Design of Synthetic Mammalian Promoters Using Highly Palindromic Subsequences

To express transgenes in specific cell types and states, promoters for endogenous genes are commonly created by truncating the sequence upstream of the transcriptional start site until the promoter is no longer functional. In this paper, we developed a method to design shorter synthetic mammalian promoters for endogenous genes by concatenating only its highly palindromic subsequences with a minimal core promoter. After developing metrics for palindromic density, analysis across all the human and mouse promoters showed higher palindromic density than expected by random. As experimental demonstrations, we applied the method to the CMV promoter (reduced to 432 nucleotides) and the mouse synapsin-1 promoter (383 nucleotides) to express fluorescent protein as reporters. Remarkably, the highly palindromic subsequences of these synthetic promoters contained sites important for strong constitutive expression and neuron-specific expression. As a resource to the community, we created enhancer sequences for all the human and mouse promoters.

Engineering a synthesis-friendly serum responsive promoter for antibiotic selection of genomic integration in cell-based therapy

For clinical cell-based therapies (e.g. CAR-T cells), the genomic integration of therapeutic genes into cells are selected using inefficient resistance genes of host origin to avoid potential immune response from using more efficient resistance genes of foreign origin. In principle, a serum-responsive promoter could express efficient resistance genes during the cell manufacturing stage that could then diminish during in vivo administration. To avoid genomic instability, we designed a synthesis-friendly serum-responsive promoter (SFSp) with no extreme GC ratios or repeats greater than 9 base pairs. SFSp was used to express a fluorescent reporter, whose expression was diminished after serum starvation. Furthermore, SFSp could be used in replacement of weak promoters (e.g. SV40p) for expressing efficient resistance genes (e.g. blasticidin resistance) from genomic integration via lentiviral infection. Thus, the regulation of resistance genes using SFSp could be a valuable tool in cell-based therapeutics to increase selection efficiency and reduce immunogenicity.

Insights on the role of chemometrics and vibrational spectroscopy in fruit metabolite analysis

•

The use of vibrational spectroscopy combined with data analytics is discussed.

•

The measure of bioactive compounds metabolites in fruit samples is presented.

•

Advantages and limitations of these techniques are discussed.

The last three decades have demonstrated the ability of combining data analytics (e.g. big data, machine learning) with modern analytical instrumental techniques such as vibrational spectroscopy (VIBSPEC) (e.g. NIR, Raman, MIR) and sensing technologies (e.g. electronic noses and tongues, colorimetric sensors) to analyse, measure and monitor a wide range of properties and samples. Developments in instrumentation, hardware and software have placed VIBSPEC as a useful tool to quantify several bioactive compounds and metabolites in a wide range of fruit and plant samples. With the incorporation of hand-held and portable instrumentation, these techniques have been valuable for the development of in-field and high throughput applications, opened new frontiers of analysis in fruits and plants. This review will present and discuss some of the current applications on the use of VIBSPEC techniques combined with data analytics on the measurement bioactive compounds and plant metabolites in different fruit samples.

Design of a synthesis-friendly hypoxia-responsive promoter for cell-based therapeutics

Towards the goal of making 'smart' cell therapies, one that recognizes disease conditions (e.g. hypoxia) and then produces mitigating biologics, it is important to develop suitable promoters. Currently, hypoxia responsive promoters are composed of strongly repeated sequences containing hypoxia response elements upstream of a minimal core promoter. Unfortunately, such repeated sequences have inherent genomic instability that may compromise the long-term consistency of cell-based therapeutics. Thus, we designed a synthesis-friendly hypoxia-inducible promoter (named SFHp) that has GC content between 25% and 75% and no repeats greater than 9 base pairs. In HEK293 cells stably integrated with genes regulated by synthetic SFHp, we demonstrated inducible reporter expression with fluorescent proteins, cell morphology rewiring with our previously engineered RhoA protein and intercellular cell signalling with secreted cytokines. These experiments exemplify the potential usage of SFHp in cell-based therapeutics with integrated genetic circuits that inducibly respond to the disease microenvironment.

Creation of a synthesis-friendly inflammation-inducible promoter suitable for cell therapy

The development of 'smart' cell-based therapeutics requires cells that first recognize conditions consistent with disease (e.g. inflammation) and then subsequently release therapeutic proteins, thereby reducing potential toxicity from otherwise continuous expression. Promoters containing NF-κB response elements are often used as reporters of inflammation; however, endogenous promoters have crosstalk with other pathways, and current synthetic promoters have many exact sequence repeats of NF-κB response elements which make them both difficult to synthesize and inherently genetically unstable. Herein, a synthesis-friendly inflammation-inducible promoter (named SFNp) was created by the packing of 14 NF-κB response elements, which have no repeats >9 bp, followed by a minimal cytomegalovirus promoter. In stably expressing human embryonic kidney 293 cells, we assessed the ability of SFNp to inducibly transcribe genes for reporting expression, changing cell morphology, and performing cell fusion. These experiments represent simple milestones for potentially using SFNp in the development of cell-based therapeutics. As strongly repeated DNA can compromise the long-term stability of genetic circuits, new designs used in 'smart' cell therapy will become more reliant on synthesis-friendly components like SFNp.

