Subpopulation behaviors in lactose metabolism by Streptococcus mutans.

When Streptococcus mutans is transferred from a preferred carbohydrate (glucose or fructose) to lactose, initiation of growth can take several hours, and substantial amounts of glucose are released during growth. Here, S. mutans strains UA159 and GS-5 were examined for stochastic behaviors in transcription of the lac operon. Using a gfp reporter fusion, we demonstrated that induction of the lac operon occurs in only a fraction of the population, with prior exposure to carbohydrate source and strain influencing the magniture of the sub-population response. Lower glucokinase activity in GS-5 was associated with release of substantially more glucose than UA159 and significantly lower lac expression. Mutants unable to use lactose grew on lactose as the sole carbohydrate when strains with an intact lac operon were also present in the cultures, indicative of the potential for population cheating. Utilizing a set of engineered obligate cheating and non-cheating strains, we confirmed that cheating can sustain a heterogeneous population. Futher, obligate cheaters of GS-5 competed well with the non-cheaters and showed a high degree of competitive fitness in a human-derived consortium biofilm model. The results show that bet-hedging behaviors in carbohydrate metabolism may substantially influence the composition and pathogenic potential of oral biofilms.

Stability and Hopf bifurcation analysis for a Lac operon model with nonlinear degradation rate and time delay.

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.

Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state.

Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation. Hence using the lac operon as an archetype, in such a region of operon-state switching, we present a fluctuating-rate model for this classical gene regulation module, incorporating the more realistic operon-state switching mechanism that was recently elucidated. We found that the positive feedback mechanism induces bistability (referred to as deterministic bistability), and that the parameter range for its occurrence is significantly broadened by stochastic operon-state switching. We further show that in the absence of positive feedback, operon-state switching must be extremely slow to trigger bistability by itself. However, in the presence of positive feedback, which stabilizes the induced state, the relatively slow operon-state switching kinetics within the physiological region are sufficient to stabilize the uninduced state, together generating a broadened parameter region of bistability (referred to as stochastic bistability). We illustrate the opposite phenotype-transition rate dependence upon the operon-state switching rates in the two types of bistability, with the aid of a recently proposed rate formula for fluctuating-rate models. The rate formula also predicts a maximal transition rate in the intermediate region of operon-state switching, which is validated by numerical simulations in our model. Overall, our findings suggest a biological function of transcriptional "variations" among genetically identical cells, for the emergence of bistability and transition between phenotypic states.

Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System.

Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli's natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or "coliroids," rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by ß-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein's local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system's performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling.

Determining the bistability parameter ranges of artificially induced lac operon using the root locus method.

This paper employs the root locus method to conduct a detailed investigation of the parameter regions that ensure bistability in a well-studied gene regulatory network namely, lac operon of Escherichia coli (E. coli). In contrast to previous works, the parametric bistability conditions observed in this study constitute a complete set of necessary and sufficient conditions. These conditions were derived by applying the root locus method to the polynomial equilibrium equation of the lac operon model to determine the parameter values yielding the multiple real roots necessary for bistability. The lac operon model used was defined as an ordinary differential equation system in a state equation form with a rational right hand side, and it was compatible with the Hill and Michaelis-Menten approaches of enzyme kinetics used to describe biochemical reactions that govern lactose metabolism. The developed root locus method can be used to study the steady-state behavior of any type of convergent biological system model based on mass action kinetics. This method provides a solution to the problem of analyzing gene regulatory networks under parameter uncertainties because the root locus method considers the model parameters as variable, rather than fixed. The obtained bistability ranges for the lac operon model parameters have the potential to elucidate the appearance of bistability for E. coli cells in in vivo experiments, and they could also be used to design robust hysteretic switches in synthetic biology.

Auto-induction-based rapid evaluation of extracellular enzyme expression from lac operator-involved recombinant Escherichia coli.

