Improving the production of a thermostable amidase through optimising IPTG induction in a highly dense culture of recombinant Escherichia coli

Engineering Escherichia coli for cost-effective production of medium-chain fatty acids from soy whey using an optimized galactose-based autoinduction system

Medium-chain fatty acids (MCFAs) are essential chemical feedstocks. Microbial production of MCFAs offers an attractive alternative to conventional methods, but the costly media and external inducers limit its practical application. To address this issue and make MCFA production more cost-effective, an E.coli platform was developed using soy whey as a medium and galactose as an autoinducer. We first designed an efficient, stringent, homogeneous, and robust galactose-based autoinduction system for the expression of pathway enzymes by rationally engineering the promoter of the galactose-proton symporter (GalP). Subsequently, the intracellular acetyl-CoA availability and NADH regeneration were enhanced to improve the reversal of the β-oxidation cycle. The resulting strain yielded 8.20 g/L and 16.42 g/L MCFA in pH-controlled batch fermentation and fed-batch fermentation with glucose added using soy whey as medium, respectively. This study provided a cost-effective and promising platform for MCFA production, as well as future strain development for other value-added chemicals production.

Degradation of Aflatoxin B1 by recombinant laccase extracellular produced from Escherichia coli

Bioenzymatic degradation of aflatoxin B1 (AFB1) is a safe, efficient and environmentally friendly detoxification technology. In this work, AFB1 was successfully degraded by recombinant laccase (fmb-rL103) in the absence of a mediator. The laccase gene was cloned from Bacillus vallismortis fmb-103, and was expressed in heterologous host Escherichia coli after codon optimization. The extracellular production of fmb-rL103 could be induced by adding methanol (6 %, v/v), and the maximum yield was 1545.6 U/L. In the 10 L bioreactor, the extracellular yield increased to 50,950.6 U/L after 20 h of induction, accounting for three quarters of the total yield. The mechanism of methanol-induced extracellular secretion was further studied by measuring acetate content, lac103 gene expression and cell membrane permeability. Furthermore, we explored the biochemical properties of fmb-rL103 and its degradation conditions on AFB1. The degradation efficiency increased constantly with increase in incubation pH and temperature, and exceeded 60 % at pH 7.0 and 37 °C. This work provides new insight into developing the large-scale production of laccase and its application to degrade AFB1.

Process study of ceramic membrane-coupled mixed-cell fermentation for the production of adenine

In order to solve the problems of high complexity, many by-products, high pollution and difficult extraction of the existing adenine production process, in this study, ceramic membrane-coupled mixed cell fermentation was used to produce adenine while reducing the synthesis of by-products and simplifying the production process of adenine. Nucleoside hydrolase (encoded by the rihC gene) was used to produce adenine by coordinated fermentation with the adenosine-producing bacterium Bacillus Subtilis XGL. The adenosine hydrolase (AdHy)-expressing strain Escherichia coli BL21-AdHy was successfully employed and the highest activity of the crude enzyme solution was found by orthogonal experiments at 170 W power, 42% duty cycle, and 8 min of sonication. The highest AdHy activity was found after 18 h of induction incubation. E. coli BL21-AdHy was induced for 18 h and sonicated under the above ultrasonic conditions and the resulting crude enzyme solution was used for co-fermentation of the strain and enzyme. Moreover, 15% (v/v) of the AdHy crude enzyme solution was added to fermentation of B. subtilis XGL after 35 h. Finally, the whole fermentation system was dialyzed using coupled ceramic membranes for 45 and 75 h, followed by the addition of fresh medium. In contrast, the AdHy crude enzyme solution was added after 35, 65, and 90 h of B. subtilis fermentation, with three additions of 15, 15, and 10% of the B. subtilis XGL fermentation system. The process was validated in a 5 L fermenter and 14 ± 0.25 g/L of adenine was obtained, with no accumulation of adenosine and d-ribose as by-products. The enzymatic activity of the AdHy crude solution treated with ultrasound was greatly improved. It also reduced the cellular activity of E. coli BL21-AdHy and reduced effects on bacterial co-fermentation. Membrane-coupled dialysis solved the problem of decreased yield due to poor bacterial survival and decreased viability, and eliminated inhibition of the product synthesis pathway by adenosine. The batch addition of crude enzyme broth allowed the continuous conversion of adenosine to adenine. This production method provides the highest yield of biologically produced adenine reported to date, reduces the cost of adenine production, and has positive implications for the industrial production of adenine by fermentation. And it provides a reference for producing other high-value-added products made by fermentation.

