Metalloprotein switches that display chemical-dependent electron transfer in cells.

Biological electron transfer is challenging to directly regulate using environmental conditions. To enable dynamic, protein-level control over energy flow in metabolic systems for synthetic biology and bioelectronics, we created ferredoxin logic gates that utilize transcriptional and post-translational inputs to control energy flow through a synthetic electron transfer pathway that is required for bacterial growth. These logic gates were created by subjecting a thermostable, plant-type ferredoxin to backbone fission and fusing the resulting fragments to a pair of proteins that self-associate, a pair of proteins whose association is stabilized by a small molecule, and to the termini of a ligand-binding domain. We show that the latter domain insertion design strategy yields an allosteric ferredoxin switch that acquires an oxygen-tolerant [2Fe-2S] cluster and can use different chemicals, including a therapeutic drug and an environmental pollutant, to control the production of a reduced metabolite in Escherichia coli and cell lysates.

Assessing nanoparticle colloidal stability with single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS).

Biological interactions, toxicity, and environmental fate of engineered nanoparticles are affected by colloidal stability and aggregation. To assess nanoparticle aggregation, analytical methods are needed that allow quantification of individual nanoparticle aggregates. However, most techniques used for nanoparticle aggregation analysis are limited to ensemble measurements or require harsh sample preparation that may introduce artifacts. An ideal method would analyze aggregate size in situ with single-nanoparticle resolution. Here, we established and validated single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS) as an unbiased high-throughput analytical technique to quantify nanoparticle size distributions and aggregation in situ. We induced nanoparticle aggregation by exposure to physiologically relevant saline conditions and applied SP-ICP-MS to quantify aggregate size and aggregation kinetics at the individual aggregate level. In situ SP-ICP-MS analysis revealed rational surface engineering principles for the preparation of colloidally stable nanoparticles. Our quantitative SP-ICP-MS technique is a platform technology to evaluate aggregation characteristics of various types of surface-engineered nanoparticles under physiologically relevant conditions. Potential widespread applications of this method may include the study of nanoparticle aggregation in environmental samples and the preparation of colloidally stable nanoparticle formulations for bioanalytical assays and nanomedicine. Graphical abstract.

Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation.

Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging.

Extracellular matrix-templating fibrous hydrogels promote ovarian tissue remodeling and oocyte growth.

Synthetic matrices which mimic the extracellular composition of native tissue create a comprehensive model for studying development and disease. Here, we have engineered a composite material which retains cell-secreted ECM for the culture of ovarian follicles by embedding electrospun dextran fibers functionalized with basement membrane binder (BMB) peptide in PEG hydrogels. In the presence of ECM-sequestering fibers, encapsulated immature primordial follicles and ovarian stromal cells aggregated into large organoid-like structures with dense deposition of laminin, perlecan, and collagen I, leading to steroidogenesis and significantly greater rates of oocyte survival and growth. We determined that cell aggregation restored key cell-cell interactions critical for oocyte survival, whereas oocyte growth was dependent on cell-matrix interactions achieved in the presence of BMB. Here we have shown that sequestration and retention of cell-secreted ECM along synthetic fibers mimics fibrous ECM structure and restores the cell-cell and cell-matrix interactions critical for engineering an artificial ovary.

High-stiffness, fast-crosslinking, cartilage matrix bioinks.

Scaffolds derived from cartilage extracellular matrix may contain intrinsic chondroinductivity and have promise for cartilage regeneration. Cartilage is typically ground into devitalized particles (DVC) and several groups have pioneered innovative methods to rebuild the DVC into a new scaffold. However, challenges remain regarding the fluid and solid biomechanics of cartilage-based scaffolds in achieving 1) high mechanical performance akin to native cartilage and 2) easy surgical delivery/retention. Fortunately, photocrosslinking bioinks may benefit clinical translation: paste-like/injectable precursor rheology facilitates surgical placement, and in situ photocrosslinking enables material retention within any size/shape of defect. While solubilized DVC has been modified with methacryloyls (MeSDVC), MeSDVC is limited by slow crosslinking times (e.g., 5-10 min). Therefore, in the current study, we fabricated a pentenoate-modified SDVC (PSDVC), to enable a faster crosslinking reaction via a thiol-ene click chemistry. The crosslinking time of the PSDVC was faster (∼1.7 min) than MeSDVC (∼4 min). We characterized the solid and fluid mechanics/printabilities of PSDVC, pentenoate-modified hyaluronic acid (PHA), and the PHA or PSDVC with added DVC particles. While the addition of DVC particles enhanced the printed shape fidelity of PHA or PSDVC, the increased clogging decreased the ease of printing and cell viability after bioprinting, and future refinement is needed for DVC-containing bioinks. However, the PSDVC alone had a paste-like rheology/good bioprintability prior to crosslinking, the fastest crosslinking time (i.e., 1.7 min), and the highest compressive modulus (i.e., 3.12 ± 0.41 MPa) after crosslinking. Overall, the PSDVC may have future potential as a translational material for cartilage repair.