Degeneration of engineered strains and decreased production of target gene products were often observed during recombinant bioprocess. Although several strategies have been developed to ensure high levels of target gene products, these methods seemed to be complex and laborious. By investigating possible factors contributing to the decreased yield, degeneration of host cells was identified as the main cause. Based on the principle of auto-induction and the fact that the interaction between colored substrates and gene products could present visible changes, a convenient and accurate screening method was developed to evaluate the production performance of engineered strains. Due to the typicality of pullulanase from genus Klebsiella, which has been a model for the research of secretion mechanism in gram-negative bacteria, an engineered E. coli producing extracellular pullulanase was employed to illustrate the method. Consequently, according to the capability to form a colorless halo, colonies could be divided into two groups, one surrounded by clear zone and the other unable to present transparent haloes. Furthermore, the high capability of these colonies was confirmed by performing pullulanase production in liquid medium. Compared with other methods for evaluating engineered strains, the visible screening technique was suggested to have the advantages of effectiveness and accuracy.

Folding LacZ in the periplasm of Escherichia coli.

Targeted, translational LacZ fusions provided the initial support for the signal sequence hypothesis in prokaryotes and allowed for selection of the mutations that identified the Sec translocon. Many of these selections relied on the fact that expression of targeted, translational lacZ fusions like malE-lacZ and lamB-lacZ42-1 causes lethal toxicity as folded LacZ jams the translocation pore. However, there is another class of targeted LacZ fusions that do not jam the translocon. These targeted, nonjamming fusions also show toxic phenotypes that may be useful for selecting mutations in genes involved in posttranslocational protein folding and targeting; however, they have not been investigated to the same extent as their jamming counterparts. In fact, it is still unclear whether LacZ can be fully translocated in these fusions. It may be that they simply partition into the inner membrane where they can no longer participate in folding or assembly. In the present study, we systematically characterize the nonjamming fusions and determine their ultimate localization. We report that LacZ can be fully translocated into the periplasm, where it is toxic. We show that this toxicity is likely due to LacZ misfolding and that, in the absence of the periplasmic disulfide bond catalyst DsbA, LacZ folds in the periplasm. Using the novel phenotype of periplasmic ß-galactosidase activity, we show that the periplasmic chaperone FkpA contributes to LacZ folding in this nonnative compartment. We propose that targeted, nonjamming LacZ fusions may be used to further study folding and targeting in the periplasm of Escherichia coli.

Axonal regeneration is compromised in NFH-LacZ transgenic mice but not in NFH-GFP mice.

To investigate neurofilament (NF) dynamics during the cytoskeleton reorganization in regenerating axons, and their electrophysiological and histological consequences, we used two transgenic lines of mice: neurofilament high (NFH)-LacZ and NFH-green fluorescent protein (GFP). In NFH-LacZ mice, NFs are retained in cell bodies and deficient in axons (Eyer and Peterson, 1994), while in NFH-GFP mice the fluorescent fusion protein is normally transported along axons (Letournel et al., 2006). Following a crush of the sciatic nerve, conduction recovery in NFH-GFP mice is similar to wild-type (wt) mice, but it is reduced in NFH-LacZ mice. Moreover, changes of axonal calibres following regeneration are similar between NFH-GFP and wt mice, but they are systematically reduced in NFH-LacZ mice. Finally, the axonal transport of NFH-GFP fusion protein and NFs is re-initiated after the crush as evidenced by the fluorescent and immunolabelling of axons distal from the crushed point, but NFs and the fusion protein are not transported along axons during regeneration in NFH-LacZ mice. Together, these results argue that the absence of axonal NFs in NFH-LacZ mice compromises the axonal regeneration, and that the NFH-GFP reporter fusion protein represents an efficient model to evaluate the NF dynamics during axonal regeneration.

Abundant LacZ activity in the absence of Cre expression in the normal and inflamed synovium of adult Col2a1-Cre; ROSA26RLacZ reporter mice.

Recent analyses of Col2a1-Cre; ROSA26R reporter mice showed that synovial fibroblasts in 7-day mice were LacZ positive, due to a history of Col2a1-Cre expression conferred by their origin in the interzone of the developing joint. We have examined LacZ staining in adult Col2a1-Cre(+/0); ROSA26R(LacZ) mice, with and without inflammatory arthritis, and found that synovial fibroblasts in normal and inflamed synovium are LacZ positive, but Cre negative. Our results suggest that Cre-mediated recombination in joint interzone cells during development endure in adult synovial cells despite the absence of ongoing Cre expression. These findings have important implications and applications for the study of synovial inflammation in models of experimental arthritis.

In vivo electroporation induces cell cycle reentry of myonuclei in rat skeletal muscle.

