Protein Expression System Research Articles

Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization

BackgroundAdaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast, in search of suitable novel promoters able to drive transcription in response to the pH signal.ResultsIn spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii.ConclusionsThis work defines in K. phaffii a subset of genes and diverse cellular pathways that are altered in response to moderate alkalinization of the medium, thus setting the basis for developing novel pH-controlled systems for heterologous protein expression in this fungus.

Development mechanism of resistant population post-exposure to tigecycline in tigecycline-heteroresistant Acinetobacter baumannii strain.

Tigecycline heteroresistance is highly prevalent in Acinetobacter baumannii clinical isolates, reducing the efficacy of tigecycline treatment. This study investigated the population dynamics of A. baumannii with tigecycline heteroresistance to determine the origin of resistance that occurs over time after antibiotic exposure. Tigecycline heteroresistance was imitated by mixing tigecycline-susceptible and -resistant A. baumannii isolates in a 1:10-6 ratio, and confirmed using population analysis profiling. Growth curves and an in-vitro competition assay found no difference in bacterial fitness between tigecycline-resistant and -susceptible populations. The green fluorescent protein (GFP) expression system and flow cytometry were used to monitor the population dynamics of the heteroresistant population, while differentiating the resistant population from the susceptible population. The mimicked tigecycline heteroresistance was confirmed to be reproducible and stable without tigecycline. The GFP-expressing population (i.e. the resistant population) nearly went undetected because it only represented approximately 10-6 of the entire population. However, when the mimicked tigecycline-heteroresistant strain was treated with tigecycline, most subpopulations expressing GFP were detected. The surviving A. baumannii population, upon exposure to tigecycline, exhibited a high minimum inhibitory concentration for tigecycline, equivalent to that of tigecycline-resistant isolates that were used to mimic heteroresistance. These results indicate that the development of resistance in tigecycline-heteroresistant A. baumannii strains, resulting in decreased antibiotic efficacy, may depend on the selection of a pre-existing resistant subpopulation.

The Effect Of Hepatitis E Virus Open Reading Frame 3 Protein on The Expression Levels of IFN-β,IL6,TNF-α and RANTES in SW480 Colon Cancer Cells

The Hepatitis E virus (HEV) could induce chronic hepatitis and liver failure with high mortality through unclear mechanisms. The purpose of this study was to determine the effect of (recombinant fusion protein, ORF3 of genotype 1 HEV) on the expression levels of cytokine or chemokine genes in colon cancer cells (SW480) using a quantitative assay of “SYBR green" real-time PCR. An ORF3 protein expression system (Orf3-GFP plasmid) was synthesized in the company of GenScript (USA) and used as an expression vector, SW480 cells were infected by (Orf3-GFP plasmid) or GFP- control vector. Result of this study was approved after assessing the expression level of the ORF3 gene in ORF3 expressing cells and in control groups using ORF3 specific primer to ensure that the transfection was performed successfully, The expression levels of three genes (IFN-β, IL-6, and TNF-α) were estimated in ORF3-expressing cells using specific primers for all genes. In addition, the role of HEV Orf3 in upregulating RANTES expression levels was revealed. In conclusion: In SW480 cells, this study found that the ORF3 protein of genotype 1 HEV is capable of regulating the expression of multiple immune response genes including Interferon- β (IFN-β), Interleukin-6 (IL-6) Tumor necrosis factor-α (TNF-α) and regulated on activation, normal T cell expressed and secreted (RANTES) which may enhance viral replication and pathogenicity.

Multiscale design of cell-free biologically active architectural structures.

Cell-free protein expression systems are here combined with 3D-printed structures to study the challenges and opportunities as biofabrication enters the spaces of architecture and design. Harnessing large-scale additive manufacturing of biological materials, we examined the addition of cell-free protein expression systems ("TXTL" i.e., biological transcription-translation machinery without the use of living cells) to printed structures. This allowed us to consider programmable, living-like, responsive systems for product design and indoor architectural applications. This emergent, pluripotent technology offers exciting potential in support of health, resource optimization, and reduction of energy use in the built environment, setting a new path to interactivity with mechanical, optical, and (bio) chemical properties throughout structures. We propose a roadmap towards creating healthier, functional and more durable systems by deploying a multiscale platform containing biologically-active components encapsulated within biopolymer lattices operating at three design scales: (i) supporting cell-free protein expression in a biopolymer matrix (microscale), (ii) varying material properties of porosity and strength within two-dimensional lattices to support biological and structural functions (mesoscale), and (iii) obtaining folded indoor surfaces that are structurally sound at the meter scale and biologically active (we label that regime macroscale). We embedded commercially available cell-free protein expression systems within silk fibroin and sodium alginate biopolymer matrices and used green fluorescent protein as the reporter to confirm their compatibility. We demonstrate mechanical attachment of freeze-dried bioactive pellets into printed foldable fibrous biopolymer lattices showing the first steps towards modular multiscale fabrication of large structures with biologically active zones. Our results discuss challenges to experimental setup affecting expression levels and show the potential of robust cell-free protein-expressing biosites within custom-printed structures at scales relevant to everyday consumer products and human habitats.

