Improving soluble recombinant SARS-CoV-2 papain-like protease production in Escherichia coli through chaperonin and maltose-binding protein tag: purification and kinetic characterization

Although COVID-19 is now becoming endemic, SARS-CoV-2 persists potential jeopardy to clinically vulnerable populations. Hence, further study is still necessary to discover novel antiviral agents against SARS-CoV-2 for proactive preparedness. SARS-CoV-2 papain-like protease (PL Pro) is a target enzyme for searching anti-Covid candidates. Our prior study revealed the major formation of inclusion bodies during PL Pro expression in E. coli RIPL. In this study, we tried using chaperonin in the E. coli Arctic Express system and both codon optimization and maltose-binding protein (MBP) fusion protein to make PL Pro more soluble. Recombinant PL Pro encoded on the pET21d(+) plasmid was expressed in E. coli Arctic express. However, the soluble protein yield remained low and unstable due to suboptimal codon usage in the insert gene. Whereas, fusion of the MBP protein with optimized codon of PL Pro enhanced the enzyme expression and solubility. Recombinant PL Pro cleaved the linker between MBP and PL Pro, which served as a cleavage site recognized by PL Pro (LKGG↓A). The purified enzyme from a 200-mL culture generated 1 mL of pure PL Pro enzyme at a 1.913 mg/mL concentration. It exhibited favorable activity against the Z-RLRGG-AMC substrate, with a Km value of 33.40 μM and a Vmax of 5.10 RFU/min.

The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli

Recombinant proteins expressed in Escherichia coli are widely used in biochemical research and industrial processes. At the same time, achieving higher protein expression levels and correct protein folding still remains the key problem, since optimization of nutrient media, growth conditions, and methods for induction of protein synthesis do not always lead to the desired result. Often, low protein expression is determined by the sequences of the expressed genes and their regulatory regions. The genetic code is degenerated; 18 out of 20 amino acids are encoded by more than one codon. Choosing between synonymous codons in the coding sequence can significantly affect the level of protein expression and protein folding due to the influence of the gene nucleotide composition on the probability of formation of secondary mRNA structures that affect the ribosome binding at the translation initiation phase, as well as the ribosome movement along the mRNA during elongation, which, in turn, influences the mRNA degradation and the folding of the nascent protein. The nucleotide composition of the mRNA untranslated regions, in particular the promoter and Shine-Dalgarno sequences, also affects the efficiency of mRNA transcription, translation, and degradation. In this review, we describe the genetic principles that determine the efficiency of protein production in Escherichia coli.

Studies on the recombinant production and anticancer activity of thermostable L- asparaginase I from Pyrococcus abyssi

L-Asparaginase catalysing the breakdown of L-Asparagine to L-Aspartate and ammonia is an enzyme of therapeutic importance in the treatment of cancer, especially the lymphomas and leukaemia. The present study describes the recombinant production, properties and anticancer potential of enzyme from a hyperthermophilic archaeon Pyrococcus abyssi. There are two genes coding for asparaginase in the genome of this organism. A 918 bp gene encoding 305 amino acids was PCR amplified and cloned in BL21 (DE3) strain of E. coli using pET28a (+) plasmid. The production of recombinant enzyme was induced under 0.5mM IPTG, purified by selective heat denaturation and ion exchange chromatography. Purified enzyme was analyzed for kinetics, in silico structure and anticancer properties. The recombinant enzyme has shown a molecular weight of 33 kDa, specific activity of 1175 U/mg, KM value 2.05mM, optimum temperature and pH 80°C and 8 respectively. No detectable enzyme activity found when L-Glutamine was used as the substrate. In silico studies have shown that the enzyme exists as a homodimer having Arg11, Ala87, Thr110, His112, Gln142, Leu172, and Lys232 being the putative active site residues. The free energy change calculated by molecular docking studies of enzyme and substrate was found as ∆G - 4.5 kJ/mole indicating the affinity of enzyme with the substrate. IC50 values of 5U/mL to 7.5U/mL were determined for FB, caco2 cells and HepG2 cells. A calculated amount of enzyme (5U/mL) exhibited 78% to 55% growth inhibition of caco2 and HepG2 cells. In conclusion, the recombinant enzyme produced and characterized in the present study offers a good candidate for the treatment of cancer. The procedures adopted in the present study can be prolonged for in vivo studies.

Development of Clostridium saccharoperbutylacetonicum as a Whole Cell Biocatalyst for Production of Chirally Pure (R)-1,3-Butanediol

Chirally pure (R)-1,3-butanediol ((R)-1,3-BDO) is a valuable intermediate for the production of fragrances, pheromones, insecticides and antibiotics. Biotechnological production results in superior enantiomeric excess over chemical production and is therefore the preferred production route. In this study (R)-1,3-BDO was produced in the industrially important whole cell biocatalyst Clostridium saccharoperbutylacetonicum through expression of the enantio-specific phaB gene from Cupriavidus necator. The heterologous pathway was optimised in three ways: at the transcriptional level choosing strongly expressed promoters and comparing plasmid borne with chromosomal gene expression, at the translational level by optimising the codon usage of the gene to fit the inherent codon adaptation index of C. saccharoperbutylacetonicum, and at the enzyme level by introducing point mutations which led to increased enzymatic activity. The resulting whole cell catalyst produced up to 20 mM (1.8 g/l) (R)-1,3-BDO in non-optimised batch fermentation which is a promising starting position for economical production of this chiral chemical.

1H, 13C and 15 N NMR assignments of solubility tag protein Msyb of Escherichia coli

Biochemical and structural characterizations of a protein are the prerequisite for the further understanding of its biological role and potential applications. The expression of recombinant protein is almost unavoidable to produce the amount of the protein required for these studies, especially at the industrial level. Escherichia coli is the single most used system for recombinant protein expression and the first choice for a trial expression. Besides the inherited defects of its prokaryotic origin, the E. coli system has problems like low protein solubility and formation of inclusion bodies. To improve the solubility while assisting correct folding of the target protein, fusing a tag protein prior to its N-terminus is one of the common approaches. GST, MBP, Trx and SUMO proteins are among the most used tags by providing different advantages during recombinant protein expression. Msyb, a small and acidic protein native to E. coli, is another example that could improve the solubility of the target protein. While the biophysical and biochemical properties of these common tag proteins have been studied to a great extent, Msyb protein remains largely uncharacterized. Here, using solution-state NMR, our near-complete resonance assignment of Msyb provides a basis for future structure determination which would help to expand its usage as a common tag protein.