Steady-state Protein Concentration Research Articles

Allometric-like scaling of AAV gene therapy for systemic protein delivery

The use of adeno-associated virus (AAV) as a gene delivery vehicle for secreted peptide therapeutics can enable a new approach to durably manage chronic protein insufficiencies in patients. Yet, dosing of AAVs have been largely empirical to date. In this report, we explore the dose-response relationship of AAVs encoding a secreted luciferase reporter to establish a mathematical model that can be used to predict steady-state protein concentrations in mice based on steady-state secretion rates invitro. Upon intravenous administration of AAV doses that scaled multiple logs, steady-state plasma concentrations of a secreted reporter protein were fit with a hyperbolic dose-response equation. Parameters for the hyperbolic model were extracted from the data and compared with create scaling factors that related invitro protein secretion rates to invivo steady-state plasma concentrations. Parathyroid hormone expressed by AAV was then used as a bioactive candidate and validated that the model, with scaling factors, could predict the plasma hormone concentrations in mice. In total, this modelsystem confirmed that plasma steady-state concentrations of secreted proteins expressed by AAVs can be guided by invitro kinetic secretion data laying groundwork for future customization and model-informed dose justification for AAV candidates.

S100A4 as a Target of the E3-Ligase Asb2β and Its Effect on Engineered Heart Tissue.

Background: S100A4 has recently emerged as an important player in cardiac disease, affecting phenotype development in animal models of myocardial infarction and pathological cardiac hypertrophy, albeit it is unclear whether S100A4 exerts a detrimental or beneficial function. The goal of the current study was to analyze S100A4 expression in models of cardiac pathology, investigate its degradation by the ubiquitin-proteasome system (UPS), and furthermore examine the functional effects of S100A4 levels in a 3D model of engineered heart tissue (EHT).Methods and Results: S100A4 mRNA and protein levels were analyzed in different models of cardiac pathology via quantitative RT-PCR and Western blot, showing a higher S100A4 steady-state protein concentration in hearts of Mybpc3-knock-in (KI) hypertrophic cardiomyopathy (HCM) mice. COS-7 cells co-transfected with plasmids encoding mutant (MUT) Asb2β lacking the E3 ligase activity in combination with V5-tagged S100A4 plasmid presented higher S100A4-V5 protein steady-state concentrations than cells co-transfected with the Asb2β wild type (WT) plasmid. This effect was blunted by treatment with the specific proteasome inhibitor epoxomicin. Adeno-associated virus serotype 6 (AAV6)-mediated S100A4 overexpression in a 3D model of EHT did not affect contractile parameters. Immunofluorescence analysis showed a cytosolic and partly nuclear expression pattern of S100A4. Gene expression analysis in EHTs overexpressing S100A4-V5 showed markedly lower steady-state concentrations of genes involved in cardiac fibrosis and pathological cardiac hypertrophy.Conclusion: We showed that S100A4 protein level is higher in cardiac tissue of Mybpc3-KI HCM mice probably as a result of a lower degradation by the E3 ligase Asb2β. While an overexpression of S100A4 did not alter contractile parameters in EHTs, downstream gene expression analysis points toward modulation of signaling cascades involved in fibrosis and hypertrophy.

Analyzing and Exploiting the Effects of Protease Sharing in Genetic Circuits

Degradation of proteins in cells plays a large role in the dynamics of gene networks. This degradation is enabled by proteases, which are found in limited quantities in the cell. Proteins that compete for protease may therefore become coupled by non-explicit interactions, which are often neglected in mathematical models. In this work, we develop a model for these non-explicit interactions in gene networks. We examine the effects of protease sharing on the number of equilibria of a system and on the steady state protein concentrations. As a consequence of this analysis, we find that protease sharing effects may be used to cancel undesirable effects due to ribosome sharing.

Steady-state protein focusing in carrier ampholyte based isoelectric focusing: Part I-Analytical solution.

The determination of an analytical solution to find the steady-state protein concentration distribution in IEF is very challenging due to the nonlinear coupling between mass and charge conservation equations. In this study, approximate analytical solutions are obtained for steady-state protein distribution in carrier ampholyte based IEF. Similar to the work of Svensson, the final concentration profile for proteins is assumed to be Gaussian, but appropriate expressions are presented in order to obtain the effective electric field and pH gradient in the focused protein band region. Analytical results are found from iterative solutions of a system of coupled algebraic equations using only several iterations for IEF separation of three plasma proteins: albumin, cardiac troponin I, and hemoglobin. The analytical results are compared with numerically predicted results for IEF, showing excellent agreement. Analytically obtained electric field and ionic conductivity distributions show significant deviation from their nominal values, which is essential in finding the protein focusing behavior at isoelectric points. These analytical solutions can be used to determine steady-state protein concentration distribution for experiment design of IEF considering any number of proteins and ampholytes. Moreover, the model presented herein can be used to find the conductivity, electric field, and pH field.