The Rheology and Printability of Cartilage Matrix-Only Biomaterials.

The potential chondroinductivity from cartilage matrix makes it promising for cartilage repair; however, cartilage matrix-based hydrogels developed thus far have failed to match the mechanical performance of native cartilage or be bioprinted without adding polymers for reinforcement. There is a need for cartilage matrix-based hydrogels with robust mechanical performance and paste-like precursor rheology for bioprinting/enhanced surgical placement. In the current study, our goals were to increase hydrogel stiffness and develop the paste-like precursor/printability of our methacryl-modified solubilized and devitalized cartilage (MeSDVC) hydrogels. We compared two methacryloylating reagents, methacrylic anhydride (MA) and glycidyl methacrylate (GM), and varied the molar excess (ME) of MA from 2 to 20. The MA-modified MeSDVCs had greater methacryloylation than GM-modified MeSDVC (20 ME). While GM and most of the MA hydrogel precursors exhibited paste-like rheology, the 2 ME MA and GM MeSDVCs had the best printability (i.e., shape fidelity, filament collapse). After crosslinking, the 2 ME MA MeSDVC had the highest stiffness (1.55 ± 0.23 MPa), approaching the modulus of native cartilage, and supported the viability/adhesion of seeded cells for 15 days. Overall, the MA (2 ME) improved methacryloylation, hydrogel stiffness, and printability, resulting in a stand-alone MeSDVC printable biomaterial. The MeSDVC has potential as a future bioink and has future clinical relevance for cartilage repair.

Conductive and injectable hyaluronic acid/gelatin/gold nanorod hydrogels for enhanced surgical translation and bioprinting.

There is growing evidence indicating the need to combine the rehabilitation and regenerative medicine fields to maximize functional recovery after spinal cord injury (SCI), but there are limited methods to synergistically combine the fields. Conductive biomaterials may enable synergistic combination of biomaterials with electric stimulation (ES), which may enable direct ES of neurons to enhance axon regeneration and reorganization for better functional recovery; however, there are three major challenges in developing conductive biomaterials: (1) low conductivity of conductive composites, (2) many conductive components are cytotoxic, and (3) many conductive biomaterials are pre-formed scaffolds and are not injectable. Pre-formed, noninjectable scaffolds may hinder clinical translation in a surgical context for the most common contusion-type of SCI. Alternatively, an injectable biomaterial, inspired by lessons from bioinks in the bioprinting field, may be more translational for contusion SCIs. Therefore, in the current study, a conductive hydrogel was developed by incorporating high aspect ratio citrate-gold nanorods (GNRs) into a hyaluronic acid and gelatin hydrogel. To fabricate nontoxic citrate-GNRs, a robust synthesis for high aspect ratio GNRs was combined with an indirect ligand exchange to exchange a cytotoxic surfactant for nontoxic citrate. For enhanced surgical placement, the hydrogel precursor solution (i.e., before crosslinking) was paste-like, injectable/bioprintable, and fast-crosslinking (i.e., 4 min). Finally, the crosslinked hydrogel supported the adhesion/viability of seeded rat neural stem cells in vitro. The current study developed and characterized a GNR conductive hydrogel/bioink that provided a refinable and translational platform for future synergistic combination with ES to improve functional recovery after SCI.

Development and quantitative characterization of the precursor rheology of hyaluronic acid hydrogels for bioprinting.

Bioprinting technologies have tremendous potential for advancing regenerative medicine due to the precise spatial control over depositing a printable biomaterial, or bioink. Despite the growing interest in bioprinting, the field is challenged with developing biomaterials for extrusion-based bioprinting. The paradigm of contemporary bioink studies relies on trial-and-error methods for discovering printable biomaterials, which has little practical use for others who endeavor to develop bioinks. There is pressing need to follow the precedent set by a few pioneering studies that have attempted to standardize bioink characterizations for determining the properties that define printability. Here, we developed a pentenoate-functionalized hyaluronic acid hydrogel (PHA) into a printable bioink and used three recommended, quantitative rheological assessments to characterize the printability: 1) yield stress, 2) viscosity, and 3) storage modulus recovery. The most important characteristic is the yield stress; we found a yield stress upper limit of ∼1000 Pa for PHA. Measuring the viscosity was advantageous for determining shear-thinning behavior, which aided in extruding highly viscous PHA through a nozzle. Post-printing recovery is required to maintain shape fidelity and we found storage modulus recoveries above ∼85% were sufficient for PHA. Two formulations had superior printability (i.e., 1.5 MDa PHA - 4 wt%, and 1 MDa PHA - 8 wt%), and increasing cell concentrations in PHA up to 9 × 106 cells/mL had minimal effects on the printability. Even so, other factors such as sterilization and peptide modifications to enhance bioactivity may influence printability, highlighting the need for investigators to consider such factors when developing new bioinks. STATEMENT OF SIGNIFICANCE: Bioprinting has potential for regenerating damaged tissues; however, there are a limited number of printable biomaterials, and developing new bioinks is challenging because the required material physical properties for extrusion-based printing are not yet known. Most new bioinks are developed by trial-and-error, which is neither efficient nor comparable across materials. There is a need for the field to begin utilizing standard methods proposed by a few pioneering studies to characterize new bioinks. Therefore, we have developed the printability of a hyaluronic acid based-hydrogel and characterized the material with three quantitative rheological tests. The current work impacts the bioprinting field by demonstrating and encouraging the use of universal bioink characterizations and by providing printability windows to advance new bioink development.

