Improving the activity of surface displayed cytochrome P450 enzymes by optimizing the outer membrane linker

Surface display system of Bacillus subtilis: A promising approach for improving the stability and applications of cellobiose dehydrogenase

Cellobiose dehydrogenase (CDH) plays a crucial role in lignocellulose degradation and bioelectrochemical industries, making it highly in demand. However, the production and purification of CDH through fungal heterologous expression methods is time-consuming, costly, and challenging. In this study, we successfully displayed Pycnoporus sanguineus CDH (psCDH) on the surface of Bacillus subtilis spores for the first time. Enzymatic characterization revealed that spore surface display enhanced the tolerance of psCDH to high temperature (80 °C) and low pH levels (3.5) compared to free psCDH. Furthermore, we found that glycerol, lactic acid, and malic acid promoted the activity of immobilized spore-displayed psCDH; glycerol has a more significant stimulating effect, increasing the activity from 16.86 ± 1.27 U/mL to 46.26 ± 3.25 U/mL. After four reuse cycles, the psCDH immobilized with spores retained 48% of its initial activity, demonstrating a substantial recovery rate. In conclusion, the spore display system, relying on cotG, enables the expression and immobilization of CDH while enhancing its resistance to adverse conditions. This system demonstrates efficient enzyme recovery and reuse. This approach provides a novel method and strategy for the immobilization and stability enhancement of CDH.

Bioconversion of vitamin D3 to bioactive calcifediol and calcitriol as high-value compounds

Biological catalysis is an important approach for the production of high-value-added compounds, especially for products with complex structures. Limited by the complex steps of chemical synthesis and low yields, the bioconversion of vitamin D₃ (VD₃) to calcifediol and calcitriol, which are natural steroid products with high added value and significantly higher biological activity compared to VD₃, is probably the most promising strategy for calcifediol and calcitriol production, and can be used as an alternative method for chemical synthesis. The conversion efficiency of VD₃ to calcifediol and calcitriol has continued to rise in the past few decades with the help of several different VD₃ hydroxylases, mostly cytochrome P450s (CYPs), and newly isolated strains. The production of calcifediol and calcitriol can be systematically increased in different ways. Specific CYPs and steroid C25 dehydrogenase (S25DH), as VD₃ hydroxylases, are capable of converting VD₃ to calcifediol and calcitriol. Some isolated actinomycetes have also been exploited for fermentative production of calcifediol and calcitriol, although the VD₃ hydroxylases of these strains have not been elucidated. With the rapid development of synthetic biology and enzyme engineering, quite a lot of advances in bioproduction of calcifediol and calcitriol has been achieved in recent years. Therefore, here we review the successful strategies of promoting VD₃ hydroxylation and provide some perspective on how to further improve the bioconversion of VD₃ to calcifediol and calcitriol.

Development of highly efficient whole-cell catalysts of cis-epoxysuccinic acid hydrolase by surface display

Bacterial cis-epoxysuccinic acid hydrolases (CESHs) are intracellular enzymes used in the industrial production of enantiomeric tartaric acids. The enzymes are mainly used as whole-cell catalysts because of the low stability of purified CESHs. However, the low cell permeability is the major drawback of the whole-cell catalyst. To overcome this problem, we developed whole-cell catalysts using various surface display systems for CESH[L] which produces L(+)-tartaric acid. Considering that the display efficiency depends on both the carrier and the passenger, we screened five different anchoring motifs in Escherichia coli. Display efficiencies are significantly different among these five systems and the InaPbN-CESH[L] system has the highest whole-cell enzymatic activity. Conditions for InaPbN-CESH[L] production were optimized and a maturation step was discovered which can increase the whole-cell activity several times. After optimization, the total activity of the InaPbN-CESH[L] surface display system is higher than the total lysate activity of an intracellular CESH[L] overexpression system, indicating a very high CESH[L] display level. Furthermore, the whole-cell InaPbN-CESH[L] biocatalyst exhibited good storage stability at 4 °C and considerable reusability. Thereby, an efficient whole-cell CESH[L] biocatalyst was developed in this study, which solves the cell permeability problem and provides a valuable system for industrial L(+)-tartaric acid production.