Generation of stable cell lines using readthrough expression from lentiviral integration

Lentiviral infection is often used to integrate genetic material into cells to stably express transgenes of interest. Depending on the location of integration into the host genome, readthrough expression of the lentiviral cargo can occur via an upstream endogenous promoter, which is typically an unwanted phenomenon because it can result in dysfunctional expression. The purpose of this study was to demonstrate that readthrough expression can be a wanted phenomenon for expressing functional proteins while at the same time reducing the size of the lentiviral transfer plasmid. Readthrough expression was used to generate HEK293 cell lines stably expressing fluorescent reporter proteins, reporter protein-antibiotic resistance fusion proteins for selection, and the vascular endothelial growth factor receptor 2. The generated proteins were all functional, as demonstrated by their ability to fluoresce, confer antibiotic resistance, and participate in receptor-mediated signalling, respectively. Therefore, we suggest that the mechanism of readthrough expression may have further applications in the expression of larger genes or genetic circuits (e.g. cell-based therapeutics), where the lentiviral cargo limit is stretched to the maximum.

EPEN-05. MUTATIONAL ANALYSIS OF THE C11ORF95 DOMAIN AND SINGLE-CELL RNA-SEQ PROFILE OF A MOUSE MODEL OF SUPRATENTORIAL EPENDYMOMA

We used a recently developed mouse model to better understand the cellular and molecular determinants of tumors driven by the oncogenic fusion protein C11orf95-RELA. Our approach makes use of in utero electroporation and a binary transposase system to introduce human C11orf95-RELA sequence, wild type and mutant forms, into neural progenitors. We used single cell RNA-seq to profile the cellular constituents within the resulting tumors in mice. We find that approximately 70% of the cells in the tumors do not express the oncogene C11orf95-RELA and these non-oncogene expressing cells are a combination of different non-tumor cell cell-types, including significant numbers of T-cells, and macrophages. The C11orf95-RELA expressing tumor cells have a unique transcriptomic profile that includes both astrocytic and neural progenitor marker genes, and is distinct from glioblastoma transcriptomic profiles. Since C11orf95-RELA is believed to function through a combination of both activation of NF-κB response genes by constitutive activation of RELA, and genes not activated by NF-κB, we assessed the expression of NF-κB response genes across the populations of cells in the tumor. Interestingly, when tumor cells highly expressing C11orf95-RELA were analyzed further, the subclusters identified were distinguished by upregulation of non-NF-kB pathways involved in cell proliferation, cell fate determination, and immune activation. We hypothesized that the C11orf95 domain may function to bring RELA transcriptional activation to inappropriate non-NF-κB targets, and we therefore performed a point mutation analysis of the C11orf95 domain. We found that mutations in either of the cysteines or histidines that make up a possible zinc finger domain in C11orf95 eliminate the ability of the fusion to induce tumors. In cell lines, these loss-of-function point mutants still trafficked to nuclei, and activated NF-κB pathways. We are currently using RNAseq and CRISPR loss-of function to identify genes downstream of C11orf95-RELA that are required for tumorigenesis.

Cryoneurolysis' outcome on pain experience (COPE) in patients with low-back pain: study protocol for a single-blinded randomized controlled trial

Background

Low-back pain, including facet joint pain, accounts for up to 20 % of all sick leaves in DenmarkA proposed treatment option is cryoneurolysis. This study aims to investigate the effect of cryoneurolysis in lumbar facet joint pain syndrome.

Methods

A single-center randomized controlled trial (RCT) is performed including 120 participants with chronic facet joint pain syndrome, referred to the Department of Neurosurgery, Aarhus University Hospital. Eligible patients receive a diagnostic anesthetic block, where a reduction of pain intensity ≥ 50 % on a numerical rating scale (NRS) is required to be enrolled. Participants are randomized into three groups to undergo either one treatment of cryoneurolysis, radiofrequency ablation or placebo. Fluoroscopy and sensory stimulation is used to identify the intended target nerve prior to administrating the above-mentioned treatments. All groups receive physiotherapy for 6 weeks, starting 4 weeks after treatment. The primary outcome is the patients’ impression of change in pain after intervention (Patient Global Impression of Change (PGIC)) at 4 weeks follow-up, prior to physiotherapy. Secondary outcomes are a reduction in low-back pain intensity (numeric rating scale) and quality of life (EQ-5D, SF-36) and level of function (Oswestry Disability Index), psychological perception of pain (Pain Catastrophizing Scale) and depression status (Major Depression Inventory).

