High Yield of Recombinant Protein in Shaken E. coli Cultures with Enzymatic Glucose Release Medium EnPresso B

Application of lactose based autoinduction for heterologous production of an active [NiFe] hydrogenase in E. coli

OBJECTIVES

This study aims to assess whether a fed-batch-based auto-induction method can enhance active hydrogenase production, encompassing cofactor formation and space-time yield.

RESULTS

The recombinant Escherichia coli strain BQF8RH8, possessing plasmids for assembly and proper maturation of Cupriavidus necator regulatory hydrogenase (RH), was cultivated in the fed-batch like EnPresso B medium with an autoinduction lactose-based system. In contrast to classical IPTG induction previously performed, we obtained active RH demonstrating the feasibility of the process for active hydrogenase production.

CONCLUSION

Our results affirm the viability of the previously developed auto-induction strategy also for a functional hydrogenase with the complex maturation process. This significantly accelerates the process and enhances hydrogenase productivity.

Identification and characterization of the functional tetrameric UDP-glucose pyrophosphorylase from Klebsiella pneumoniae

In all kingdoms of life, the enzyme uridine diphosphate-glucose pyrophosphorylase (UGP) occupies a central role in metabolism, as its reaction product uridine diphosphate-glucose (UDP-Glc) is involved in various crucial cellular processes. Pathogens, including fungi, parasites, and bacteria, depend on UGP for the synthesis of virulence factors; in particular, various bacterial species utilize UDP-Glc and its derivatives for the synthesis of lipopolysaccharides, capsular polysaccharides, and biofilm exopolysaccharides. UGPs have, therefore, gained attention as anti-bacterial drug target candidates, prompting us to study their structure-function relationships to provide a basis for the rational development of specific inhibitors. UGP function is tied to its oligomeric state, and the majority of bacterial homologs have been described as tetramers encoded by the galU gene. Uniquely, enterobacterial species harbor a second gene, galF, encoding a protein with high homology to UGP, whose function is somewhat controversial. Here, we show that the galF gene of the opportunistic pathogen Klebsiella pneumoniae encodes a dimeric protein that has lost UGP activity, likely due to a combination of active site mutations and an inability to tetramerize, whereas the functional K. pneumoniae UGP, encoded by galU, is an active tetramer. Our AlphaFold-assisted structure-function relationship studies underline that tetramerization is essential for bacterial UGP function and is facilitated by a common mechanism utilizing conserved key residues. Targeting the respective molecular interfaces, which are absent in human UGP, could provide a means of selectively inhibiting the bacterial virulence factor UGP and potentially rendering pathogenic species avirulent.IMPORTANCEThe enzyme uridine diphosphate-glucose pyrophosphorylase (UGP) is important for the virulence of bacterial pathogens and, therefore, a potential drug target. In this study, we identify the gene encoding the functional UGP in Klebsiella pneumoniae, a bacterium notoriously causing severe antibiotic-resistant infections in humans, and reveal structural and functional features that may aid in the development of new antibiotics.

Engineering and Expression Strategies for Optimization of L-Asparaginase Development and Production

Genetic engineering for heterologous expression has advanced in recent years. Model systems such as Escherichia coli, Bacillus subtilis and Pichia pastoris are often used as host microorganisms for the enzymatic production of L-asparaginase, an enzyme widely used in the clinic for the treatment of leukemia and in bakeries for the reduction of acrylamide. Newly developed recombinant L-asparaginase (L-ASNase) may have a low affinity for asparagine, reduced catalytic activity, low stability, and increased glutaminase activity or immunogenicity. Some successful commercial preparations of L-ASNase are now available. Therefore, obtaining novel L-ASNases with improved properties suitable for food or clinical applications remains a challenge. The combination of rational design and/or directed evolution and heterologous expression has been used to create enzymes with desired characteristics. Computer design, combined with other methods, could make it possible to generate mutant libraries of novel L-ASNases without costly and time-consuming efforts. In this review, we summarize the strategies and approaches for obtaining and developing L-ASNase with improved properties.

Glucose transport engineering allows mimicking fed-batch performance in batch mode and selection of superior producer strains

Background

Fed-batch mode is the standard culture technology for industrial bioprocesses. Nevertheless, most of the early-stage cell and process development is carried out in batch cultures, which can bias the initial selection of expression systems. Cell engineering can provide an alternative to fed-batch cultures for high-throughput screening and host selection. We have previously reported a library of Escherichia coli strains with single and multiple deletions of genes involved in glucose transport. Compared to their wild type (W3110), the mutant strains displayed lower glucose uptake, growth and aerobic acetate production rates. Therefore, when cultured in batch mode, such mutants may perform similar to W3110 cultured in fed-batch mode. To test that hypothesis, we evaluated the constitutive expression of the green fluorescence protein (GFP) in batch cultures in microbioreactors using a semi defined medium supplemented with 10 or 20 g/L glucose + 0.4 g yeast extract/g glucose.

