Optimization of recombinant gene expression in Escherichia coli

NeuralCodOpt: Codon optimization for the development of DNA vaccines

Inefficient gene translation, driven by organisms' codon preferences, is an emerging research area since this results in sluggish processes and diminished protein yields. Our research culminates in deriving efficient, optimized codon sequences by considering organism-specific Relative Codon Adaptiveness (RCA) ranges. In this research work, we have developed a novel algorithm, Neural Codon Optimization (NeuralCodOpt), to automate the process of codon optimization tailored to a specific organism and input sequence. Our algorithm has two main parts: the target Codon Adaptation Index generation using K-Means and the automation of sequence optimization using reinforcement learning. This algorithm has been tested across a set of 130 species, yielding highly optimal results that are quite significant compared to the previous works. NeuralCodOpt has shown a high accuracy of 86.7%, which would substantially contribute to Deoxyribonucleic Acid (DNA) vaccines by improving the efficiency of DNA expression vectors. These vectors are crucial in DNA vaccination and gene therapy as they enhance protein expression levels. By further incorporating it into plasmid construction, the translational efficiency of DNA vaccines will be significantly improved.

Tuning constitutive recombinant gene expression in Lactobacillus plantarum

Background

Lactobacillus plantarum constitutes a well-recognized food-grade system for the expression of recombinant proteins in the field of industrial and medical biotechnology. For applications in vivo or in biotechnological processes, the level of expression of e.g. antigens or enzymes is often critical, as expression levels should be of a certain effectiveness, yet, without putting too much strain to the overall system. The key factors that control gene expression are promoter strength, gene copy number and translation efficiency. In order to estimate the impact of these adjusting screws in L. plantarum CD033, we have tested several constitutive promoters in combination with high and low copy number plasmid backbones and varying space between the Shine-Dalgarno sequence and the start-codon.

Results

By combining strong promoters, such as transcription elongation factor promoters, isolated from L. plantarum CD033 and L. buchneri CD034, a synthetic promoter, originally derived from L. plantarum WCSF1 and a heterologous promoter derived from L. buchneri CD034 with a high and a low copy number origin of replication we demonstrated various expression levels of the model protein mCherry. All promoters were feasible for protein expression and in all cases, the high copy number origin of replication increased expression twofold. We found that the optimal spacer between the Shine-Dalgarno sequence and the start codon in L. plantarum consists of 8 nucleotides and elongation as well as shortening this sequence gradually down-regulates gene expression.

Conclusions

We have evaluated the effects of a set of gene regulatory tools to fine tune recombinant gene expression in L. plantarum CD033. We have thus, provided potential expression vectors useful for constitutive protein expression in lactic acid bacteria ranging from moderate to strong production levels.

Enhancing the protein production levels in Escherichia coli with a strong promoter

In biotechnology, the use of Escherichia coli for recombinant protein production has a long tradition, although the optimal production conditions for certain proteins are still not evident. The most favorable conditions for protein production vary with the gene product. Temperature and induction conditions represent parameters that affect total protein production, as well as the amount of soluble protein. Furthermore, the choice of promoter and bacterial strain will have large effects on the production of the target protein. In the present study, the effects of three different promoters (T7, trc and lacUV5) on E. coli production of target proteins with different characteristics are presented. The total amount of target protein as well as the amount of soluble protein were analyzed, demonstrating the benefits of using a strong promoter such as T7. To understand the underlying causes, transcription levels have been correlated with the total amount of target protein and protein solubility in vitro has been correlated with the amount of soluble protein that is produced. In addition, the effects of two different E. coli strains, BL21(DE3) and Rosetta(DE3), on the expression pattern were analyzed. It is concluded that the regulation of protein production is a combination of the transcription and translation efficiencies. Other important parameters include the nucleotide-sequence itself and the solubility of the target protein.

Optimization of recombinant protein expression level in Escherichia coli by flow cytometry and cell sorting

Overexpression of recombinant proteins in Escherichia coli often leads to a severe growth retardation of the host cells. The phage T7 promoter phi10 in a pET vector was utilized to express human superoxide dismutase. Induction with IPTG lead to an increase in protein content and cell size and a termination of cell division, due to the deviation of the general metabolic fluxes from all cellular processes to plasmid maintenance and foreign protein synthesis. To generate promoter mutants which are better tolerated by the host cells we constructed a random mutation library by PCR with degenerated primers in a part of the promoter involved in the binding to the RNA polymerase and the initiation of transcription. This library was sorted by flow cytometry for cells with a lower total protein content as an indicator for continued cell replication and hence a less severe stress situation. The clones obtained had a similar SOD production compared to the original strain, but were able to reach higher densities in a batch culture, which resulted in a higher total yield.