Data will be assessed at baseline (T0), randomization (T1), day one (T2), 4 weeks (T3), 3 (T4), 6 (T5) and 12 months (T6).

Discussion

This study will provide information on the effectiveness of cryoneurolysis vs. the effectiveness of radiofrequency ablation or placebo for patients with facet joint pain, and help to establish whether cryoneurolysis should be implemented in clinical practice for this patient population.

Trial registration

The trial is approved by the ethical committee of Central Jutland Denmark with registration number 1-10-72-27-19 and the Danish Data Protection Agency with registration number 666,852. The study is registered at Clinicaltrial.gov with the ID number NCT04786145.

Engineering a Synthesis-Friendly Constitutive Promoter for Mammalian Cell Expression

Since cell-based therapies require the constitutive and stable expression of therapeutic transgenes, lentiviral infection is commonly used to integrate gene material regulated by standard constitutive promoters. Unfortunately, none of the standard or synthetic constitutive promoters can be easily synthesized at low cost due to the presence of repeated subsequences. Thus, in this paper, we designed a synthetic constitutive promoter (named SFCp) that can drive the expression of fluorescent proteins that subsequently trafficked to intended subcellular localizations and the expression of synthetic proteins that rewired the cellular response of Ca²⁺ to cell morphology changes. Furthermore, SFCp can be used to avoid sequence homology that can theoretically result in loss of genetic material by homologous recombination in tandem constructs. As gene synthesis becomes an indispensable tool in the arsenal of synthetic biology, it is essential to develop a toolbox of gene synthesis friendly components for cell engineering such as constitutive promoters.

Synthetic Biology Approaches in Immunology

Breakthroughs in gene synthesis has allowed synthetic biologists the ability to design any DNA sequence of interest, enabling the possibility to create complex systems inside cells with novel functions to tackle problems in immunology. Synthetic immunology of mammalian cells expressing natural or synthetic genes can guide and induce immune responses in patients. Through recent developments in engineering chimeric receptors, it is now feasible to customize control over engineered cells to target the disease sites with specificity. These cells can avoid immune rejection if derived from expandable cell types (e.g., stem cells or T cells) and then can be grown in abundance before implantation. However, safety concerns of engineered cells in circulation necessitates the development of a wide range of mechanisms to kill cells after their therapeutic life ends. This therapeutic effect is still predominantly the secretion of therapeutic proteins, but novel therapeutic interventions have been explored by synthetic biologists. In the pursuit of engineering new cell functions for synthetic immunology, it is possible that many problems previously thought intractable may actually be possible.

A monoclonal antibody acts as a migratory cue via Ca2+ re-wiring

As monoclonal antibodies have two epitopes for their target ligand, they should theoretically dimerize target receptors upon binding. In particular, the dimerization of the vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) stimulates early events occurring within minutes (e.g. Ca²⁺ signal generation) and late events occurring over hours and days (e.g. cell migration in angiogenesis). Although studies have noted that antibodies targeting VEGFR2 (anti-VEGFR2) inhibited cell migration in angiogenesis, we show in this paper that an anti-VEGFR2 stimulus nevertheless triggered a Ca²⁺ signal in VEGFR2 expressing cells. This Ca²⁺ signal was then re-wired to promote cell migration by co-expressing an engineered Ca²⁺ activated RhoA (called CaRQ), thereby engineering the opposite anticipated effect of an anti-VEGFR2 antibody. In these cells, the anti-VEGFR2 antibody stimulus induced cellular blebbing, migration across a membrane, and in vitro scratch wound healing. This work expands the utility of monoclonal antibodies to induce tailored responses in engineered cells such as changes in cell fluorescence via Ca²⁺ reporters or migration patterns via CaRQ.

Genetically Encoded Circuit for Remote Regulation of Cell Migration by Magnetic Fields

Magnetoreception can be generally defined as the ability to transduce the effects of a magnetic field into a cellular response. Magnetic stimulation at the cellular level is particularly attractive due to its ability for deep penetration and minimal invasiveness, allowing remote regulation of engineered biological processes. Previously, a magnetic-responsive genetic circuit was engineered using the transient receptor potential vanilloid 1 (TRPV1) and the iron containing ferritin protein (i.e., the TF circuit). In this study, we combined the TF circuit with a Ca²⁺ activated RhoA protein (CaRQ) to allow a magnetic field to remotely regulate cell migration. Cells expressing the TF circuit and CaRQ exhibited consistent dynamic protrusions, leading to migration along a porous membrane, directed spreading in response to a magnetic field gradient, as well as wound healing. This work offers a compelling interface for programmable electrical devices to control the migration of living systems for potential applications in cell-based therapy.