A statistical approach to boost soluble expression of E. coli-derived virus-like particles in shake-flask cultivation

Hepatitis B core virus-like particles (HBc-VLP) have been widely used as carrier platforms to present an epitope of interest. Escherichia coli expression system is cost effective and produces high yields of recombinant protein. However major drawbacks include difficulties in obtaining soluble expression and tendency to form inclusion bodies. To boost solubility of proteins during expression of E. coli-derived HBc-VLPs carrying EBNA1 epitope, a statistical approach involving fractional factorial design (FFD) and response surface methodology (RSM) was used. For the first time, this approach was applied to quantitatively determine the impact of key parameters in shake-flask cultivation. Expression conditions including post-induction temperature and shaker-speed, and cell density at induction were optimized. Based on native agarose gel electrophoresis, optimized soluble protein cellular yield was 210.5mgg^-1 dry cell mass and volumetric yield was 272mgL^-1 of culture media. Findings highlight: 1) the significant interaction between post-induction temperature and shaker-speed on production, and; 2) sufficient oxygen level is required during induction. It is concluded that this statistical approach can be practically applied to optimize expression of HBc-VLP in shake-flask cultivation, and to determine key parameters for large-scale productions.

Cell Catalysis of Citrate to Itaconate by Engineered Halomonas bluephagenesis

Itaconic acid (IA), an important five-carbon unsaturated dicarboxylic acid, is one of the top 12 renewable chemicals with an urgent need to reduce industrial production costs. Halomonas bluephagenesis, which possesses the potential for cost-effective bioproduction of chemicals and organic acids due to its ability to grow under open nonsterile conditions and high tolerance to organic acid salts, was genetically engineered and used to produce IA from citrate by a cell catalytic strategy. Here, two essential genes (cis-aconitate decarboxylase encoding gene cadA and aconitase (ACN) encoding gene acn) were introduced into H. bluephagenesis to construct an IA biosynthesis pathway. Further engineering modifications including coexpression of molecular chaperones GroESL, increasing the copy number of the gene encoding rate-limiting enzyme ACN, and weakening the competing pathway were implemented. Under the optimized condition for the cell catalytic system, the engineered strain TAZI-08 produced 451.45 mM (58.73 g/L) IA from 500 mM citrate, with 93.24% conversion in 36 h and a productivity of 1.63 g/(L h). An intermittent feeding strategy further increased the IA titer to 488.86 mM (63.60 g/L). The IA titer and citrate conversion in H. bluephagenesis are the highest among heterologous hosts reported so far, demonstrating that this strain is a suitable chassis for hyperproduction of IA.

Identification of Optimal Expression Parameters and Purification of a Codon-Optimized Human GLIS1 Transcription Factor from Escherichia coli

GLIS1 has multiple roles in embryonic development and in deriving induced pluripotent stem cells by aiding signaling pathways and chromatin assembly. An inexpensive and simple method to produce human GLIS1 protein from Escherichia coli (E. coli) is demonstrated in this study. Various parameters such as codon usage bias, E. coli strains, media, induction conditions (such as inducer concentration, cell density, time, and temperature), and genetic constructs were investigated to obtain soluble expression of human GLIS1 protein. Using identified expression conditions and an appropriate genetic construct, the human GLIS1 protein was homogeneously purified (purity > 90%) under native conditions. Importantly, the purified protein has upheld a stable secondary structure, as demonstrated by circular dichroism spectroscopy. To the best of our knowledge, this is the first study to report the ideal expression conditions of human GLIS1 protein in E. coli to achieve soluble expression and purification under native conditions, upholding its stable secondary structure post-purification. The biological activity of the purified GLIS1 fusion protein was further assessed in MDA-MB-231 cells. This biologically active human GLIS1 protein potentiates new avenues to understand its molecular mechanisms in different cellular functions in various cancers and in the generation of induced pluripotent stem cells.

Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli

Biological functions of bacteria can be regulated by monitoring their own population density induced by the quorum sensing system. However, quantitative insight into the system’s dynamics and regulatory mechanism remain challenging. Here, we construct a comprehensive mathematical model of the synthetic quorum sensing circuit that controls population density in Escherichia coli. Simulations agree well with experimental results obtained under different ribosome-binding site (RBS) efficiencies. We present a quantitative description of the component dynamics and show how the components respond to isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The optimal IPTG-induction range for efficiently controlling population density is quantified. The controllable area of population density by acyl-homoserine lactone (AHL) permeability is quantified as well, indicating that high AHL permeability should be treated with a high dose of IPTG, while low AHL permeability should be induced with low dose for efficiently controlling. Unexpectedly, an oscillatory behavior of the growth curve is observed with proper RBS-binding strengths and the oscillation is greatly restricted by the bacterial death induced by toxic metabolic by-products. Moreover, we identify that the mechanism underlying the emergence of oscillation is determined by the negative feedback loop structure within the signaling. Bifurcation analysis and landscape theory are further employed to study the stochastic dynamic and global stability of the system, revealing two faces of toxic metabolic by-products in controlling oscillatory behavior. Overall, our study presents a quantitative basis for understanding and new insights into the control mechanism of quorum sensing system, providing possible clues to guide the development of more rational control strategy.

Automated multi-scale cascade of parallel stirred-tank bioreactors for fast protein expression studies

Automation, parallelization and autonomous operation of standard lab equipment, usually applied for manual bioprocess development, is considered as the key for reduction of bioprocess development time and costs. An automated bioreactor system with 4 stirred-tank bioreactors on a L-scale was combined with a custom-made biomass transfer system to distribute the cell suspensions produced on the L-scale into 48 parallel stirred-tank bioreactors on a mL-scale. Afterwards parallel protein expression studies automated by a liquid handling system with integrated fluorescence reader were performed. Isopropyl β-D-1-thiogalactopyranoside-induced (IPTG) expression of the red fluorescence protein mCherry was studied as an example of using fed-batch processes with recombinant Escherichia coli. In a first automated study, IPTG concentrations were varied in 48 parallel fed-batch processes with E. coli cells produced at a growth rate of 0.1 h^-1 on an L-scale and transferred automatically to the mL-scale. The mCherry expression rate increased with increasing inducer concentration until the highest protein expression rate was observed at > 9 μM IPTG. In a second automated study, the growth rate of E. coli was varied between 0.1-0.2 h^-1 in parallelly-operated stirred-tank bioreactors on a L-scale. The cells were automatically transferred and distributed into the stirred-tank bioreactors on a mL-scale and the concentration of the inducer IPTG was varied as before in parallel fed-batch processes. An increased growth rate during the production of the recombinant E. coli cells and/or higher cell densities during protein expression resulted in the increased IPTG concentrations necessary to achieve identical expression rates compared to a growth rate of 0.1 h^-1 with the exception of very low inducer concentrations and inducer concentrations in excess. The new automated multi-scale cascade of parallel stirred-tank bioreactors should easily be applicable for performing fast optimisation studies with other microbial production systems and will have the potential to reduce bioprocess development time and staff assignment considerably.

A highly active heparinase I from Bacteroides cellulosilyticus: Cloning, high level expression, and molecular characterization

As one of the most extensively studied glycosaminoglycan lyases, heparinase I has been used in producing low or ultra-low molecular weight heparin. Its' important applications are to neutralize the heparin in human blood and analyze heparin structure in the clinic. However, the low productivity and activity of the enzyme have greatly hindered its applications. In this study, a novel Hep-I from Bacteroides cellulosilyticus (BcHep-I) was successfully cloned and heterologously expressed in E. coli BL21 (DE3) as a soluble protein. The molecular mass and isoelectric point (pI) of the enzyme are 44.42 kDa and 9.02, respectively. And the characterization of BcHep-I after purified with Ni-NTA affinity chromatography suggested that it is a mesophilic enzyme. BcHep-I can be activated by 1 mM Ca2+, Mg2+, and Mn2+, while severely inhibited by Zn2+, Co2+, and EDTA. The specific activity of the enzyme was 738.3 U·mg-1 which is the highest activity ever reported. The Km and Vmax were calculated as 0.17 mg·mL-1 and 740.58 U·mg-1, respectively. Besides, the half-life of 300 min at 30°C showed BcHep-I has practical applications. Homology modeling and substrate docking revealed that Gln15, Lys74, Arg76, Lys104, Arg149, Gln208, Tyr336, Tyr342, and Lys338 were mainly involved in the substrate binding of Hep-I, and 11 hydrogen bonds were formed between heparin and the enzyme. These results indicated that BcHep-I with high activity has great potential applications in the industrial production of heparin, especially in the clinic to neutralize heparin.