Adult urodele amphibians such as newts are capable of regenerating lost structures including their limbs. In these species, dedifferentiation of myofiber is essential for the regenerative process. Upon terminal differentiation, nuclei of myofiber (myonuclei) are withdrawn from cell cycle, but prior to dedifferentiation, myonuclei reenter the cell cycle. In contrast with urodele amphibians, it is generally accepted that mammalian myofibers are not able to dedifferentiate in response to muscle injury. A recent study has suggested that electroporation can induce dedifferentiation response of skeletal muscle in newt limbs. In the present study, we examined whether myonuclei of skeletal muscle of mammals are capable of reentering the cell cycle by means of electroporation. Electroporation was applied to tibialis anterior muscle of the rat with or without plasmid DNA. Histological analyses revealed that, while electroporation induces degenerative/regenerative responses in skeletal muscle irrespective of the presence of plasmid DNA, the expression of proliferating cell nuclear antigen (PCNA) in myonuclei was observed only in the presence of plasmid DNA. The present results indicate that myonuclei of skeletal muscle are capable of reentering the cell cycle and suggest that in vivo electroporation can induce dedifferentiation of mammalian skeletal muscle.

Integration of H-2Z1, a somatosensory cortex-expressed transgene, interferes with the expression of the Satb1 and Tbc1d5 flanking genes and affects the differentiation of a subset of cortical interneurons.

H-2Z1 is an enhancer trap transgenic mouse line in which the lacZ reporter delineates the somatosensory area of the cerebral cortex where it is expressed in a subset of layer IV neurons. In the search of somatosensory specific genes or regulatory sequences, we mapped the H-2Z1 transgene insertion site to chromosome 17, 100 and 460 kb away from Tbc1d5 and Satb1 flanking genes. We show here that insertion of the H-2Z1 transgene results in three distinct outcomes. First, a genetic background-sensitive expression of lacZ in several brain and body structures. While four genes in a 1 Mb region around the insertion are expressed in the barrel cortex, H-2Z1 expression resembles more that of its two direct neighbors. Moreover, H-2Z1 closely reports most of the body and brain expression sites of the Satb1 chromatin remodeling gene including tooth buds, thymic epithelium, pontine nuclei, fastigial cerebellar nuclei, and cerebral cortex. Second, the H-2Z1 transgene causes insertional mutagenesis of Tbc1d5 and Satb1, leading to a strong decrease in their expressions. Finally, insertion of H-2Z1 affects the differentiation of a subset of cortical GABAergic interneurons, a possible consequence of downregulation of Satb1 expression. Thus, the H-2Z1 "somatosensory" transgene is inserted in the regulatory landscape of two genes highly expressed in the developing somatosensory cortex and reports for a subdomain of their expression profiles. Together, our data suggest that regulation of H-2Z1 expression results from local and remote genetic interactions.

The human ubiquitin C promoter drives selective expression in principal neurons in the brain of a transgenic mouse line.

The specificity of promoters used to drive the expression of proteins of interest is a crucial determinant of transgenesis. Numerous strategies have been developed to restrict expression on a certain cell population. On the other hand it has also remained challenging to obtain ubiquitous expression of transgenes which is needed for example to generate recombination reporter mice or to induce expression by recombination mediated excision of STOP-cassettes. We have generated transgenic mice with the expression of nuclear ß-galactosidase driven by the human ubiquitin C promoter thought to mediate ubiquitous expression. However, in the brains of these transgenic mice the expression of the transgene was strikingly limited to principal neurons, while no expression was detected in interneurons or glial cells. These results indicate that the human ubiquitin C promoter might be useful to selectively target projections neurons of the brain.

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.

Combined inadequacies of multiple B vitamins amplify colonic Wnt signaling and promote intestinal tumorigenesis in BAT-LacZxApc1638N mice.