Antibody-Based Fusion Proteins Allow Ca2+ Rewiring to Most Extracellular Ligands

The Ca2+ signaling toolkit is the set of proteins used by living systems to generate and respond to Ca2+ signals. The selective expression of these proteins in particular tissues, cell types and subcellular locations allows the Ca2+ signal to regulate a diverse set of cellular processes. Through synthetic biology, the Ca2+ signaling toolkit can be expanded beyond the natural repertoire to potentially allow a non-natural ligand to control downstream cellular processes. To realize this potential, we exploited the ability of an antibody to bind its antigen exclusively in combination with the ability of the cytoplasmic domain of vascular endothelial growth factor receptor 2 (VEGFR2) to generate a Ca2+ signal upon oligomerization. Using protein fusions between antibody variants (i.e., nanobody, single-chain antibody and the monoclonal antibody) and the VEGFR2 cytoplasmic domain, Ca2+ signals were generated in response to extracellular stimulation with green fluorescent protein, mCherry, tumor necrosis factor alpha and soluble CD14. The Ca2+ signal generation by the stimulus did not require a stringent transition from monomer to oligomer state, but instead only required an increase in the oligomeric state. The Ca2+ signal generated by these classes of antibody-based fusion proteins can be rewired with a Ca2+ indicator or with an engineered Ca2+ activated RhoA to allow for antigen screening or migration to most extracellular ligands, respectively.

Engineered cell migration to lesions linked to autoimmune disease

The damaging and degenerative effects in autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and Crohn's disease often manifests as the formation of lesions that feature a high local concentration of granulocyte-macrophage colony-stimulating factor (GM-CSF). GM-CSF along with other pro-inflammatory factors form a positive feedback loop that ultimately perpetuate the lesions. Hence, to engineer chemotaxis to GM-CSF, we created a new chimeric GM-CSF receptor alpha subunit (GMRchi) that was coupled with a previously engineered Ca²⁺ -activated RhoA. When these proteins were expressed in mammalian cells, it allowed migration to chemical and cellular sources of GM-CSF. As a possible therapeutic intervention, we further implemented the mechanism of cell-cell membrane fusion and subsequent death. Since the microenvironment of lesions is more than just GM-CSF secretion, the further ability to recognize a combination of other features such as tissue markers will be needed for greater specificity. Nonetheless, this work represents a first step to enable cell-based therapy of autoimmune lesions.

Light directed migration of a cluster of cells in the centimeter scale

Protein-based systems for light directed migration of cells have been demonstrated up to distances of several hundred microns, but larger distances in the centimeter scale would allow new possible applications. Light activated migration in mammalian cells can be achieved by cells expressing channelrhodopsin-2 and an engineered Ca²⁺ sensitive Rac1 protein called RACer. In this study, light was used to induce wound healing, localize cells into a region of interest, and move cells over centimeter scale distances. Given the spatially complex organization of different types of cells in real tissue, light directed migration over the centimeter scale could potentially organize cell type arrangement to help develop more realistic tissues for transplantation.

Engineering a temperature sensitive tobacco etch virus protease

Since tobacco etch virus protease (TEVp) has a high specificity and efficiency in cleaving its target substrates, many groups have attempted to engineer conditional control of its activity. Temperature induction is widely used for modulating gene function because it has fast temporal response, good penetrability and applicability to many model organisms. Here, we engineered a temperature sensitive TEVp (tsTEVp) by using N-terminal truncations to TEVp that achieved efficient proteolysis on a timescale of 4 h after 30°C induction, while remaining relatively inactive at 37°C. As demonstration, tsTEVp was used to generate temperature-induced biological responses for protein translocation, protein degradation and Ca2+-mediated cellular blebbing. Lastly, tsTEVp and their engineered target substrates could find applications in engineered synthetic biological systems.

Autonomous Cell Migration to CSF1 Sources via a Synthetic Protein-Based System

Inflammatory lesions, often seen in diseases such as rheumatoid arthritis, atherosclerosis and cancer, feature an acidic (i.e., low pH) microenvironment rampant with cytokines, such as CSF1. For potential therapeutic intervention targeted at these CSF1 sources, we have assembled a system of four proteins inside a cell (i.e., HEK293) that initially had no natural CSF1-seeking ability. This system included a newly engineered CSF1 chimera receptor (named CSF1Rchi), the previously engineered Ca²⁺ activated RhoA (i.e., CaRQ), vesicular stomatitis virus glycoprotein G (VSVG) and thymidine kinase (TK). The binding of CSF1 to the CSF1Rchi generated a Ca²⁺ signal that activated CaRQ-mediated cellular blebbing, allowing autonomous cell migration toward the CSF1 source. Next, the VSVG protein allowed these engineered cells to fuse with the CSF1 source cells, upon low pH induction. Finally, these cells underwent death postganciclovir treatment, via the TK suicide mechanism. Hence, this protein system could potentially serve as the basis of engineering a cell to target inflammatory lesions in diseases featuring a microenvironment with high levels of CSF1 and low pH.

