A convenient and rapid method for genetic transformation of E. coli with plasmids

Molecular Cloning of a New Bi-Functional Fusion Protein of Clostridium perfringens Type A Alpha and Clostridium septicum Alpha Toxin Genes in E. coli

Background: A synthetic construct bi-functional protein fusion includes two protein domains, or proteins bind by a fragment. The synthetic construct is designed to achieve better characterize and new functionality. Therefore, having proper cells is essential for cloning fusion genes. Clostridium perfringens type A produces the alpha-toxin and can cause gas gangrene and gastrointestinal diseases. C. septicum produces the alpha-toxin and can cause non-traumatic and traumatic gas gangrene. Objectives: The current study aimed to investigate molecular cloning of a new bi-functional fusion protein of C. perfringens alpha (cpa) and C. septicum alpha (csa) toxin genes in E. coli TOP10. In silico analysis was used for the chimeric fusion protein structural prediction. Methods: To produce chimeric fusion protein, the alpha-alpha (α-α) fusion gene was designed according to nucleotide sequences of cpa (KY584046.1) and csa (JN793989.2) genes. Tertiary structural prediction and validation of the fusion protein were determined by online software. In the new synthetic construction, α-α fusion protein genes are bind via the linker AEAAAKEAAAKA. The linker was introduced between the two domains by fusion PCR. The synthetic fusion gene was cloned into the pUC57cloning vector and then transferred into the host cell. Results: Analysis of the chimeric protein fusion is showed using the I-TASSER server as C-score equal to -2.68 as well as Rampage software in order to confirm the geometrical model as a natural like protein. Also, 1.0% agarose gel electrophoresis of fusion PCR product and sequencing analysis revealed a DNA fragment length of 2346 bp. Screening gel electrophoresis showed 996 bp length, which the designed linker was contained in it. Gel electrophoresis of extracted and purified recombinant plasmid (pUC57/αα) showed that a pUC57/αα of 5056 bp. The digested recombinant pUC57/αα showed one 2.3 kb (our fusion gene) band and one 2.7 kb (pUC57) band. Conclusions: This study presented a new approach for the fusion of cpa and csa genes based on the fusion PCR strategy. According to the latest information, this is the first time that α-α fusion gene is designed and cloned into a suitable cloning vector.

The optimization system for preparation of TG1 competent cells and electrotransformation

An efficient electrotransformation system that includes electrocompetent cells is a critical component for the success of large‐scale gene transduction and replication. The conditions of TG1 competent cell preparation and optimal electrotransformation were evaluated by investigating different parameters. Certain parameters for preparation of TG1 competent cells (≥8 × 10¹⁰ colony forming units (cfu)/μg DNA) include optimum culture time of monoclonal bacteria (8–10 hr), amplification growth concentration (approximately OD₆₀₀ = 0.45), and culture volume (400 ml in 2 L conical flask). With increased storage of competent cells at −80°C, electrotransformation efficiency gradually decreased, but it remains greater than ≥ 10¹⁰ cfu/μg DNA 3 months later. Moreover, the recovery time of electrotransformation also influenced electrotransformation efficiency (1.5–2 hr for optimization). The optimized transformation efficiency of TG1 (≥8 × 10¹⁰ cfu/μg DNA) was observed under suitable electric voltage (2.5 kV), electric intensity (15 kV/cm), and electric time (3.5 ms) of electricity for plasmid transformation. Optimized DNA amount (0.01–100 ng) dissolved in water led to the high efficiency of plasmid transformation (≥8 × 10¹⁰ cfu/μg DNA), but had low efficiency when dissolved in T4 ligation buffer (≤3 × 10¹⁰ cfu/μg DNA). These results indicated that an optimized TG1 transformation system is useful for high electrotransformation efficiency under general laboratory conditions. The optimized TG1 transformation system might facilitate large‐scale gene transduction for phage display library construction.

Enhanced Gene Delivery in Bacterial and Mammalian Cells Using PEGylated Calcium Doped Magnetic Nanograin

BACKGROUND

Beyond viral carriers which have been widely used in gene delivery, non-viral carriers can further improve the delivery process. However, the high cytotoxicity and low efficiency impedes the clinical application of non-viral systems. Therefore, in this work, we fabricated polyethylene glycol (PEG) coated, calcium doped magnetic nanograin (PEG/Ca(II)/Fe3O4) as a genome expression enhancer.

METHODS

Monodisperse magnetic nanograins (MNGs) with tunable size were synthesized by a solvothermal method. The citrate anions on the spherical surface of MNGs capture Ca2+ ions by an ion exchange process, which was followed by surface capping with PEG. The synthesized PEG/Ca(II)/Fe3O4 was characterized using Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS) spectra, vibrating sample magnetometer (VSM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). MTT test was utilized to assess the toxicity of PEG/Ca(II)/Fe3O4. Real time qPCR was applied for quantification of gene expression.

RESULTS

DLS spectra and TEM images confirmed a thin layer of PEG on the nanocarrier surface. Shifting the zeta potential in the biological pH window from -23.9 mV (for Fe3O4) to ≈ +11 mV (for PEG/Ca(II)/Fe3O4) confirms the MNGs surface protonation. Cytotoxicity results show that cell viability and proliferation were not hindered in a wide range of nanocarrier concentrations and different incubation times.