The Wnt pathway is a pivotal signaling cascade in colorectal carcinogenesis. The purpose of this work is to determine whether depletion of folate and other metabolically related B vitamins induces in vivo activation of intestinal Wnt signaling and whether this occurs in parallel with increased tumorigenesis. A hybrid mouse was created by crossing a Wnt-reporter animal (BAT-LacZ) with a model of colorectal cancer (Apc1638N). A mild depletion of folate and vitamins B2, B6, and B12 was induced over 16 wk, and the control animals in each instance were pair fed a diet containing the basal requirement of these nutrients. The multiplicity of macroscopic tumors and aberrant crypt foci both increased by ~50% in the hybrid mice fed the depletion diet (P<0.05). A 4-fold elevation in Wnt signaling was produced by the depletion diet (P<0.05) and was accompanied by significant changes in the expression of a number of Wnt-related genes in a pattern consistent with its activation. Proliferation and apoptosis of the colonic mucosa both changed in a protransformational direction (P<0.05). In summary, mild depletion of multiple B vitamins produces in vivo activation of colonic Wnt signaling, implicating it as a key pathway by which B-vitamin inadequacies enhance intestinal tumorigenesis.

Nrf2 degron-fused reporter system: a new tool for specific evaluation of Nrf2 inducers.

The transcription factor Nrf2 is degraded through the proteasome pathway, but is stabilized in response to oxidative and electrophilic stresses, and activates cytoprotective enzyme genes through binding to the antioxidant/electrophile response element (ARE/EpRE). Nrf2 inducers thus have considerable potential as therapeutic drugs. Although ARE-driven reporters are commonly employed to validate Nrf2 inducers, these reporters are relatively nonspecific. We have generated a new reporter, Nrf2d-LacZ, which may prove to be a better tool for validation of Nrf2 inducers. We made the Nrf2d-LacZ reporter by fusing the N-terminus of Nrf2 harboring a Neh2 degron to ß-galactosidase (LacZ), and compared its activity in immortalized mouse embryo fibroblasts (MEFs) with conventional ARE-luciferase (ARE-Luc) reporters in 293T cells, and in MEFs. Nrf2d-LacZ was degraded in unstressed conditions, but stabilized upon exposure to stresses. LacZ activity was induced by electrophiles in a dose-dependent manner, and the induction was detected much more rapidly compared with ARE-Luc. Nrf2d-LacZ was activated not only by electrophiles but also by a variety of other Nrf2 inducing stresses. Although ARE-Luc was activated by 12-O-Tetradecanoylphorbol 13-acetate in an Nrf2-independent manner, Nrf2d-LacZ was not activated by TPA, thus emphasizing the specificity of the Nrf2d-LacZ reporter system for validation of Nrf2 inducers.

GPR39, a putative receptor of Zn2+, is region specifically localized in different lobes of the mouse prostate.

OBJECTIVES: To define the expression pattern of the putative zinc receptor GPR39 at different regions of the mouse prostate. METHODS: We used a mouse strain harboring a LacZ reporter at 1 allele of gpr39 (gpr39(+/LacZ)). LacZ staining of adult prostate was performed by whole-mount staining followed by tissue section. The expression results were also confirmed at protein level by immunohistochemistry staining using GPR39 antibody in adult male mice. RESULTS: Whole-mount LacZ staining and tissue sections clearly revealed that GPR39 mRNA is intensely expressed at the epithelial cells of dorsal and anterior prostates, with lower intensity at the lateral prostate and very low or no expression in the ventral prostate. Immunohistochemistry staining results were consistent with those for LacZ staining. CONCLUSIONS: These data demonstrate that the putative zinc receptor GPR39 is spatially expressed at different regions of the mouse prostate with various intensities, suggesting that GPR39 might play an important role in mediating zinc function for normal prostate health in a region-specific manner. GPR39 expression in human prostate under normal and pathologic conditions is an interesting issue that warrants further investigation.

Reciprocal expression of connexin 40 and 45 during phenotypical changes in renin-secreting cells.

Gap junctional coupling of renin-producing cells is of major functional importance for the control of renin synthesis and release. This study was designed to determine the relevance of the vascular gap junction protein connexin 45 (Cx45) for the control of renin expression and secretion. By crossbreeding mice which drive Cre recombinase under the control of the endogenous renin promoter with mice harboring floxed Cx45 gene alleles, we generated viable mice with a deletion of Cx45 in the renin cell lineage. These mice were normotensive, and renin cells in their kidneys were normal with regard to localization and number. Sodium deficiency induced typical recruitment of renin-producing cells along afferent arterioles, whereas sodium overload resulted in a decrease in the number of cells expressing renin. Regulation of renin secretion by perfusion pressure, catecholamines, and angiotensin II from isolated kidneys of mice with renin cell-specific deletion of Cx45 was normal. Analyzing Cx45 promoter activity in cells of the preglomerular arteriolar tree by using mice driving the reporter gene LacZ under the control of the Cx45 promoter revealed strong staining in smooth muscle cells of the media, whereas renin-expressing cells were almost devoid of LacZ staining. Conversely, renin-producing cells, but not vascular smooth muscle cells expressed the gap junction protein Cx40. These findings suggest that Cx45 plays no major functional role in renin-producing cells, probably because the expression of Cx45 is downregulated in these cells. Since renin-producing cells in the adult kidney can reversibly transform into vascular smooth muscle cells and vice versa, our findings on connexin expression indicate that these phenotype switches are paralleled by characteristic reciprocal changes in the transcriptional activity of Cx40 and Cx45 genes.