Enzyme cascade converting cyclohexanol into ε-caprolactone coupled with NADPH recycling using surface displayed alcohol dehydrogenase and cyclohexanone monooxygenase on E. coli

The application of enzymes as biocatalysts in industrial processes has great potential due to their outstanding stereo-, regio- and chemoselectivity. Using autodisplay, enzymes can be immobilized on the cell surface of Gram-negative bacteria such as Escherichia coli. In the present study, the surface display of an alcohol dehydrogenase (ADH) and a cyclohexanone monooxygenase (CHMO) on E. coli was investigated. Displaying these enzymes on the surface of E. coli resulted in whole-cell biocatalysts accessible for substrates without further purification. An apparent maximal reaction velocity VMAX(app) for the oxidation of cyclohexanol with the ADH whole-cell biocatalysts was determined as 59.9 mU ml-1 . For the oxidation of cyclohexanone with the CHMO whole-cell biocatalysts a VMAX(app) of 491 mU ml-1 was obtained. A direct conversion of cyclohexanol to ε-caprolactone, which is a known building block for the valuable biodegradable polymer polycaprolactone, was possible by combining the two whole-cell biocatalysts. Gas chromatography was applied to quantify the yield of ε-caprolactone. 1.12 mM ε-caprolactone was produced using ADH and CHMO displaying whole-cell biocatalysts in a ratio of 1:5 after 4 h in a cell suspension of OD578nm 10. Furthermore, the reaction cascade as applied provided a self-sufficient regeneration of NADPH for CHMO by the ADH whole-cell biocatalyst.

Towards synthetic PETtrophy: Engineering Pseudomonas putida for concurrent polyethylene terephthalate (PET) monomer metabolism and PET hydrolase expression

BACKGROUND

Biocatalysis offers a promising path for plastic waste management and valorization, especially for hydrolysable plastics such as polyethylene terephthalate (PET). Microbial whole-cell biocatalysts for simultaneous PET degradation and growth on PET monomers would offer a one-step solution toward PET recycling or upcycling. We set out to engineer the industry-proven bacterium Pseudomonas putida for (i) metabolism of PET monomers as sole carbon sources, and (ii) efficient extracellular expression of PET hydrolases. We pursued this approach for both PET and the related polyester polybutylene adipate co-terephthalate (PBAT), aiming to learn about the determinants and potential applications of bacterial polyester-degrading biocatalysts.

RESULTS

P. putida was engineered to metabolize the PET and PBAT monomer terephthalic acid (TA) through genomic integration of four tphII operon genes from Comamonas sp. E6. Efficient cellular TA uptake was enabled by a point mutation in the native P. putida membrane transporter MhpT. Metabolism of the PET and PBAT monomers ethylene glycol and 1,4-butanediol was achieved through adaptive laboratory evolution. We then used fast design-build-test-learn cycles to engineer extracellular PET hydrolase expression, including tests of (i) the three PET hydrolases LCC, HiC, and IsPETase; (ii) genomic versus plasmid-based expression, using expression plasmids with high, medium, and low cellular copy number; (iii) three different promoter systems; (iv) three membrane anchor proteins for PET hydrolase cell surface display; and (v) a 30-mer signal peptide library for PET hydrolase secretion. PET hydrolase surface display and secretion was successfully engineered but often resulted in host cell fitness costs, which could be mitigated by promoter choice and altering construct copy number. Plastic biodegradation assays with the best PET hydrolase expression constructs genomically integrated into our monomer-metabolizing P. putida strains resulted in various degrees of plastic depolymerization, although self-sustaining bacterial growth remained elusive.

CONCLUSION

Our results show that balancing extracellular PET hydrolase expression with cellular fitness under nutrient-limiting conditions is a challenge. The precise knowledge of such bottlenecks, together with the vast array of PET hydrolase expression tools generated and tested here, may serve as a baseline for future efforts to engineer P. putida or other bacterial hosts towards becoming efficient whole-cell polyester-degrading biocatalysts.

Redox metabolism for improving whole-cell P450-catalysed terpenoid biosynthesis

The growing preference for producing cytochrome P450-mediated natural products in microbial systems stems from the challenging nature of the organic chemistry approaches. The P450 enzymes are redox-dependent proteins, through which they source electrons from reducing cofactors to drive their activities. Widely researched in biochemistry, most of the previous studies have extensively utilised expensive cell-free assays to reveal mechanistic insights into P450 functionalities in presence of commercial redox partners. However, in the context of microbial bioproduction, the synergic activity of P450- reductase proteins in microbial systems have not been largely investigated. This is mainly due to limited knowledge about their mutual interactions in the context of complex systems. Hence, manipulating the redox potential for natural product synthesis in microbial chassis has been limited. As the potential of redox state as crucial regulator of P450 biocatalysis has been greatly underestimated by the scientific community, in this review, we re-emphasize their pivotal role in modulating the in vivo P450 activity through affecting the product profile and yield. Particularly, we discuss the applications of widely used in vivo redox engineering methodologies for natural product synthesis to provide further suggestions for patterning on P450-based terpenoids production in microbial platforms.