Engineering mammalian cells to seek senescence-associated secretory phenotypes

Since the removal of senescent cells in model organisms has been linked to rejuvenation and increased lifespan, senotherapies have emerged to target senescent cells for death. In particular, interleukin-6 (IL6) is a prominent senescence-associated secretory phenotype (SASP) and, thus, seeking IL6 could potentially localize engineered cells to senescent cells for therapeutic intervention. Here, we engineered a chimeric IL6 receptor (IL6Rchi) that generates a Ca²⁺ signal in response to IL6 stimulation. When IL6Rchi was co-expressed with an engineered Ca²⁺-activated RhoA (CaRQ), it enabled directed migration to IL6 in cells that have no such natural ability. Next, the removal of target cells was accomplished by the mechanism of membrane fusion and subsequent death. This work represents a first step towards engineering a cell to target senescent cells that secrete high levels of IL6. For increased specificity to senescent cells, it will likely be necessary for an engineered cell to recognize multiple SASPs simultaneously.

Engineered Proteins Program Mammalian Cells to Target Inflammatory Disease Sites

Disease sites in atherosclerosis and cancer feature cell masses (e.g., plaques/tumors), a low pH extracellular microenvironment, and various pro-inflammatory cytokines such as tumor necrosis factor α (TNFα). The ability to engineer a cell to seek TNFα sources allows for targeted therapeutic delivery. To accomplish this, here we introduced a system of proteins: an engineered TNFα chimeric receptor (named TNFR1chi), a previously engineered Ca²⁺-activated RhoA (named CaRQ), vesicular stomatitis virus glycoprotein G (VSVG), and thymidine kinase. Upon binding TNFα, TNFR1chi generates a Ca²⁺ signal that in turn activates CaRQ-mediated non-apoptotic blebs that allow migration toward the TNFα source. Next, the addition of VSVG, upon low pH induction, causes membrane fusion of the engineered and TNFα source cells. Finally, after ganciclovir treatment cells undergo death via the thymidine kinase suicide mechanism. Hence, we assembled a system of proteins that forms the basis of engineering a cell to target inflammatory disease sites characterized by TNFα secretion and a low-pH microenvironment.

Engineering Synthetic Proteins to Generate Ca2+ Signals in Mammalian Cells

The versatility of Ca²⁺ signals allows it to regulate diverse cellular processes such as migration, apoptosis, motility and exocytosis. In some receptors (e.g., VEGFR2), Ca²⁺ signals are generated upon binding their ligand(s) (e.g., VEGF-A). Here, we employed a design strategy to engineer proteins that generate a Ca²⁺ signal upon binding various extracellular stimuli by creating fusions of protein domains that oligomerize to the transmembrane domain and the cytoplasmic tail of the VEGFR2. To test the strategy, we created chimeric proteins that generate Ca²⁺ signals upon stimulation with various extracellular stimuli (e.g., rapamycin, EDTA or extracellular free Ca²⁺). By coupling these chimeric proteins that generate Ca²⁺ signals with proteins that respond to Ca²⁺ signals, we rewired, for example, dynamic cellular blebbing to increases in extracellular free Ca²⁺. Thus, using this design strategy, it is possible to engineer proteins to generate a Ca²⁺ signal to rewire a wide range of extracellular stimuli to a wide range of Ca²⁺-activated processes.

Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells

Background

To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells.

Results

While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca²⁺ signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions.

Conclusions

This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0320-7) contains supplementary material, which is available to authorized users.

The spatiotemporal relationship between local Ca(2+) signaling and P2X2R-activated membrane blebbing

Mammalian P2X receptors (P2XRs), a family of seven ionotropic purinergic receptors, function as ion channels modulating diverse cellular processes such as secretion, apoptosis and proliferation in response to extracellular ATP. Previously, it was shown that upon ATP stimulus, the P2X7 receptor (a member of P2XR family) triggers plasma membrane (PM) blebbing in HEK293 cells. In this study, we demonstrate that this phenomenon extends to another member of the P2XR family-P2X2 receptor (P2X2R). Similar to P2X7 receptor, P2X2R blebbing is dependent on Ca(2+)-calmodulin and ROCK-I. To elucidate the spatiotemporal relationship between Ca(2+) signaling and blebbing, protein biosensors and switches were used to image and generate Ca(2+) signals, respectively, while observing PM blebbing in cells. Blebbing cannot be initiated by Ca(2+) influx from the endoplasmic reticulum or by Ca(2+) transport across the PM by other Ca(2+) channels. To trigger blebbing, it is necessary for Ca(2+) to enter specifically through the P2X2R. Lastly, a local Ca(2+) signal near a fragment that encodes the intracellular P2X2R C-terminus tail is sufficient to trigger blebbing.