CONCLUSION

PEGylated calcium doped magnetic nanograin enhanced PUC19 plasmid expression into E. Coli and GFP protein expression in HEK-293 T cells compared to control. A polymerase chain reaction of the NeoR test shows that the transformed plasmids are of high quality.

An Improved Method of Preparing High Efficiency Transformation Escherichia coli with Both Plasmids and Larger DNA Fragments

The high-throughput, cost-efficient transformation systems determine the success of gene cloning and functional analysis. Among various factors that affect this transformation systems, the competence ability of target cells is one of the most important factors. We found antimicrobial peptides LFcin-B can increase the permeability of the cell membrane, and their lethal antibacterial properties can be inhibited by moderately high concentrations of Ca2+ and Mn2+. In this study, we established a convenient and rapid method (CRM) by adding small concentrations of (0.35 mg/L) and moderately high concentrations of MnCl2 (50 mM) and CaCl2 (30 mM) in transformation buffer. The transformation efficiency of E. coli cells (DH5α, JM109 and TOP10) prepared by CRM were comparable with electroporation for plasmid transformation (3.1 ± 0.3 × 109 cfu/µg). Unlike competent cells prepared using other chemical methods, those obtained using CRM method are extremely competent for receiving larger size DNA fragments (> 5000 bp) into plasmid vectors. The competent E. coli cells prepared by CRM method are particularly useful for most high-efficiency transformation experiments under normal laboratory conditions.

Why Johnny can't clone: Common pitfalls and not so common solutions

The demand for cloned genes has increased incessantly over the past 32 years, but some who need recombinant plasmids struggle to produce them. While the pitfalls of traditional ligation-dependent cloning are non-trivial, most can be avoided with sufficient effort and attention to detail. Here, the chemical properties of enzymes and reagents used to clone genes into plasmids are reviewed to draw attention to the most pertinent details. In particular, the virtues of agarose gel electrophoresis monitoring, the nature of the interactions between DNA and silica, and challenges associated with thermostable DNA polymerases, restriction endonucleases, and T4 DNA ligase are explored. Common pitfalls associated with Escherichia coli transformation and DNA modifying enzymes are also described. A thorough understanding of established methods is essential for troubleshooting, implementing alternative approaches, and inventing new techniques in response to changes in technology and demand.

A convenient colony-based transformation method for high-throughput changing of plasmid hosts

We have developed a convenient Escherichia coli transformation method, termed colony-based transformation, in which a single fresh colony of plasmid-containing donor strain is used instead of extracted plasmid to transform E. coli recipient cell. Thus the need for plasmid extraction and competent cell preparation is avoided. Additionally, a high-throughput transformation process based on this method was designed in which samples are prepared in a 96-well PCR plate and hundreds of transformations can be performed simultaneously in a thermocycler. We therefore suggest that this method may serve as a substitute of current transformation methods based on plasmid extraction.

A cyclophilin A CPR1 overexpression enhances stress acquisition in Saccharomyces cerevisiae

Cyclophilins are conserved cis-trans peptidyl-prolyl isomerase that are implicated in protein folding and function as molecular chaperones. We found the expression of cyclophilin A, Cpr1, changes in response to exposure to yeast Saccharomyces cerevisiae to abiotic stress conditions. The effect of Cpr1 overexpression in stress responses was therefore examined. The CPR1 gene was cloned to the yeast expression vector pVTU260 under regulation of an endogenous alcohol dehydrogenase (ADH) promoter. The overexpression of Cpr1 drastically increased cell viability of yeast in the presence of stress inducers, such as cadmium, cobalt, copper, hydrogen peroxide, tert-butyl hydroperoxide (t-BOOH), and sodium dodecyl sulfate (SDS). The Cpr1 expression also enhanced the cell rescue program resulting in a variety of antioxidant enzymes including thioredoxin system (particularly, thioredoxin peroxidase), metabolic enzymes (glucose-6-phosphate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase), and molecular chaperones (Hsp104, Hsp90, Hsp60 and Hsp42). Thus, our study illustrates the importance of Cpr1 as a molecular chaperone that improves cellular stress responses through collaborative relationships with other proteins when yeast cells are exposed to adverse conditions, and it also premises the improvement of yeast strains.

A colony-to-lawn method for efficient transformation of Escherichia coli

AIMS

To develop a fast, convenient, inexpensive and efficient Escherichia coli transformation method for changing hosts of plasmids, which can also facilitate the selection of positive clones after DNA ligation and transformation.

METHODS AND RESULTS

A single fresh colony from plasmid-containing donor strain is picked up and suspended in 75% ethanol. Cells are pelleted and resuspended in CaCl(2) solution and lysed by repetitive freeze-thaw cycles to obtain plasmid-containing cell lysate. The E. coli recipient cells are scraped from the lawn of LB plate and directly suspended in the plasmid-containing cell lysate for transformation. Additionally, a process based on colony-to-lawn transformation and protein expression was designed and conveniently used to screen positive clones after DNA ligation and transformation.

CONCLUSIONS

With this method, a single colony from plasmid-containing donor strain can be directly used to transform recipient cells scraped from lawn of LB plate. Additionally, in combination with this method, screening of positive clones after DNA ligation and transformation can be convenient and time-saving.

SIGNIFICANCE AND IMPACT OF THE STUDY

Compared with current methods, this procedure saves the steps of plasmid extraction and competent cell preparation. Therefore, the method should be highly valuable especially for high-throughput changing hosts of plasmids during mutant library creation.