Diagnostic and vaccine potential of Zika virus envelope protein (E) derivates produced in bacterial and insect cells.

In the present study we evaluated the features of different recombinant forms of Zika virus (ZIKV) proteins produced in either bacterial (Eschericha coli) or insect cells (Drosophila melanogaster). The ZIKV-envelope glycoprotein (EZIKV) is responsible for virus entry into host cells, is the main target of neutralizing antibodies and has been used as a target antigen either for serological tests or for the development of subunit vaccines. The EZIKV is composed of three structural and functional domains (EDI, EDII, and EDIII), which share extensive sequence conservation with the corresponding counterparts expressed by other flaviviruses, particularly the different dengue virus (DENV) subtypes. In this study, we carried out a systematic comparison of the antigenicity and immunogenicity of recombinant EZIKV, EDI/IIZIKV and EDIIIZIKV produced in E. coli BL21 and Drosophila S2 cells. For the antigenicity analysis we collected 88 serum samples from ZIKV-infected participants and 57 serum samples from DENV-infected. For immunogenicity, C57BL/6 mice were immunized with two doses of EZIKV, EDI/IIZIKV and EDIIIZIKV produced in E. coli BL21 and Drosophila S2 cells to evaluate humoral and cellular immune response. In addition, AG129 mice were immunized with EZIKV and then challenge with ZIKV. Testing of samples collected from ZIKV-infected and DENV-infected participants demonstrated that the EZIKV and EDIIIZIKV produced in BL21 cells presented better sensitivity and specificity compared to proteins produced in S2 cells. In vivo analyses were carried out with C57BL/6 mice and the results indicated that, despite similar immunogenicity, antigens produced in S2 cells, particularly EZIKV and EDIIIZIKV, induced higher ZIKV-neutralizing antibody levels in vaccinated mice. In addition, immunization with EZIKV expressed in S2 cells delayed the onset of symptoms and increased survival rates in immunocompromised mice. All recombinant antigens, either produced in bacteria or insect cells, induced antigen-specific CD4+ and CD8+ T cell responses. In conclusion, the present study highlights the differences in antigenicity and immunogenicity of recombinant ZIKV antigens produced in two heterologous protein expression systems.

Key amino acids residues enhance the ability of CpcR to activate cry gene expression in Bacillus thuringiensis

Typical Bacillus thuringiensis (Bt) produces one or more parasporal crystals composed of insecticidal Cry proteins during the sporulation, and the parasporal crystals and spores are produced from the same cell. Strain Bt LM1212 is different from typical Bt strains in that its crystals and spores are produced in different cells. Previous studies have found that the cell differentiation process of Bt LM1212 is related to the transcription factor CpcR which activates the cry-gene promoters. In addition, CpcR could activate the Bt LM1212 cry35-like gene promoter (P35) when introduced in the heterologous HD73- strain. It was shown that P35 was only activated in non-sporulating cells. In this study, the peptidic sequences of CpcR homologous proteins found in other strains of the Bacillus cereus group were used as references to identify two key amino acid sites for CpcR activity. The function of these amino acids was investigated by measuring P35 activation by CpcR in strain HD73-. These results will lay a foundation for the optimization of the insecticidal protein expression system in non-sporulating cells.

Development of Corynebacterium glutamicum as Staphylococcal-Targeting Chassis via the Construction of Autoinducing Peptide (AIP)-Responsive Expression System