An Engineered Split Intein for Photoactivated Protein Trans-Splicing

Protein splicing is mediated by inteins that auto-catalytically join two separated protein fragments with a peptide bond. Here we engineered a genetically encoded synthetic photoactivatable intein (named LOVInC), by using the light-sensitive LOV2 domain from Avena sativa as a switch to modulate the splicing activity of the split DnaE intein from Nostoc punctiforme. Periodic blue light illumination of LOVInC induced protein splicing activity in mammalian cells. To demonstrate the broad applicability of LOVInC, synthetic protein systems were engineered for the light-induced reassembly of several target proteins such as fluorescent protein markers, a dominant positive mutant of RhoA, caspase-7, and the genetically encoded Ca2+ indicator GCaMP2. Spatial precision of LOVInC was demonstrated by targeting activity to specific mammalian cells. Thus, LOVInC can serve as a general platform for engineering light-based control for modulating the activity of many different proteins.

Photoswitchable protein degradation: a generalizable control module for cellular function?

In this issue of Chemistry & Biology, Renicke et al. report a photosensitive degron (psd) consisting of the LOV2 domain fused to a protein degradation sequence. This design enabled light-dependent protein degradation in yeast. When psd was fused to cell-cycle-dependent proteins, it controlled cell cycle by light with spatiotemporal precision.

Programming membrane fusion and subsequent apoptosis into mammalian cells

By the delivery of specific natural or engineered proteins, mammalian cells can be programmed to perform increasingly sophisticated and useful functions. Here, we introduce a set of proteins that has potential value in cell-based therapies by programming a cell to target tumor cells. First, the delivery of VSV-G (vesicular stomatitis virus glycoprotein) allowed the cell to undergo membrane fusion with adjacent cells to form syncytia (i.e., a multinucleated cell) in conditions of low pH typically occurring at a tumor site. The formation of syncytia caused the clustering of nuclei along with an integration of the microtubule network and ER. Interestingly, the formation of syncytia between cells that are dynamically blebbing, a mode of migration preferred during tumor metastasis, resulted in the loss of these morphology changes. Lastly, the codelivery of VSV-G with L57R (an engineered photoactivated caspase-7) allowed cells to undergo low pH-dependent membrane fusion followed by blue light-dependent apoptosis. In cell-based therapies, the clearance of syncytia between tumor cells might further trigger an immune response against the tumor.

Relativistic quantum teleportation with superconducting circuits

We study the effects of relativistic motion on quantum teleportation and propose a realizable experiment where our results can be tested. We compute bounds on the optimal fidelity of teleportation when one of the observers undergoes nonuniform motion for a finite time. The upper bound to the optimal fidelity is degraded due to the observer's motion. However, we discuss how this degradation can be corrected. These effects are observable for experimental parameters that are within reach of cutting-edge superconducting technology.

Simultaneous assembly of two target proteins using split inteins for live cell imaging

Inteins are protein elements that covalently reassemble proteins from two precursor fragments in a process known as protein splicing. They are commonly used to reassemble a single target protein by protein splicing, but a second target protein can potentially reassemble by intein dimerization. Here, we use the naturally occurring split DnaE intein from Nostoc punctiforme (NpuDnaE) to demonstrate the simultaneous assembly of two target proteins in several examples studied with live cell imaging: yellow fluorescent protein (YFP) with monomeric red fluorescent protein (mRFP), dominant positive mutant of RhoA GTPase with YFP and GCaMP2 Ca(2+) indicator with mRFP. These examples showed the versatility of the strategy along with some interesting attributes: first, the two target proteins are in equal stoichiometry; second, the extent of protein splicing can be reported by a fluorescent protein. In particular, the split GCaMP2 with mRFP could find applications in tissue-specific Ca(2+) imaging in transgenic organisms, where mRFP could control for motion-related intensity changes.

Engineered networks of synthetic and natural proteins to control cell migration

Mammalian cells reprogrammed with engineered transgenes have the potential to be useful therapeutic platforms because they can support large genetic networks, can be taken from a host or patient, and perform useful functions such as migration and secretion. Successful engineering of mammalian cells will require the development of modules that can perform well-defined, reliable functions, such as directed cell migration toward a chemical or physical signal. One inherently modular cellular pathway is the Ca(2+) signaling pathway: protein modules that mobilize and respond to Ca(2+) are combined across cell types to create complexity. We have designed a chimera of Rac1, a GTPase that controls cell morphology and migration, and calmodulin (CaM), a Ca(2+)-responsive protein, to control cell migration. The Rac1-CaM chimera (named RACer) controlled lamellipodia growth in response to Ca(2+). RACer was combined with LOVS1K (a previously engineered light-sensitive Ca(2+)-mobilizing module) and cytokine receptors to create protein networks where blue light and growth factors regulated cell morphology and, thereby, cell migration. To show the generalizability of our design, we created a Cdc42-CaM chimera that controls filopodia growth in response to Ca(2+). The insights that have been gained into Ca(2+) signaling and cell migration will allow future work to combine engineered protein systems to enable reprogrammed cell sensing of relevant therapeutic targets in vivo.