Genetic and genomic analysis of RNases in model cyanobacteria.

Cyanobacteria are diverse photosynthetic microbes with the ability to convert CO2 into useful products. However, metabolic engineering of cyanobacteria remains challenging because of the limited resources for modifying the expression of endogenous and exogenous biochemical pathways. Fine-tuned control of protein production will be critical to optimize the biological conversion of CO2 into desirable molecules. Messenger RNAs (mRNAs) are labile intermediates that play critical roles in determining the translation rate and steady-state protein concentrations in the cell. The majority of studies on mRNA turnover have focused on the model heterotrophic bacteria Escherichia coli and Bacillus subtilis. These studies have elucidated many RNA modifying and processing enzymes and have highlighted the differences between these Gram-negative and Gram-positive bacteria, respectively. In contrast, much less is known about mRNA turnover in cyanobacteria. We generated a compendium of the major ribonucleases (RNases) and provide an in-depth analysis of RNase III-like enzymes in commonly studied and diverse cyanobacteria. Furthermore, using targeted gene deletion, we genetically dissected the RNases in Synechococcus sp. PCC 7002, one of the fastest growing and industrially attractive cyanobacterial strains. We found that all three cyanobacterial homologs of RNase III and a member of the RNase II/R family are not essential under standard laboratory conditions, while homologs of RNase E/G, RNase J1/J2, PNPase, and a different member of the RNase II/R family appear to be essential for growth. This work will enhance our understanding of native control of gene expression and will facilitate the development of an RNA-based toolkit for metabolic engineering in cyanobacteria.

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.

Transcription, mRNA decay, translation and protein degradation are essential processes during eukaryotic gene expression, but their relative global contributions to steady-state protein concentrations in multi-cellular eukaryotes are largely unknown. Using measurements of absolute protein and mRNA abundances in cellular lysate from the human Daoy medulloblastoma cell line, we quantitatively evaluate the impact of mRNA concentration and sequence features implicated in translation and protein degradation on protein expression. Sequence features related to translation and protein degradation have an impact similar to that of mRNA abundance, and their combined contribution explains two-thirds of protein abundance variation. mRNA sequence lengths, amino-acid properties, upstream open reading frames and secondary structures in the 5' untranslated region (UTR) were the strongest individual correlates of protein concentrations. In a combined model, characteristics of the coding region and the 3'UTR explained a larger proportion of protein abundance variation than characteristics of the 5'UTR. The absolute protein and mRNA concentration measurements for >1000 human genes described here represent one of the largest datasets currently available, and reveal both general trends and specific examples of post-transcriptional regulation.

Seed ageing-induced inhibition of germination and post-germination root growth is related to lower activity of plasma membrane H +-ATPase in maize roots

Seeds of most crops can be severely damaged and lose vigor when stored under conditions of high humidity and temperature. The aged seeds are characterized by delayed germination and slow post-germination growth. To date, little is known about the physiological mechanisms responsible for slow root growth of seedlings derived from aged seeds. Plasma membrane H(+)-ATPase is a universal H(+) pump in plant cells and is involved in various physiological processes including the elongation growth of plant cells. In the present study, we investigated the effect of a mild seed ageing treatment on plasma membrane H(+)-ATPase activity of seedling roots. Maize (Zea mays L.) seeds with 17% water content were aged at 45 degrees C for 30h. The aged seeds showed a 20% reduction in germination. Seedlings from aged seeds grew slowly during an experimental period of 120h after imbibition. Plasma membranes of maize seedling roots were isolated for investigation in vitro. Plasma membrane H(+)-ATPase (EC 3.6.3.6) activity was 14% lower for seedling roots developed from aged seeds as compared to control seeds. Protein gel immunoblotting analysis demonstrated that the reduced activity of plasma membrane H(+)-ATPase was attributed to a decrease in steady-state protein concentration of this enzyme. In conclusion, seed ageing causes a lower steady-state enzyme concentration of the H(+)-ATPase in the plasma membrane, which is related to slow germination and post-germination growth of seedling roots.