Despite increasing reports of antimicrobial activities of commensal and non-pathogenic bacteria such as Corynebacterium spp., previous studies on bioengineered therapeutics traditionally employed probiotics and food-grade bacteria which limits further advancements into microbial therapeutics research. In this study, Corynebacterium glutamicum, a generally recognised as safe (GRAS) and model bacterium was employed as a new chassis for the development of bioengineered corynebacterial chassis tailored towards Staphylococcus sp. via autoinducer peptide (AIP)-based quorum sensing (QS) interactions. To develop C. glutamicum as a staphylococcal-targeting chassis, the bacteria were transformed with the pResponse plasmid harboring AIP-responding accessory regulatory proteins agrAC and red fluorescent protein (RFP) genes under the control of the PaceA and P3 promoter, respectively, which was expected to stimulate the production of fluorescence signals in the presence of AIPs. Fluorescence activity of the C. glutamicum pResponse strain was compared to control C. glutamicum pRFP strain containing only the P3-RFP gene without the agrAC gene cassette. Using AIP-I as the input biomolecule, C. glutamicum pResponse strain fluoresced under different concentrations of AIP-I whereas no fluorescence was observed in the control C. glutamicum pRFP strain. When tested with S. aureus culture supernatant, the pResponse strain exhibited increasing fluorescence over the incubation period with the highest fluorescence signal of 183 relative fluorescence units (R.F.U) was observed at a 48 h point thereby demonstrating a functional QS-responsive protein expression system in bioengineered C. glutamicum. These findings demonstrated the feasibility and promising potential of developing bioengineered C. glutamicum as a staphylococcal-responsive and -targeting chassis.

Design of an artificial transcriptional system for production of high levels of recombinant proteins in tobacco (Nicotiana benthamiana).

Plants have recently received much attention as a means of producing recombinant proteins because they are easy to grow at a low cost and at a large scale. Although many plant protein expression systems have been developed, there remains a need for improved systems that deliver high yields of recombinant proteins. Transcription of the recombinant gene is a key step in increasing the yield of recombinant proteins. However, revealed strong promoters, terminators, and transcription factors that have been identified do not necessarily lead to high level production of recombinant proteins. Thus, in this study, a robust expression system was designed to produce high levels of recombinant protein consisting of a novel hybrid promoter, FM'M-UD, coupled with an artificial terminator, 3PRt. FM'M-UD contained fragments from three viral promoters (the promoters of Mirabilis mosaic caulimovirus (MMV) full-length transcript, the MMV subgenomic transcript, and figwort mosaic virus subgenomic transcript) and two types of cis-acting elements (four GAL4 binding sites and two zinc finger binding sites). The artificial terminator, 3PRt, consisted of the PINII and 35S terminators plus RB7, a matrix attachment region. The FM'M-UD promoter increased protein levels of reporters GFP, RBD : SD1 (part of S protein from SARS-CoV-2), and human interleukin-6 (hIL6) by 4-6-fold, 2-fold, and 6-fold, respectively, relative to those of the same reporters driven by the CaMV 35S promoter. Furthermore, when the FM'M-UD/3PRt expression cassette was expressed together with GAL4/TAC3d2, an artificial transcription factor that bound the GAL4 binding sites in FM'M-UD, levels of hIL6 increased by 10.7-fold, relative to those obtained from the CaMV 35S promoter plus the RD29B terminator. Thus, this novel expression system led to the production of a large amount of recombinant protein in plants.

Exploring temperature-mediated plasmid replication as a reversible and switchable protein expression system in genetic Escherichia coli

Exploring temperature-mediated plasmid replication as a reversible and switchable protein expression system in genetic Escherichia coli

Characterization of the off-flavor from Pichia pastoris GS115 during the overexpression of an α-l-rhamnosidase.

The methylotrophic yeast Pichia pastoris is an important host for the industrial expression of functional proteins. In our previous studies, P. pastoris strains have been sniffed with a strong off-flavor during the overexpression of various functional proteins, limiting the application of these proteins. Although many yeast strains have been reported with off-flavor, no attention has been paid to characterize the off-flavor in P. pastoris so far. Considering that P. pastoris has advantages over other established expression systems of functional proteins, it is of interest to identify the compounds with off-flavor synthesized in the overexpression of functional proteins with P. pastoris strains. In this study, the off-flavor synthesized from P. pastoris GS115 was characterized during the overexpression of an α-l-rhamnosidase, which helps understand the aromatic metabolites with off-flavor of P. pastoris strains. In addition, 2-acetylbutyrolactone and dodecanol were newly revealed with plastic and metallic notes, enriching the aromatic contributors of biological products. Thus, this study is important for understanding the metabolites with off-flavor of P. pastoris strains and other organisms, providing important knowledge to improve the flavor of products yielding with P. pastoris strains and other organisms. Characterize the sensory and chemical profile of the off-flavor produced by one strain of P. pastoris in vitro.

Unlocking the strength of inducible promoters in Gram-negative bacteria.

