measured expression with combinations of inducer concentrations. We found a wide range of regulatory functions. Several functions were similar to the one observed in a reference lab strain, whereas others depended weakly on the presence of cAMP. Some characteristics of the regulatory function were explained by the genetic relatedness of strains, indicating that differences varied on relatively short time scales. The regulatory characteristics explained by genetic relatedness were among those that best predicted the initial growth of strains following transition to a lactose environment, suggesting a role for selection. Finally, we transferred the operon, with the regulatory gene, from five natural isolate strains into a reference lab strain. The regulatory function of these hybrid strains revealed the effect of local and global regulatory elements in controlling expression. Together, this work demonstrates that regulatory functions can be varied within a species and that there is variation within a species to best match a function to particular environments. The operon of is a classic model for studying gene regulation. This study has uncovered features such as the environmental input logic controlling gene expression, as well as gene expression bistability and hysteresis. Most operon studies have focused on a few lab strains, and it is not known how generally those findings apply to the diversity of strains. We examined the environmental dependence of gene regulation in 20 natural isolates of and found a wide range of regulatory responses. By transferring genes from natural isolate strains into a common reference strain, we found that regulation depends on both the genes themselves and on the broader genetic background, indicating potential for still-greater regulatory diversity following horizontal gene transfer. Our results reveal that there is substantial natural variation in the regulation of the operon and indicate that this variation can be ecologically meaningful.
Topics: Escherichia coli; Evolution, Molecular; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genes, Regulator; Genetic Background; Genetic Variation; Lac Operon; Mutation; Phenotype; Phylogeny; Polymorphism, Genetic
PubMed: 31719176
DOI: 10.1128/mBio.02232-19 -
Structure (London, England : 1993) Mar 1996Crystal and cocrystal structures of the LacI and PurR repressors reveal a novel use of hinge alpha helices which bind in the minor groove of the operator and mediate... (Review)
Review
Crystal and cocrystal structures of the LacI and PurR repressors reveal a novel use of hinge alpha helices which bind in the minor groove of the operator and mediate transmission of the allosteric signals that modulate DNA-binding activity.
Topics: Bacterial Proteins; Binding Sites; Crystallography, X-Ray; Escherichia coli Proteins; Lac Operon; Lac Repressors; Models, Molecular; Protein Conformation; Protein Structure, Secondary; Repressor Proteins; Transcription, Genetic
PubMed: 8805532
DOI: 10.1016/s0969-2126(96)00025-1 -
Mathematical Biosciences and... Mar 2019In this paper, we construct a discrete time delay Lac operon model with nonlinear degradation rate for mRNA, resulting from the interaction among several identical mRNA...
In this paper, we construct a discrete time delay Lac operon model with nonlinear degradation rate for mRNA, resulting from the interaction among several identical mRNA pieces. By taking a discrete time delay as bifurcation parameter, we investigate the nonlinear dynamical behaviour arising from the model, using mathematical tools such as stability and bifurcation theory. Firstly, we discuss the existence and uniqueness of the equilibrium for this system and investigate the effect of discrete delay on its dynamical behaviour. Absence or limited delay causes the system to have a stable equilibrium, which changes into a Hopf point producing oscillations if time delay is increased. These sustained oscillation are shown to be present only if the nonlinear degradation rate for mRNA satisfies specific conditions. The direction of the Hopf bifurcation giving rise to such oscillations is also determined, via the use of the so-called multiple time scales technique. Finally, numerical simulations are shown to validate and expand the theoretical analysis. Overall, our findings suggest that the degree of nonlinearity of the model can be used as a control parameter for the stabilisation of the system.
Topics: Algorithms; Computational Biology; Computer Simulation; DNA; Gene Expression Profiling; Humans; Lac Operon; Models, Biological; Nonlinear Dynamics; Oscillometry; Proteins; RNA; Time Factors
PubMed: 31137182
DOI: 10.3934/mbe.2019083 -
International Journal of Molecular... Oct 2023Laccase genes produce laccase enzymes that play a crucial role in the production of lignin and oxidation reactions within plants. Lignin is a complex polymer that... (Review)
Review
Laccase genes produce laccase enzymes that play a crucial role in the production of lignin and oxidation reactions within plants. Lignin is a complex polymer that provides structure and toughness to the cell walls of numerous fruit plants. The genes that encode laccase enzymes play vital roles in plant physiology, including the synthesis of pigments like PA that contribute to the colors of fruits, and in defending against pathogens and environmental stresses. They are crucial for fruit development, ripening, structural maintenance in plants, and adaptation to various environmental factors. As such, these genes and enzymes are essential for plant growth and development, as well as for various biotechnological applications in environmental remediation and industrial processes. This review article emphasizes the significance of genes encoding laccase enzymes during fruit growth, specifically pertaining to the strengthening of the endocarp through lignification. This process is crucial for ensuring fruit defense and optimizing seed scattering. The information gathered in this article will aid breeders in producing future fruit-bearing plants that are resistant to disease, cost-effective, and nutrient-rich.
Topics: Fruit; Lignin; Laccase; Lac Operon; Seeds; Gene Expression Regulation, Plant
PubMed: 37958753
DOI: 10.3390/ijms242115768 -
Genetics Dec 1992
Review
Topics: DNA Repair; DNA Replication; Escherichia coli; Gene Amplification; Lac Operon; Models, Biological; Mutagenesis; Rec A Recombinases; Recombination, Genetic; Transcription, Genetic
PubMed: 1459440
DOI: 10.1093/genetics/132.4.865 -
Journal of Bacteriology Nov 2000
Topics: Artificial Gene Fusion; Genetic Code; Lac Operon
PubMed: 11029410
DOI: 10.1128/JB.182.21.5935-5938.2000