A peritoneal-based automated wearable artificial kidney

Work on wearable kidneys has evolved around the technology of hemodialysis or hemofiltration, which call for continuous anticoagulation of the extracoporeal circulation and are encumbered with potential immunologic and non-immunologic complications of continuous blood-artificial membrane interactions. A peritoneal-based automated wearable artificial kidney (AWAK) requires no extracorporeal circulation and is therefore "bloodless." Because AWAK is designed to continuously regenerate and reuse the spent dialysate in perpetuity, it is also "waterless." A sorbent-based assembly regenerates both the aqueous and the protein components (AqC and PrC) of the spent dialysate, producing a novel, autologous protein-containing dialysate. The regenerated AqC has the same composition as the commercially available peritoneal dialysate, but contains bicarbonate instead of lactate and has a more physiological pH. The regenerated PrC is recycled back into the peritoneal cavity, thereby ameliorating or eliminating protein loss. Depending on the steady-state protein concentrations that can be achieved (under the condition of continuous dialysate regeneration and recycling), the PrC also has the potential of both augmenting ultrafiltration and mediating the removal of protein-bound toxins. Additional sorbents can be incorporated into AWAK for the removal of middle molecular weight uremic toxins. At a regeneration rate of 4 l/h, AWAK provides a dialysate flow of 96 l/day (8-12 times the current rate). Round-the-clock dialysis and ultrafiltration provide steady-state metabolic-biochemical and fluid balance regulation, thereby eliminating "shocks" of abrupt changes in these parameters that characterize the current dialytic modalities. Dialysis-on-the-go, made possible by AWAK's "wearability" and automation, frees end-stage renal failure patients from the servitude that is demanded by the current dialytic regimentations.

High‐level expression and stabilization of recombinant human chitinase produced in a continuous constitutive Pichia pastoris expression system

A continuous fermentation process has been developed in Pichia pastoris (P. pastoris) with the glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter in order to produce large quantities of recombinant human chitinase (rh-chitinase) for preclinical studies as a potential high-dose antifungal drug. Expression levels of about 200 to 400 mg/L have been demonstrated in fed-batch fermentations using strains with either the traditional methanol-inducible or the constitutive GAP promoter. Proteolytic degradation of the enzyme was typically seen in fed-batch fermentations. Continuous production of the enzyme by P. pastoris with the GAP promoter was demonstrated in a 1.5-L working volume fermentor using either glucose or glycerol as the carbon source. The fermentation could be extended for >1 month with a steady-state protein concentration of approximately 300 mg/L. Cell densities were >400 g/L wet cell weight (WCW) (approximately 100 g/L dry cell weight [DCW]) at a dilution rate (D) of 0.83 day(-1) or 1.2 volume exchanges per day (VVD). No proteolytic degradation of the enzyme was seen in the continuous fermentation mode.

Designer gene networks: Towards fundamental cellular control.

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model formulation leads to computational and analytical approaches relevant to nonlinear dynamics and statistical physics. We first review the relevant work on synthetic gene networks, highlighting the important experimental findings with regard to genetic switches and oscillators. We then present the derivation of a deterministic model describing the temporal evolution of the concentration of protein in a single-gene network. Bistability in the steady-state protein concentration arises naturally as a consequence of autoregulatory feedback, and we focus on the hysteretic properties of the protein concentration as a function of the degradation rate. We then formulate the effect of an external noise source which interacts with the protein degradation rate. We demonstrate the utility of such a formulation by constructing a protein switch, whereby external noise pulses are used to switch the protein concentration between two values. Following the lead of earlier work, we show how the addition of a second network component can be used to construct a relaxation oscillator, whereby the system is driven around the hysteresis loop. We highlight the frequency dependence on the tunable parameter values, and discuss design plausibility. We emphasize how the model equations can be used to develop design criteria for robust oscillations, and illustrate this point with parameter plots illuminating the oscillatory regions for given parameter values. We then turn to the utilization of an intrinsic cellular process as a means of controlling the oscillations. We consider a network design which exhibits self-sustained oscillations, and discuss the driving of the oscillator in the context of synchronization. Then, as a second design, we consider a synthetic network with parameter values near, but outside, the oscillatory boundary. In this case, we show how resonance can lead to the induction of oscillations and amplification of a cellular signal. Finally, we construct a toggle switch from positive regulatory elements, and compare the switching properties for this network with those of a network constructed using negative regulation. Our results demonstrate the utility of model analysis in the construction of synthetic gene regulatory networks. (c) 2001 American Institute of Physics.

Noise-based switches and amplifiers for gene expression.

The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network. Engineered control of cellular function through the design and manipulation of such networks lies within the constraints of current technology. Here we develop a model describing the regulation of gene expression and elucidate the effects of noise on the formulation. We consider a single network derived from bacteriophage lambda and construct a two-parameter deterministic model describing the temporal evolution of the concentration of lambda repressor protein. Bistability in the steady-state protein concentration arises naturally, and we show how the bistable regime is enhanced with the addition of the first operator site in the promotor region. We then show how additive and multiplicative external noise can be used to regulate expression. In the additive case, we demonstrate the utility of such control through the construction of a protein switch, whereby protein production is turned "on" and "off" by using short noise pulses. In the multiplicative case, we show that small deviations in the transcription rate can lead to large fluctuations in the production of protein, and we describe how these fluctuations can be used to amplify protein production significantly. These results suggest that an external noise source could be used as a switch and/or amplifier for gene expression. Such a development could have important implications for gene therapy.