Results

The mutant strains cultured in batch mode displayed a fast-growth phase (growth rate between 0.40 and 0.60 h⁻¹) followed by a slow-growth phase (growth rate between 0.05 and 0.15 h⁻¹), similar to typical fed-batch cultures. The phase of slow growth is most probably caused by depletion of key amino acids. Three mutants attained the highest GFP fluorescence. Particularly, a mutant named WHIC (ΔptsHIcrr, ΔmglABC), reached a GFP fluorescence up to 14-fold greater than that of W3110. Strain WHIC was cultured in 2 L bioreactors in batch mode with 100 g/L glucose + 50 g/L yeast extract. These cultures were compared with exponentially fed-batch cultures of W3110 maintaining the same slow-growth of WHIC (0.05 h⁻¹) and using the same total amount of glucose and yeast extract than in WHIC cultures. The WHIC strain produced approx. 450 mg/L GFP, while W3110 only 220 mg/L.

Conclusion

The combination of cell engineering and high throughput screening allowed the selection of a particular mutant that mimics fed-batch behavior in batch cultures. Moreover, the amount of GFP produced by the strain WHIC was substantially higher than that of W3110 under both, batch and fed-batch schemes. Therefore, our results represent a valuable technology for accelerated bioprocess development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01906-1.

High cell density cultivation of E. coli in shake flasks for the production of recombinant proteins

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True fed-batch strategy for high cell density cultivation of E. coli in shake flask.

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Cybernetic model-based optimization of the feeding recipe.

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Biomass of 19.9–21.5 g DCW/L, in agreement with the model prediction.

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Volumetric productivity for tested proteins increased 8–34-fold compared to batch.

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Scale up of fed-batch recipe to bioreactor resulted in further 2.8-fold increase.

Batch cultivation of recombinant bacteria in shake flasks typically results in low cell density due to nutrient depletion. Previous studies on high cell density cultivation in shake flasks have relied mainly on controlled release mechanisms. Here, we report a true fed-batch strategy to achieve high cell density of recombinant E. coli in shake flasks in 24 h by feeding a mixture of glycerol and yeast extract with a syringe pump. Feed composition and feed rate were obtained by cybernetic model-based, multi-objective optimization. Model parameters were estimated from time-course measurement of substrate, biomass, and dissolved oxygen levels. The optimized process yielded 20.7 g dry cell weight/L, in agreement with the model prediction. Volumetric protein productivity improved by 10–34-fold compared to batch cultivation with 2.8-fold further improvement when the fed-batch process was replicated in a 3 L bioreactor. The process has significance in the routine laboratory cultivations and in scaleup studies.

Implementing Multi-Enzyme Biocatalytic Systems Using Nanoparticle Scaffolds

Interest in multi-enzyme synthesis outside of cells (in vitro) is becoming far more prevalent as the field of cell-free synthetic biology grows exponentially. Such synthesis would allow for complex chemical transformations based on the exquisite specificity of enzymes in a "greener" manner as compared to organic chemical transformations. Here, we describe how nanoparticles, and in this specific case-semiconductor quantum dots, can be used to both stabilize enzymes and further allow them to self-assemble into nanocomplexes that facilitate high-efficiency channeling phenomena. Pertinent protocol information is provided on enzyme expression, choice of nanoparticulate material, confirmation of enzyme attachment to nanoparticles, assay format and tracking, data analysis, and optimization of assay formats to draw the best analytical information from the underlying processes.

High-yield expression of periplasmic single-chain variable fragments by solid Escherichia coli cultures

High-yield expression of quality antibody fragments is indispensable for research and diagnosis. Most recombinant antibody fragments are expressed in Escherichia coli using liquid cultures; however, their yields and quality are often poor. Here the authors expressed a single-chain variable fragment in E. coli cultivated on the wet surface of a solid support. Compared with a liquid culture, the authors obtained 2.5-times more single-chain variable fragments with membrane-cultivated E. coli. This method has two important advantages: it enables high yields of periplasmic single-chain variable fragments compared with liquid culture and offers simple and rapid expression and extraction.

So you want to express your protein in Escherichia coli?

Recombinant proteins have been extensively employed as therapeutics for the treatment of various critical and life-threatening diseases and as industrial enzymes in high-value industrial processes. Advances in genetic engineering and synthetic biology have broadened the horizon of heterologous protein production using multiple expression platforms. Selection of a suitable expression system depends on a variety of factors ranging from the physicochemical properties of the target protein to economic considerations. For more than 40 years, Escherichia coli has been an established organism of choice for protein production. This review aims to provide a stepwise approach for any researcher embarking on the journey of recombinant protein production in E. coli. We present an overview of the challenges associated with heterologous protein expression, fundamental considerations connected to the protein of interest (POI) and designing expression constructs, as well as insights into recently developed technologies that have contributed to this ever-growing field.