Efficient in vivo doxycycline and cre recombinase-mediated inducible transgene activation in the murine trabecular meshwork.

PURPOSE: To generate new mouse lines that facilitate inducible gene activation in the murine trabecular meshwork in vivo. METHODS: Two expression cassettes were knocked into the 3'-UTR of the Myocilin (Myoc) locus, an abundantly expressed extracellular matrix protein produced by cells of the trabecular meshwork. The first cassette directs expression of an inducible form of Cre recombinase, CreER(T2), which is activated by tamoxifen administration under the control of endogenous Myoc regulatory elements. The second cassette contains a reverse tetracycline transactivator, rtTA(M2), which directs the expression of tetracycline-operator transgenes on exposure of animals to doxycycline (Dox). These lines were crossed to GFP and lacZ reporter mice to assay for tamoxifen or Dox-induced transgene expression. RESULTS: Both the Myoc-CreER(T2) and the Myoc-rtTA(M2) lines were capable of directing efficient and inducible expression of transgenes in the murine trabecular meshwork in vivo. In addition, activation of transgenes by Myoc-rtTA(M2) was reversible with loss of transgene expression after Dox withdrawal. Examination of multiple tissues demonstrates efficient transgene activation in the trabecular meshwork, with additional sites of transgene activation including cells in the retina, sclera, lung, kidney, and abundant activation in the neocortex and hippocampus. CONCLUSIONS: Two new mouse lines have been generated that allow for efficient and inducible transgene activation in the murine trabecular meshwork in vivo.

Spatial p21 expression profile in the mid-term mouse embryo.

Throughout development cells make the decision to proliferate, arrest or die. Control of this process is essential for normal development, with unrestrained cell proliferation and cell death underlying the origin and progression of disease. The cell-cycle is tightly regulated by a number of factors including the cyclin-dependent kinase inhibitor 1A (Cdkn1a), termed p21 (or Cip1 or WAF1). p21 acts as a negative regulator of cell-cycle progression by binding and inhibiting complexes formed between the cyclin-dependent kinases and their catalytic partners the cyclins. In this report we identify the temporal spatial expression profile of p21 in the developing mid-term mouse embryo using a p21-LacZ reporter mouse line. Expression of p21 was restricted to specific regions with a correspondence to both areas of terminal differentiation and active remodelling. A complex temporal and spatial relationship between p21 expression and regions of apoptosis was evident. A protective role with regard to apoptosis for p21 is proposed.

On multistability of delayed genetic regulatory networks with multivariable regulation functions.

Many genetic regulatory networks (GRNs) have the capacity to reach different stable states. This capacity is defined as multistability which is an important regulation mechanism. Multiple time delays and multivariable regulation functions are usually inevitable in such GRNs. In this paper, multistability of GRNs is analyzed by applying the control theory and mathematical tools. This study is to provide a theoretical tool to facilitate the design of synthetic gene circuit with multistability in the perspective of control theory. By transforming such GRNs into a new and uniform mathematical formulation, we put forward a general sector-like regulation function that is capable of quantifying the regulation effects in a more precise way. By resorting to up-to-date techniques, a novel Lyapunov-Krasovskii functional (LKF) is introduced for achieving delay dependence to ensure less conservatism. New conditions are then proposed to ensure the multistability of a GRN in the form of linear matrix inequalities (LMIs) that are dependent on the delays. Our multistability conditions are applicable to several frequently used regulation functions especially the multivariable ones. Two examples are employed to illustrate the applicability and usefulness of the developed theoretical results.