High-level expression of a truncated wall-associated protein A from the dental cariogenic Streptococcus mutans

Streptococcus mutans plays a primary role in the formation of dental caries. Previously, in our laboratory, an S. mutans genomic library was prepared, and the wapA gene was cloned into the shuttle vector, pSA4/4B2. To generate overexpression of wapA and to facilitate efficient purification of the WapA protein for use as an immunogen, an expression vector with the strong tac promoter was used. In order to answer questions regarding the optimization of solubility and expression based on gene size or the hydrophobicity of the protein product, 12 truncated constructs of the wapA gene were prepared using PCR. The truncated products were subcloned into the pGEX-6P-1 glutathione S-transferase (GST) fusion vector and expressed in E. coli BL21. The fusion proteins were analyzed by SDS-PAGE and confirmed by analysis with anti-GST and anti-WapA antibodies. Our study suggests that abrogation of the wapA promoter is necessary for expression of this gene in this expression system. Deletion of the signal peptide and the hydrophobic C terminus of WapA increased expression compared with the full-length construct, and truncation at the protease cleavage site of the C-terminal region greatly increased the stability of the protein without a loss in reactivity with the anti-WapA antibody. Western immunoblot analysis with anti-WapA antiserum clearly showed that the majority of the epitopes of the GST-WapA fusions are located in the N-terminal region of WapA. The immunogenicity of the various WapA fusion products is being examined in mice and rats to further map the immunologically dominant regions of the protein. This method effectively increased the expression of WapA and should contribute to the further understanding of gene expression of E. coli, as well as aid in the characterization of this protein for future immunologic evaluation.

Genetically engineered polymers for drug delivery

Genetic engineering methodology offers the ability to synthesize protein-based polymers with precisely controlled structures. Protein-based polymers synthesized by recombinant techniques have a well-defined monomer composition and sequence, stereochemistry, and a narrow molecular weight distribution. The structure of the polymeric carrier at the molecular level influences its biological disposition and drug release profile. Current methodologies of polymer synthesis (chemical polymerization) result in the production of polymers with heterogeneous molecular weights, and with monomer sequences and compositions defined in terms of statistical distributions. Genetic engineering methodologies can be used to design new polymeric drug carriers with improved properties, such as better-defined biorecognition, pharmacokinetic, biodegradation, and drug release profiles. In this review article the rationale and methodology of polymer synthesis using genetic engineering techniques, the status of such polymers in drug delivery to-date, and the potential of these polymers for the development of new systems in the future are discussed.

Flow cytometric analysis of metabolic stress effects due to recombinant plasmids and proteins in Escherichia coli production strains

Overexpression of recombinant proteins in Escherichia coli often leads to a severe growth retardation of the host cells. Using flow cytometry, we analyzed the temporal development of the cellular content of DNA, total protein, and the recombinant product (human superoxide dismutase) in different strains. In cells carrying plasmids utilizing the phage T7 promoter 10 (pET vectors), induction with IPTG leads to an increase in protein content and size, an increase and a wide spreading of DNA content distribution, and a termination of cell division. These effects occurred with pET plasmids with or without an insert, but not with another plasmid which utilizes the tac promoter.

Rational design of an improved induction scheme for recombinant Escherichia coli

In Escherichia coli, strong overexpression of a recombinant protein has been shown to be deleterious due to a heavy metabolic burden on the host cell, which may completely cease cell growth before maximum product accumulation has occurred. Aiming at a reduction of very high product formation rates, we engineered E. coli strains by mutating the Leloir pathway for galactose metabolization, so that galactose can be utilized to induce lac derived promoters. The induction with galactose was effective in every strain and expression construct tested, and it reduced the metabolic burden on a highly overproducing clone so that cell growth and product accumulation could be maintained for several generations.

Regulation and expression of human Fabs under the control of the Escherichia coli arabinose promoter, PBAD

BACKGROUND

The L-arabinose operon from E. coli contains an inducible promoter PBAD which has been extensively studied for the control of gene expression. PBAD has a number of potential advantages over Plac, and has been used successfully to promote high level expression of recombinant proteins.

OBJECTIVES

The aim of this study was to investigate PBAD as an alternative system to Plac for the bacterial expression of recombinant Fabs.

STUDY DESIGN

The promoter PBAD from the E. coli arabinose operon araBAD and the gene encoding the regulator of this promoter, were cloned into the phagemid expression vector MCO1. Expression of human recombinant tetanus toxoid (TT) and c-erbB2 Fabs under the control of PBAD was compared at two induction temperatures with the same Fabs produced under the control of Plac.

RESULTS

Expression of TT and c-erbB2 Fabs under the control of PBAD was comparable to Fab expression from Plac. However, highly expressed TT Fab under the control of PBAD was localised to the soluble periplasmic fraction whereas under the control of Plac, there was greater leakage of Fab into the culture supernatant. In addition, Fab expression from PBAD could be more tightly repressed than from Plac.

CONCLUSION

PBAD is a useful and cheaply inducible alternative to the more commonly used Plac for the rapid expression of soluble recombinant human antibody fragments.

Developments in metabolic engineering

The complete sequencing of several microbial genomes has resulted in the increased availability of genes for metabolic engineering. The number of databases and computational tools to deal with this information has also increased. This development has stimulated, and will continue to stimulate, advances in metabolic engineering. Specific recent advances include improvement of pathways for aromatic metabolites, the development of a more complete understanding of the effect of bacterial hemoglobin on cell performance, the development of NMR-based methods for the monitoring of intracellular metabolites and metabolic flux, and the application of metabolic control analysis and metabolic flux analysis to a variety of systems.