Inducible bacterial promoters are ubiquitous biotechnology tools that have a consistent architecture including two key elements: the operator region recognized by the transcriptional regulatory proteins, and the -10 and -35 consensus sequences required to recruit the sigma (σ) 70 subunits of RNA polymerase to initiate transcription. Despite their widespread use, leaky transcription in the OFF state remains a challenge. We have updated the architecture of the lac and tet promoters to improve their strength, control and portability by the adaptation of the consensus -10 and -35 sequence boxes strongly targeted by σ70 , incorporation of a strong ribosome binding site recognized broadly by Gram-negative bacteria, and independent control of the transcriptional regulators by constitutive promoters. To test the promoters, we use the far-red fluorescent protein mCardinal, which significantly improves the signal-to-background ratio of promoter measurements over widely utilized green fluorescent proteins. We validate the improvement in OFF state control and inducibility by demonstrating production of the toxic and aggregate-prone cocaine esterase enzyme CocE. We further demonstrate portability of the promoters to additional Gram-negative species Pseudomonas putida and Vibrio natriegens. Our results represent a significant improvement over existing protein expression systems that will enable advances in protein production for various biotechnology applications.

The role of lipid bilayer composition in cell-free expressed ABC transporter folding.

Cell-free protein expression systems provide a powerful tool to mechanistically probe how membrane composition, and the resulting biophysical properties, affect membrane protein (MP) complex folding and function. These systems can be designed without translocons, insertases, and chaperones commonly used to assist in membrane protein folding to isolate the impact of membrane properties on the folding process. In this study we investigate the ABC transporter, SapABCDF, in the gram-negative non-typeable Haemophilus influenzae (NTHI). This transporter sequesters heme and antimicrobial peptides (AMPs) from the periplasm into the cytoplasm via ATPase activity and understanding factors that contribute to MP complex folding and function is critical for developing antimicrobial treatments for NTHI and reduce the severity of infection. Using a cell-free protein expression system, we expressed each protein in the SapABCDF transporter in the presence of small unilamellar lipid vesicles (SUVs). We developed a sucrose flotation assay to evaluate protein colocalization to fluorescently labeled SUVs after cell-free expression and found that all components of the SapBCDF system express and colocalize to vesicles, suggesting their membrane integration and assembly. We then conducted a co-translational MP folding assay with a C-terminal mEGFP tag to determine membrane compositions that promote MP folding and expression. Analysis of cell-free expression products via western blot suggests that one transmembrane domain, SapC, expresses preferentially into SUVs containing phosphatidylethanolamine (PE). Ongoing studies aim to characterize transporter functionality and biophysically characterize the impact of bilayer biophysical properties on MP folding. Together, our results should improve our understanding of the biophysical requirements for properly folded and functioning ABC transporters.

Structure study reveals active and inactive conformations of protein kinase C B1.

A human cell-based recombinant protein expression system is advantageous for large scale protein expression and purification as it provides native and nearly ideal conditions for correct folding and post-translational modification of protein products. Recently, we developed an affinity tag system using llama single-domain antibodies (a.k.a. nanobodies) generated against the fluorescent proteins YFP and mCherry. These nanobodies are highly efficient, with high binding capacity while exhibiting binding affinities that are down to the sub-nanomolar Kd, serving as ideal affinity-matrices for routine protein expression and purification in a mammalian system. These mCherry-tag and YFP-tag systems have enabled us to successfully express and purify numerous recombinant human proteins with productive yields and high quality. Here, we utilize the YFP-tag system to express and purify recombinant full-length human Protein Kinase C βI (PKCβI) using HEK293F cells. We have determined structures of purified PKCβI protein using X-ray crystallography that define two distinct conformations of the enzyme, providing structural insights behind their inhibition and activation mechanisms.

Tuning the composition of supported lipid bilayers in a QCMD to uncover rules of membrane protein incorporation.

Cells are not very cooperative when it comes to helping us understand them better. They are small, needy, complex, and they have their own lives to run. To circumvent these flaws of cells our lab has developed the all E. coli cell-free protein expression system called TXTL. TXTL can express genes and execute genetic programs in-vitro using the transcriptional and translational machinery of E. coli cells without the E. coli cells themselves. So far with TXTL our lab has probed both fundamental and applied ideas in gene regulation, metabolism, self-assembly, and encapsulation.