Optimized expression conditions for enhancing production of two recombinant chitinolytic enzymes from different prokaryote domains

Enhancing functional gene expression is key to high-level production of active chitinases. For this purpose, the effects of culture cell density, inducer concentration, post-induction time and induction temperatures on the functional expression of two different chitinases (HsChiA1p, a family 18 archaeal chitinase and PtChi19p, a family 19 bacterial chitinase) were comparatively investigated. Results showed that the effect of each parameter on the activity of both chitinases was specific to each enzyme. In addition, different Escherichia coli host strains compatible with the expression in pET systems were assayed for active protein overexpression. When using BL21 Star (DE3), a significant increase of 60% in expression was observed for the active archaeal chitinase HsChiA1p as compared to that found when using BL21 (DE3), indicating that the rne131 gene mutation efficiently stabilizes the mRNA for HsChiA1p. Using the Codon Adaptation Index value, rare codon analysis of the archaeal HschiA1 and bacterial Ptchi19 genes revealed that both DNA sequences were not optimal for maximal expression in E. coli. Different E. coli host strains possess extra copies of some of the tRNA genes for rare codons. For the Rosetta 2 (DE3) and the BL21 RP (DE3) strains, a significant increase of 40% was reached for the activity of HsChiA1p and PtChi19p. Finally, as part of the protein still remained insoluble, the best conditions for recovering biologically active protein from inclusion bodies were established for each enzyme.

Biotechnology Based Process for Production of a Disulfide-Bridged Peptide

A disulfide-bridged peptide drug development candidate contained two oligopeptide chains with 11 and 12 natural amino acids joined by a disulfide bond at the N-terminal end. An efficient biotechnology based process for the production of the disulfide-bridged peptide was developed. Initially, the two individual oligopeptide chains were prepared separately by designing different fusion proteins and expressing them in recombinant E. coli. Enzymatic or chemical cleavage of the two fusion proteins provided the two individual oligopeptide chains which could be conjugated via disulfide bond by conventional chemical reaction to the disulfide-bridged peptide. A novel heterodimeric system to bring the two oligopeptide chains closer and induce disulfide bond formation was designed by taking advantage of the self-assembly of a leucine zipper system. The heterodimeric approach involved designing fusion proteins with the acidic and basic components of the leucine zipper, additional amino acids to optimize interaction between the individual chains, specific cleavage sites, specific tag to ensure separation, and two individual oligopeptide chains. Computer modeling was used to identify the nature and number of amino acid residue to be inserted between the leucine zipper and oligopeptides for optimum interaction. Cloning and expression in rec E. coli, fermentation, followed by cell disruption resulted in the formation of heterodimeric protein with the interchain disulfide bond. Separation of the desired heterodimeric protein, followed by specific cleavage at methionine by cyanogen bromide provided the disulfide-bridged peptide.

Experimental design approach in recombinant protein expression: determining medium composition and induction conditions for expression of pneumolysin from Streptococcus pneumoniae in Escherichia coli and preliminary purification process

Background

Streptococcus pneumoniae (S. pneumoniae) causes several serious diseases including pneumonia, septicemia and meningitis. The World Health Organization estimates that streptococcal pneumonia is the cause of approximately 1.9 million deaths of children under five years of age each year. The large number of serotypes underlying the disease spectrum, which would be reflected in the high production cost of a commercial vaccine effective to protect against all of them and the higher level of amino acid sequence conservation as compared to polysaccharide structure, has prompted us to attempt to use conserved proteins for the development of a simpler vaccine. One of the most prominent proteins is pneumolysin (Ply), present in almost all the serotypes known at the moment, which shows an effective protection against S. pneumoniae infections.

Results

We have cloned the pneumolysin gene from S. pneumoniae serotype 14 and studied the effects of eight variables related to medium composition and induction conditions on the soluble expression of rPly in Escherichia coli (E. coli) and a 2^8-4 factorial design was applied. Statistical analysis was carried out to compare the conditions used to evaluate the expression of soluble pneumolysin; rPly activity was evaluated by hemolytic activity assay and served as the main response to evaluate the proper protein expression and folding. The optimized conditions, validated by the use of triplicates, include growth until an absorbance of 0.8 (measured at 600 nm) with 0.1 mM IPTG during 4 h at 25°C in a 5 g/L yeast extract, 5 g/L tryptone, 10 g/L NaCl, 1 g/L glucose medium, with addition of 30 μg/mL kanamycin.