Engineered regulation of lysozyme by the SH3-CB1 binding interaction

The ability to design proteins with desired properties by using protein structural information will allow us to create high-value therapeutic and diagnostic products. Using the protein structures of lambda lysozyme and the SH3 domain of human Crk, we designed a synthetic protein switch that controls the activity of lysozyme by sterically hindering its active cleft through the binding of SH3 to its CB1 peptide-binding partner. First, several fusion protein designs with lysozyme and CB1 were modeled to determine the one with greatest steric effect in the presence of SH3. Next, the selected fusion protein was created and tested in vitro. In the absence of SH3, the lysozyme-CB1 fusion protein functioned normally. In the presence of SH3, the lysozyme activity was inhibited and with the addition of excess CB1 peptides to compete for SH3 binding, the lysozyme activity was restored. Lastly, this structure-based strategy can be used to engineer synthetic regulation by peptide-domain-binding interfaces into a variety of proteins.

Parts-based assembly of synthetic transmembrane proteins in mammalian cells

Transmembrane proteins span cellular membranes such as the plasma membrane and endoplasmic reticulum (ER) membrane to mediate inter- and intracellular interactions. An N-terminal signal peptide and transmembrane helices facilitate recruitment to the ER and integration into the membrane, respectively. Using a parts-based assembly approach in this study, we confirm that the minimum requirement to create a transmembrane protein is indeed only a transmembrane helix (TM). When transfected in mammalian cells, our fusion proteins in the schematic form X-TM-Y were localized to vesicles, the golgi apparatus, the nuclear envelope, or the endoplasmic reticulum, consistent with ER targeting. Further studies to determine orientation showed that X was facing the cytoplasm, and Y the lumen. Lastly, in our fusion proteins with an N-terminal TM, the TM effectively reversed the orientation of X and Y. This knowledge can be applied to the parts-based engineering of synthetic transmembrane proteins with varied functions and biological applications.

Engineering a photoactivated caspase-7 for rapid induction of apoptosis

Apoptosis is a cell death program involved in the development of multicellular organisms, immunity, and pathologies ranging from cancer to HIV/AIDS. We present an engineered protein that causes rapid apoptosis of targeted cells in monolayer culture after stimulation with blue light. Cells transfected with the protein switch L57V, a tandem fusion of the light-sensing LOV2 domain and the apoptosis-executing domain from caspase-7, rapidly undergo apoptosis within 60 min after light stimulation. Constant illumination of under 5 min or oscillating with 1 min exposure had no effect, suggesting that cells have natural tolerance to a short duration of caspase-7 activity. Furthermore, the overexpression of Bcl-2 prevented L57V-mediated apoptosis, suggesting that although caspase-7 activation is sufficient to start apoptosis, it requires mitochondrial contribution to fully commit.

Effects of rapamycin-induced oligomerization of parvalbumin, Stim1 and Orai1 in puncta formation

Elevations of cytosolic Ca2+ from the endoplasmic reticulum (ER) regulate a diverse range of cellular processes. When these luminal stores become depleted, the transmembrane ER protein Stim1 oligomerizes and translocates within the ER membrane to puncta junctions to couple with Orai1 channels, activating store-operated calcium entry (SOCE). Stim1 oligomerization and puncta formation have generally been associated with its luminal domains, however, studies have implicated that the cytoplasmic domains may contribute to this oligomerization. Studies have also suggested that intermediate or regulating elements may be required to fine-tune puncta formation and activation of SOCE. Here we made fusion proteins of Stim1 and Orai1 with FRB and FKBP12 domains that associate in the presence of rapamycin. Rapamycin-induced coupling of Stim1 to Stim1, Orai1 to Orai1 and Stim1 to Orai1 was found to be insufficient for puncta formation. Rapamycin was then used to recruit the cytosolic Ca2+ buffer protein parvalbumin (Pav) to Stim1 in order to buffer the local cytosolic Ca2+ near the ER membrane. Interestingly, Pav buffering near the ER caused puncta formation that was indistinguishable from those caused by thapsigargin. Our results suggest that Stim1 oligomerization and puncta formation may be additionally regulated either by local Ca2+ levels near the ER membrane or by as yet unidentified Ca2+-dependent proteins interacting with the cytoplasmic domains of Stim1.