A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit.

Monitoring the aggregation of proteins within the cellular environment is key to investigating the molecular mechanisms underlying the formation of off-pathway protein assemblies associated with the development of disease and testing therapeutic strategies to prevent the accumulation of non-native conformations. It remains challenging, however, to couple protein aggregation events underlying the cellular pathogenesis of a disease to genetic circuits and monitor their progression in a quantitative fashion using synthetic biology tools. To link the aggregation propensity of a target protein to the expression of an easily detectable reporter, we investigated the use of a transcriptional AND gate system based on complementation of a split transcription factor. We first identified two-fragment tetracycline repressor (TetR) variants that can be regulated via ligand-dependent induction and demonstrated that split TetR variants can function as transcriptional AND gates in both bacteria and mammalian cells. We then adapted split TetR for use as an aggregation sensor. Protein aggregation was detected by monitoring complementation between a larger TetR fragment that serves as a "detector" and a smaller TetR fragment expressed as a fusion to an aggregation-prone protein that serves as a "sensor" of the target protein aggregation status. This split TetR represents a novel genetic component that can be used for a wide range of applications in bacterial as well as mammalian synthetic biology and a much needed cell-based sensor for monitoring a protein's conformational status in complex cellular environments.

Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid.

Transcriptional control can be used to program cells to label proteins with noncanonical amino acids by regulating the expression of orthogonal aminoacyl tRNA synthetases (aaRSs). However, we cannot yet program cells to control labeling in response to aaRS and ligand binding. To identify aaRSs whose activities can be regulated by interactions with ligands, we used a combinatorial approach to discover fragmented variants of Escherichia coli methionyl tRNA synthetase (MetRS) that require fusion to associating proteins for maximal activity. We found that these split proteins could be leveraged to create ligand-dependent MetRS using two approaches. When a pair of MetRS fragments was fused to FKBP12 and the FKBP-rapamycin binding domain (FRB) of mTOR and mutations were introduced that direct substrate specificity toward azidonorleucine (Anl), Anl metabolic labeling was significantly enhanced in growth medium containing rapamycin, which stabilizes the FKBP12-FRB complex. In addition, fusion of MetRS fragments to the termini of the ligand-binding domain of the estrogen receptor yielded proteins whose Anl metabolic labeling was significantly enhanced when 4-hydroxytamoxifen (4-HT) was added to the growth medium. These findings suggest that split MetRS can be fused to a range of ligand-binding proteins to create aaRSs whose metabolic labeling activities depend upon post-translational interactions with ligands.

The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation.

Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement in which native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein's functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AKs with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and it reveals a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection.

Early myogenic responses to acute exercise before and after resistance training in young men.

To enable dynamic regulation of muscle mass and myofiber repair following injury, a satellite cell precursor population exists to supply additional nuclei. Activated satellite cells express many genes and associated proteins necessary for maturation and incorporation into the damaged fiber. There is little knowledge about the response of these markers following whole-body resistance exercise training. We investigated the impact of 12 weeks of progressive whole-body resistance training on the expression of MRFs, PAX7, NCAM, and FA1, incorporating both acute and chronic resistance exercise components. Ten young recreationally active males (21.2 ± 3.5 years) performed 12 weeks of whole-body resistance training at 70-85% of their predetermined one-repetition maximum (1RM). At the initiation and completion of the training period, muscular strength was assessed by RM and dynamometer testing, and vastus lateralis samples were obtained prior to and 3 h following an acute resistance exercise test (both whole-body and isometric exercises). Increased mRNA expression of PAX7 (threefold), NCAM (threefold), MYF5 (threefold), MYOD (threefold) and MYOGENIN (twofold) was observed 3 h after the acute resistance exercise test, both pre and posttraining. Similarly, PAX7 (11-fold) and FA1 (twofold) protein abundance increased after acute exercise, while resting NCAM (eightfold) and FA1 (threefold) protein abundance increased following 12 weeks of resistance training. It is possible that these molecular changes are primarily due to the preceding exercise bout, and are not modified by long-term or whole-body exercise training.