Conclusions

This experimental design methodology allowed the development of an adequate process condition to attain high levels (250 mg/L) of soluble expression of functional rPly in E. coli, which should contribute to reduce operational costs. It was possible to recover the protein in its active form with 75% homogeneity.

The influence of microbial physiology on biocatalyst activity and efficiency in the terminal hydroxylation of n-octane using Escherichia coli expressing the alkane hydroxylase, CYP153A6

BACKGROUND

Biocatalyst improvement through molecular and recombinant means should be complemented with efficient process design to facilitate process feasibility and improve process economics. This study focused on understanding the bioprocess limitations to identify factors that impact the expression of the terminal hydroxylase CYP153A6 and also influence the biocatalytic transformation of n-octane to 1-octanol using resting whole cells of recombinant E. coli expressing the CYP153A6 operon which includes the ferredoxin (Fdx) and the ferredoxin reductase (FdR).

RESULTS

Specific hydroxylation activity decreased with increasing protein expression showing that the concentration of active biocatalyst is not the sole determinant of optimum process efficiency. Process physiological conditions including the medium composition, temperature, glucose metabolism and product toxicity were investigated. A fed-batch system with intermittent glucose feeding was necessary to ease overflow metabolism and improve process efficiency while the introduction of a product sink (BEHP) was required to alleviate octanol toxicity. Resting cells cultivated on complex LB and glucose-based defined medium with similar CYP level (0.20 μmol gDCW-1) showed different biocatalyst activity and efficiency in the hydroxylation of octane over a period of 120 h. This was influenced by differing glucose uptake rate which is directly coupled to cofactor regeneration and cell energy in whole cell biocatalysis. The maximum activity and biocatalyst efficiency achieved presents a significant improvement in the use of CYP153A6 for alkane activation. This biocatalyst system shows potential to improve productivity if substrate transfer limitation across the cell membrane and enzyme stability can be addressed especially at higher temperature.

CONCLUSION

This study emphasises that the overall process efficiency is primarily dependent on the interaction between the whole cell biocatalyst and bioprocess conditions.

lac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA

Most commonly used expression systems in bacteria are based on the Escherichia coli lac promoter. Furthermore, lac operon elements are used today in systems and synthetic biology. In the majority of the cases the gratuitous inducers IPTG or TMG are used. Here we report a systematic comparison of lac promoter induction by TMG and IPTG which focuses on the aspects inducer uptake, population heterogeneity and a potential influence of the transacetylase, LacA. We provide induction curves in E. coli LJ110 and in isogenic lacY and lacA mutant strains and we show that both inducers are substrates of the lactose permease at low inducer concentrations but can also enter cells independently of lactose permease if present at higher concentrations. Using a gfp reporter strain we compared TMG and IPTG induction at single cell level and showed that bimodal induction with IPTG occurred at approximately ten-fold lower concentrations than with TMG. Furthermore, we observed that lac operon induction is influenced by the transacetylase, LacA. By comparing two Plac-gfp reporter strains with and without a lacA deletion we could show that in the lacA(+) strain the fluorescence level decreased after few hours while the fluorescence further increased in the lacA(-) strain. The results indicate that through the activity of LacA the IPTG concentration can be reduced below an inducing threshold concentration-an influence that should be considered if low inducer amounts are used.

Improvement of the expression and purification of Mycobacterium tuberculosis arylamine N-acetyltransferase (TBNAT) a potential target for novel anti-tubercular agents

Arylamine N-acetyltransferase from Mycobacterium tuberculosis (TBNAT) has been proposed as a drug target for latent tuberculosis treatment. The enzyme is essential for the survival of the mycobacterium in macrophages. However, TBNAT has been very difficult to generate as a soluble protein. In this work we describe production of soluble recombinant TBNAT at a reasonable yield achieved by subcloning the tbnat gene with a purification His-tag into the pVLT31 plasmid, and subsequent optimisation of the induction conditions. The expression system results in soluble protein optimised upon extended (60 h) low level isopropyl β-D-1-thiogalactopyranoside level induction (100 μM) at a temperature of 15 °C. The level of TBNAT expression obtained in E. coli has been significantly improved from ∼2 mg to a final yield of up to 16 mg per litre of culture at a purity level suitable for structural studies. The molecular mass of 31310 Da was confirmed using mass spectroscopy and the oligomerisation state was determined. The stability of TBNAT in different buffer systems was investigated by thermal shift assays and sufficient protein is now available for the screening of chemical libraries for inhibitors.