A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum

The presence and distribution of hybrid individuals and the existence of a hybrid zone between the catadromous Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum were investigated throughout the range of both species in Australia. Bayesian analyses and genotypic simulations identified 140 putative hybrids (11·5% of the total sample) with varying levels of introgression. Most hybrids were observed in an area extending from the Snowy River to the Albert River suggesting a hybrid zone in the eastern Bass Strait region. Sixteen hybrids, however, were found outside this zone, possibly reflecting the movement of hybrid offspring between estuaries or their inadvertent release during fish stocking programmes. Biparental backcrossing was found to occur suggesting that hybrids were fertile. These results have implications for the management of the extensive stocking programme in M. novemaculeata and for understanding the potential role of habitat degradation and reduced water flow in facilitating hybridization in species with migratory life histories.

TEV protease-facilitated stoichiometric delivery of multiple genes using a single expression vector

Delivery and expression of multiple genes is an important requirement in a range of applications such as the engineering of synthetic signaling pathways and the induction of pluripotent stem cells. However, conventional approaches are often inefficient, nonstoichiometric and may limit the maximum number of genes that can be simultaneously expressed. We here describe a versatile approach for multiple gene delivery using a single expression vector by mimicking the protein expression strategy of RNA viruses. This was accomplished by first expressing the genes together with TEV protease as a single fusion protein, then proteolytically self-cleaving the fusion protein into functional components. To demonstrate this method in E. coli cells, we analyzed the translation products using SDS-PAGE and showed that the fusion protein was efficiently cleaved into its components, which can then be purified individually or as a binding complex. To demonstrate this method in mammalian cells, we designed a differential localization scheme and used live cell imaging to observe the distinctive subcellular targeting of the processed products. We also showed that the stoichiometry of the processed products was consistent and corresponded with the frequency of appearance of their genes on the expression vector. In summary, the efficient expression and separation of up to three genes was achieved in both E. coli and mammalian cells using a single TEV protease self-processing vector.

Structure based design of a Ca2+-sensitive RhoA protein that controls cell morphology

The Rho proteins are important regulators of cell morphology, and the prototypical protein RhoA is known to regulate contraction, blebbing and bleb retraction. We have identified and experimentally confirmed that RhoA has a binding site for calmodulin, a ubiquitous transducer of the Ca(2+) second messenger. Using structural modeling, a fusion protein was designed wherein RhoA activity was controlled by Ca(2+) via calmodulin. Living cells transfected with this synthetic protein underwent Ca(2+) sensitive and calmodulin-dependent bleb retraction within minutes. Further, the modularity of Ca(2+) signaling was exploited to induce bleb retraction in response to blue light (using channelrhodopsin-2) or exogenous chemicals (with acetylcholine receptor), showing input signal versatility. The widespread use of Ca(2+) signaling in nature suggests that fully exploring its signaling potential may allow powerful applications to other synthetic biological systems.

Fluorescent protein-based methods for on-plate screening of gene insertion

BACKGROUND

Unlike the commonly used method of blue-white screening for gene insertion, a fluorescent protein-based screening method offers a gain-of-function screening process without using any co-factors and a gene fusion product with a fluorescent protein reporter that is further useful in cell imaging studies. However, complications related to protein-folding efficiencies of the gene insert in fusion with fluorescent protein reporters prevent effective on-plate bacterial colony selection leading to its limited use.

METHODOLOGY/PRINCIPAL FINDINGS

Here, we present three methods to tackle this problem. Our first method promotes the folding of the gene insert by using an N-terminal protein such as calmodulin that is well folded and expressed. Under this method, fluorescence was increased more than 30x over control allowing for enhanced screening. Our second method creates a fluorescent protein that is N-terminal to the gene upon insertion, thereby reducing the dependency of the fluorescent protein reporter on the folding of the gene insert. Our third method eliminates any dependence of the fluorescent protein reporter on the folding of the gene insert by using a stop and start sequence for protein translation.

CONCLUSIONS/SIGNIFICANCE

The three methods together will expand the usefulness of fluorescence on-plate screening and offer a powerful alternative to blue-white screening.

Design of fluorescent fusion protein probes

Many fluorescent probes depend on the fluorescence resonance energy transfer (FRET) between fluorescent protein pairs. The efficiency of energy transfer becomes altered by conformational changes of a fused sensory protein in response to a cellular event. A structure-based approach can be taken to design probes better with improved dynamic ranges by computationally modeling conformational changes and predicting FRET efficiency changes of candidate biosensor constructs. FRET biosensors consist of at least three domains fused together: the donor protein, the sensory domain, and the acceptor protein. To more efficiently subclone fusion proteins containing multiple domains, a cassette-based system can be used. Generating a cassette library of commonly used domains facilitates the rapid subcloning of future fusion biosensor proteins. FRET biosensors can then be used with fluorescence microscopy for real-time monitoring of cellular events within live cells by tracking changes in FRET efficiency. Stimulants can be used to trigger a range of cellular events including Ca(2+) signaling, apoptosis, and subcellular translocations.