P450-driven plastic-degrading synthetic bacteria

Plastic contamination currently threatens a wide variety of ecosystems and presents damaging repercussions and negative consequences for many wildlife species. Sustainable plastic waste management is an important approach to environmental protection and a necessity in the current life cycle of plastics in nature. Plastic biodegradation by microorganisms is a notable possible solution. This opinion article includes a proposal to use hypothetical P450 enzymes with an engineered active site as potent trigger biocatalysts to biodegrade polyethylene (PE) via in-chain hydroxylation into smaller products of linear aliphatic alcohols and alkanoic acids based on cascade enzymatic reactions. Furthermore, we propose the adoption of P450 into plastic-eating synthetic bacteria for PE biodegradation. This strategy can be applicable to other dense plastics, such as polypropylene (PP) and polystyrene (PS).

An integrative approach to improving the biocatalytic reactions of whole cells expressing recombinant enzymes

Biotransformation is a selective, stereospecific, efficient, and environment friendly method, compared to chemical synthesis, and a feasible tool for industrial and pharmaceutical applications. The design of biocatalysts using enzyme engineering and metabolic engineering tools has been widely reviewed. However, less importance has been given to the biocatalytic reaction of whole cells expressing recombinant enzymes. Along with the remarkable development of biotechnology tools, a variety of techniques have been applied to improve the biocatalytic reaction of whole cell biotransformation. In this review, techniques related to the biocatalytic reaction are examined, reorganized, and summarized via an integrative approach. Moreover, equilibrium-shifted biotransformation is reviewed for the first time.

Autodisplay of human PIP5K1α lipid kinase on Escherichia coli and inhibitor testing

The human phosphatidylinositol 4-phosphate 5-kinase type I α (hPIP5K1α) plays a major role in the PI3K/AKT/mTOR signaling pathway. As it has been shown before that hPIP5K1α is involved in the development of different types of cancer in particular prostate cancer, inhibitors of the enzyme might be a new option for the treatment of this disease. Here we report on the expression of hPIP5K1α on the surface of E. coli using Autodisplay. Autodisplay is defined as the surface display of a recombinant protein on a gramnegative bacterium by the autotransporter secretion pathway. After verification of surface expression, enzyme activity of whole cells displaying hPIP5K1α was determined by a capillary electrophoresis based assay. When using cells at an OD₅₇₈ of 2.5, the artificial substrate phosphatidylinositol4-phosphate (PI(4)P) fluorescein was converted by a rate of 10.7 ± 0.2 fmol/min. Using this substrate inhibition of three pyranobenzoquinone type compounds was tested. The most active compound was 4-(2-amino-3-cyano-6-hydroxy-5,8-dioxo-7-undecyl-5,8-dihydro-4H-chromen-4-yl) benzoic acid with an IC₅₀ value of 8.6 μM. Because until now, all attempts to purify hPIP5K1α failed, we suggest the use of whole cells of E. coli displaying the enzyme as a convenient tool for inhibitor identification.

protaTETHER: A method for the incorporation of linkers in biomacromolecules

The impacts of linkers on dynamics, expression, and activity of biomacromolecules are often overlooked. This may be due, in part, to the lack of facile methods for incorporation and analysis of linkers that vary iteratively in both length and sequence composition. The protaTETHER method addresses this gap by enabling the incorporation of focused linker libraries at potentially any region in a protein sequence. In this chapter, we describe the generation and incorporation of linkers in a PKAc-GFP fusion protein and provide methods for the application and evaluation of the protaTETHER process.

Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution

We report a first of its kind functional cell surface display of nucleic acid polymerase and its directed evolution to efficiently incorporate 2'-O-methyl nucleotide triphosphates (2'-OMe-NTPs). In the development of polymerase cell surface display, two autotransporter proteins (Escherichia coli adhesin involved in diffuse adherence and Pseudomonas aeruginosa esterase A [EstA]) were employed to transport and anchor the 68-kDa Klenow fragment (KF) of E. coli DNA polymerase I on the surface of E. coli. The localization and function of the displayed KF were verified by analysis of cell outer membrane fractions, immunostaining, and fluorometric detection of synthesized DNA products. The EstA cell surface display system was applied to evolve KF for the incorporation of 2'-OMe-NTPs and a KF variant with a 50.7-fold increased ability to successively incorporate 2'-OMe-NTPs was discovered. Expanding the scope of cell-surface displayable proteins to the realm of polymerases provides a novel screening tool for tailoring polymerases to diverse application demands in a polymerase chain reaction and sequencing-based biotechnological and medical applications. Especially, cell surface display enables novel polymerase screening strategies in which the heat-lysis step is bypassed and thus allows the screening of mesophilic polymerases with broad application potentials ranging from diagnostics and DNA sequencing to replication of synthetic genetic polymers.