Genome-wide nonessential gene identification of Autographa californica multiple nucleopolyhedrovirus

The Baculovirus Expression Vector System (BEVS) is an insect cell-based heterologous protein expression system that possesses powerful potential in the development of protein drugs and vaccines. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most widely-used vector in BEVS with 151 open reading frames (ORFs) containing essential and nonessential genes. Deletion of nonessential genes has many advantages including increased foreign gene insertion. In this study, the λ red recombination system was used to knock out genes in a modified AcMNPV that carried an enhanced yellow fluorescent protein (eYFP) at the Ac126-Ac127 locus. Eighty genes were almost completely deleted respectively and 69 gene knockout AcMNPVs (KOVs) were obtained to evaluate their infection efficiency. After infecting Spodoptera frugiperda 9 (Sf9) cells, 51 KOVs including 62 genes showed similar infectivity as wide type (WT) and hence were defined as nonessential genes. However, 18 KOVs produced fewer infectious virions, indicating that these genes were influential in the production of progeny viruses. Combining our research with previous studies, a desired minimal AcMNPV genome containing 86 ORFs and all of the homologous regions (hrs) was brought up, facilitating genetic modification of baculovirus vectors and improvement of recombinant protein expression in the future.

Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline.

We present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parametrizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in a cell-free protein expression system. We build on existing Python tools─BioCRNpyler, AutoReduce, and Bioscrape─to create this pipeline. For enzyme-mediated DNA recombination in a cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model; hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parametrization.

T7Max transcription system

BackgroundEfficient cell-free protein expression from linear DNA templates has remained a challenge primarily due to template degradation. In addition, the yields of transcription in cell-free systems lag behind transcriptional efficiency of live cells. Most commonly used in vitro translation systems utilize T7 RNA polymerase, which is also the enzyme included in many commercial kits.ResultsHere we present characterization of a variant of T7 RNA polymerase promoter that acts to significantly increase the yields of gene expression within in vitro systems. We have demonstrated that T7Max increases the yield of translation in many types of commonly used in vitro protein expression systems. We also demonstrated increased protein expression yields from linear templates, allowing the use of T7Max driven expression from linear templates.ConclusionsThe modified promoter, termed T7Max, recruits standard T7 RNA polymerase, so no protein engineering is needed to take advantage of this method. This technique could be used with any T7 RNA polymerase- based in vitro protein expression system.

An Inducible T7 Polymerase System for High-Level Protein Expression in Diverse Gram-Negative Bacteria

A broad host range (BHR)-inducible T7 RNA polymerase system was developed, enabling induction with isopropyl-β-d-thiogalactopyranoside (IPTG), similar to the Escherichia coli strain BL21(DE3) protocol, but it is now applicable in a wide range of bacteria. This system allows for high protein yields and purification from diverse Gram-negative bacteria, including the native host.

Recent advances in genetic tools for engineering probiotic lactic acid bacteria.

Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities. Lactic acid bacteria (LAB) are considered appropriate chassis organisms that can be genetically engineered for therapeutic and industrial applications. Here, we have reviewed comprehensively various synthetic biology techniques for engineering probiotic LAB strains, such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 mediated genome editing, homologous recombination, and recombineering. In addition, we also discussed heterologous protein expression systems used in engineering probiotic LAB. By combining computational biology with genetic engineering, there is a lot of potential to develop next-generation synthetic LAB with capabilities to address bottlenecks in industrial scale-up and complex biologics production. Recently, we started working on Lactochassis project where we aim to develop next generation synthetic LAB for biomedical application.

CRISPR/Cas9-Mediated Multiplexed Genome Editing in Aspergillus oryzae.

Aspergillus oryzae has great potential and competitive advantages to be developed as an excellent expression system, owing to its powerful protein secretion ability, complex post-translational modification, and safety characteristics. However, the low efficiency of genetic modification and gene function analysis is an urgent problem to be solved in A. oryzae and other filamentous fungal systems. Therefore, establishing efficient genetic transformation and multiplexed genome editing tools is significant for developing A. oryzae expression systems, and revealing its intrinsic mechanisms. In this study, the high-efficiency transformation of A. oryzae was achieved by optimizing the preparation conditions of protoplasts, and the random editing efficiency of the CRISPR/Cas9 system in A. oryzae for single and double genes reached 37.6% and 19.8%, respectively. With the aid of the selection marker, such as color or resistance, the editing efficiency of single and double genes can reach 100%. Based on the developed CRISPR/Cas9 genome editing method, the heterologous lipase gene (TLL) achieves precise integration at different genetic loci in one step. The efficient and accurate acquisition of positive transformants indicated that the morphological gene yA could be used as a helpful selection marker for genome editing in A. oryzae. In conclusion, the developed system improves the efficiency of transformation and multiplexed genome editing for A. oryzae. It provides a practical method for developing the A. oryzae high-efficiency expression system for heterologous proteins.