Thrombin-Mediated Transcriptional Regulation Using DNA Aptamers in DNA-Based Cell-Free Protein Synthesis

Realizing the potential of cell-free systems will require development of ligand-sensitive gene promoters that control gene expression in response to a ligand of interest. Here, we describe an approach to designing ligand-sensitive transcriptional control in cell-free systems that is based on the combination of a DNA aptamer that binds thrombin and the T7 bacteriophage promoter. Placement of the aptamer near the T7 promoter, and using a primarily single-stranded template, results in up to a 6-fold change in gene expression in a ligand concentration-dependent manner. We further demonstrate that the sensitivity to thrombin concentration and the fold change in expression can be tuned by altering the position of the aptamer. The results described here pave the way for the use of DNA aptamers to achieve modular regulation of transcription in response to a wide variety of ligands in cell-free systems

Effect of tetO on LacI mediated repression of T7lacO when tetO is in between the two lac operators (in vivo).

<p>Shown in (A) are the plasmid constructs pDRT7 14 and pDRT7 77. B) Displays the responses of these plasmids to presence /absence of 30 μM IPTG and 200 ng/ml aTc. C) Gene expression response, as determined by the normalized fluorescence response, of the pDRT7 77 plasmid to a range of IPTG and aTc concentrations. aTc concentration (ng/mL) is displayed on the X axis and the Y-axis denotes IPTG concentrations (μM). GFP fluorescence measurements in B and C are expressed as µM/OD₆₀₀. D) is a schematic of the IMPLIES logic gate realized using the pDRT7 77 plasmid. Error bars depict standard deviation of triplicate measurements.</p

Multi-Input Regulation and Logic with T7 Promoters in Cells and Cell-Free Systems

<div><p>Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in an <i>E. coli</i> cell-free protein expression system. Our results expand the utility of T7 promoters in cell based as well as cell-free synthetic biology applications.</p> </div

Design strategy for achieving combinatorial regulation of expression from T7 promoters.

<p>A) An auxiliary lacO is placed upstream to a conventional T7lacO promoter to create stronger LacI repressible T7 promoters. DNA looping is induced by the binding of a single LacI tetramer to both of the lacO binding sites. B) TetR binding regions (tetO) placed within this DNA looping framework, at regions indicated by grey box, can enable multi-input regulation by interfering with LacI mediated looping.</p

Effect of auxiliary operators on LacI mediated repression of T7lacO promoters (in vivo).

<p>A) illustrates promoter sequences containing T7lacO promoters with auxiliary operator sequences of different strengths. B) Protein expression responses to 30 μM IPTG from the constructs depicted in A). GFP concentration units are expressed as µM/OD₆₀₀. C) Dose responses to IPTG from the different constructs. Fluorescence response values are normalized to cell counts as determined by optical density values. Error bars depict standard deviation of triplicate measurements. Lines depict nonlinear regression fits to the Hill equation.</p

Effect of tetO on LacI mediated repression of T7lacO when tetO is in between the two lac operators in cell free systems.

<p>A) Fluorescence response from pDRT7 77 to LacI and TetR proteins. B) Shows fluorescence response from pDRT7 14 and pDRT7 77 plasmids to presence of 300 μM IPTG and/or 200ng/ml aTc. Error bars in the figure depict standard deviations of triplicate measurements.</p

Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis

Cell-free protein synthesis (CFPS) has the potential to produce enzymes, therapeutic agents, and other proteins, while circumventing difficulties associated with in vivo heterologous expression. However, the contents of the cell-free extracts used to carry out synthesis are generally not characterized, which hampers progress toward enhancing yield or functional activity of the target protein. We explored the utility of mass spectrometry (MS)-based proteomics for characterizing the bacterial extracts used for transcribing and translating gene sequences into proteins as well as the products of CFPS reactions. Full proteome experiments identified over 1000 proteins per reaction. The complete set of proteins necessary for transcription and translation were found, demonstrating the ability to define potential metabolic capabilities of the extract. Further, MS-based techniques allowed characterization of the CFPS product and provided insight into the synthesis reaction and potential functional activity of the product. These capabilities were demonstrated using two different CFPS products, the commonly used standard green fluorescent protein (GFP, 27 kDa) and the polyketide synthase DEBS1 (394 kDa). For the large, multidomain DEBS1, substantial premature termination of protein translation was observed. Additionally, MS/MS analysis, as part of a conventional full proteomics workflow, identified post-translational modifications, including the chromophore in GFP, as well as the three phosphopantetheinylation sites in DEBS1. A hypothesis-driven approach focused on these three sites identified that all were correctly modified for DEBS1 expressed in vivo but with less complete coverage for protein expressed in CFPS reactions. These post-translational modifications are essential for functional activity, and the ability to identify them with mass spectrometry is valuable for judging the success of the CFPS reaction. Collectively, the use of MS-based proteomics will prove advantageous for advancing the application of CFPS and related techniques