Improving the autotransporter-based surface display of enzymes in Pseudomonas putida KT2440

Pseudomonas putida can be used as a host for the autotransporter‐mediated surface display of enzymes (autodisplay), resulting in whole‐cell biocatalysts with recombinant functionalities on their cell envelope. The efficiency of autotransporter‐mediated secretion depends on the N‐terminal signal peptide as well as on the C‐terminal translocator domain of autotransporter fusion proteins. We set out to optimize autodisplay for P. putida as the host bacterium by comparing different signal peptides and translocator domains for the surface display of an esterase. The translocator domain did not have a considerable effect on the activity of the whole‐cell catalysts. In contrast, by using the signal peptide of the P. putida outer membrane protein OprF, the activity was more than 12‐fold enhanced to 638 mU ml⁻¹ OD⁻¹ compared with the signal peptide of V. cholerae CtxB (52 mU ml⁻¹ OD⁻¹). This positive effect was confirmed with a β‐glucosidase as a second example enzyme. Here, cells expressing the protein with N‐terminal OprF signal peptide showed more than fourfold higher β‐glucosidase activity (181 mU ml⁻¹ OD⁻¹) than with the CtxB signal peptide (42 mU ml⁻¹ OD⁻¹). SDS‐PAGE and flow cytometry analyses indicated that the increased activities correlated with an increased amount of recombinant protein in the outer membrane and a higher number of enzymes detectable on the cell surface.

Purification-independent immunoreagents obtained by displaying nanobodies on bacteria surface

The availability of preimmune libraries of antibody fragments allows for the fast generation of binders which can be expressed in both eukaryotic and prokaryotic systems. We exploited the recombinant nature of antibody fragments to demonstrate the possibility of expressing them as functional proteins displayed on the surface of Escherichia coli and by such a way to generate living reagents ready-to-use for diagnostics. Such immunoreagents were effectively exploited without the necessity of any purification step to prepare immunocapture surfaces suitable for the diagnostic of both cancer cells and toxic microalgae. The same nanobody-displaying bacteria were also engineered to coexpress GFP in their cytoplasm. Suspensions of such living fluorescent immunoreagents effectively bound to eukaryotic cells making them visible and quantifiable by flow cytometry analysis and using 96-well plate readers. The collected data showed the suitability of such living immunoreagents for reproducible and inexpensive diagnostic applications.

Autotransporter-Mediated Display of a Naïve Affibody Library on the Outer Membrane of Escherichia coli

Development of new affinity proteins using combinatorial protein engineering is today established for generation of monoclonal antibodies and also essential for discovery of binders that are based on non-immunoglobulin proteins. Phage display is most frequently used, but yeast display is becoming increasingly popular, partly due to the option of utilizing fluorescence-activated cell sorting (FACS) for isolation of new candidates. Escherichia coli has several valuable properties for library applications and in particular the high transformation efficiency. The use of various autotransporters and intimins for secretion and anchoring on the outer membrane have shown promising results and particularly for directed evolution of different enzymes. Here, the authors report on display of a large naïve affibody library on the outer membrane of E. coli using the autotransporter Adhesin Involved in Diffuse Adherence (AIDA-I). The expression cassette is first engineered by removing non-essential sequences, followed by introduction of an affibody library, comprising more than 10⁹ variants, into the new display vector. The quality of the library and general performance of the method is assessed by FACS against five different targets, which resulted in a panel of binders with down to nanomolar affinities, suggesting that the method has potential as a complement to phage display for generation of affibody molecules.

Orientation and density control of proteins on solid matters by outer membrane coating: Analytical and diagnostic applications

Autodisplay is an expression system for the display of recombinant proteins on the outer membrane (OM) of gram negative bacteria and has been developed for translocation studies, whole cell biocatalysis, bioremediation, inhibitor screening, and enzyme refolding. Recently, affinity proteins such as IgG-binding Z-domains and biotin-binding streptavidin have been autodisplayed on the OM of Escherichia coli for analytical and biomedical applications. The secretion mechanism of the autodisplay system was used and orientation and density control of these affinity proteins were determined. Affinity protein-autodisplaying E. coli cells have been used to coat solid supports in immunoassays. For this purpose, the OM of autodisplayed E. coli cells was separated and isolated by the aid of detergents. The structure of the resulting OM liposomes as well as their physico-chemical parameters, were analyzed. OM liposomes were used subsequently for coating various solid matters including microplates and biosensor transducer surfaces and the formation of OM layers were monitored. OM layer formation on solid matters was shown to increase the sensitivity of immunoassays and biosensors. In this review, analytical and diagnostic applications are described in particular concerning orientation and density control of autodisplayed affinity proteins.