Cytotoxicity Induced by Engineered Silver Nanocrystallites Is Dependent on Surface Coatings and Cell Types

Due to their unique antimicrobial properties silver nanocrystallites have garnered substantial attention and are used extensively for biomedical applications as an additive to wound dressings, surgical instruments and bone substitute materials. They are also released into unintended locations such as the environment or biosphere. Therefore it is imperative to understand the potential interactions, fate and transport of nanoparticles with environmental biotic systems. Numerous factors including the composition, size, shape, surface charge, and capping molecule of nanoparticles are known to influence cell cytotoxicity. Our results demonstrate that the physical/chemical properties of the silver nanoparticles including surface charge, differential binding and aggregation potential, which are influenced by the surface coatings, are a major determining factor in eliciting cytotoxicity and in dictating potential cellular interactions. In the present investigation, silver nanocrystallites with nearly uniform size and shape distribution but with different surface coatings, imparting overall high negativity to high positivity, were synthesized. These nanoparticles included poly­(diallyldimethylammonium) chloride-Ag, biogenic-Ag, colloidal-Ag (uncoated), and oleate-Ag with zeta potentials +45 ± 5, −12 ± 2, −42 ± 5, and −45 ± 5 mV, respectively; the particles were purified and thoroughly characterized so as to avoid false cytotoxicity interpretations. A systematic investigation on the cytotoxic effects, cellular response, and membrane damage caused by these four different silver nanoparticles was carried out using multiple toxicity measurements on mouse macrophage (RAW-264.7) and lung epithelial (C-10) cell lines. Our results clearly indicate that the cytotoxicity was dependent on various factors such as surface charge and coating materials used in the synthesis, particle aggregation, and the cell-type for the different silver nanoparticles that were investigated. Poly­(diallyldimethylammonium)-coated Ag nanoparticles were found to be the most toxic, followed by biogenic-Ag and oleate-Ag nanoparticles, whereas uncoated or colloidal silver nanoparticles were found to be the least toxic to both macrophage and lung epithelial cells. Also, based on our cytotoxicity interpretations, lung epithelial cells were found to be more resistant to the silver nanoparticles than the macrophage cells, regardless of the surface coating

Layer-by-Layer Templated Assembly of Silica at the Nanoscale

Bioinspired bottom-up assembly and layer-by-layer (LbL) construction of inorganic materials from lithographically defined organic templates enables the fabrication of nanostructured systems under mild temperature and pH conditions. Such processes open the door to low-impact manufacturing and facile recycling of hybrid materials for energy, biology, and information technologies. Here, templated LbL assembly of silica was achieved using a combination of electron beam lithography, chemical lift-off, and aqueous solution chemistry. Nanopatterns of lines, honeycomb-lattices, and dot arrays were defined in polymer resist using electron beam lithography. Following development, exposed areas of silicon were functionalized with a vapor deposited amine-silane monolayer. Silicic acid solutions of varying pH and salt content were reacted with the patterned organic amine-functional templates. Vapor treatment and solution reaction could be repeated, allowing LbL deposition. Conditions for the silicic acid deposition had a strong effect on thickness of each layer, and the morphology of the amorphous silica formed. “Defects” in the arrays of silica nanostructures were minor and do not affect the overall organization of the layers. The bioinspired method described here facilitates the bottom-up assembly of inorganic nanostructures defined in three dimensions and provides a path, via LbL processing, for the construction of layered hybrid materials under mild conditions

<i>In Vivo</i> Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale

Selectively labeled GroEL protein was produced in living deuterated bacterial cells to enhance its neutron scattering signal above that of the intracellular milieu. Quasi-elastic neutron scattering shows that the in-cell diffusion coefficient of GroEL was (4.7 ± 0.3) × 10^–12 m²/s, a factor of 4 slower than its diffusion coefficient in buffer solution. Internal protein dynamics showed a relaxation time of (65 ± 6) ps, a factor of 2 slower compared to the protein in solution. Comparison to the literature suggests that the effective diffusivity of proteins depends on the length and time scale being probed. Retardation of in-cell diffusion compared to the buffer becomes more significant with the increasing probe length scale, suggesting that intracellular diffusion of biomolecules is nonuniform over the cellular volume. The approach outlined here enables investigation of protein dynamics within living cells to open up new lines of research using “in-cell neutron scattering” to study the dynamics of complex biomolecular systems