Protein engineering of cellobiose dehydrogenase from Phanerochaete chrysosporium in yeast Saccharomyces cerevisiae InvSc1 for increased activity and stability

Protein Stability: Enhancement and Measurement

This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.

Carotenoid Biosynthesis: Genome-Wide Profiling, Pathway Identification in Rhodotorula glutinis X-20, and High-Level Production

Rhodotorula glutinis, as a member of the family Sporidiobolaceae, is of great value in the field of biotechnology. However, the evolutionary relationship of R. glutinis X-20 with Rhodosporidiobolus, Sporobolomyces, and Rhodotorula are not well understood, and its metabolic pathways such as carotenoid biosynthesis are not well resolved. Here, genome sequencing and comparative genome techniques were employed to improve the understanding of R. glutinis X-20. Phytoene desaturase (crtI) and 15-cis-phytoene synthase/lycopene beta-cyclase (crtYB), key enzymes in carotenoid pathway from R. glutinis X-20 were more efficiently expressed in S. cerevisiae INVSc1 than in S. cerevisiae CEN.PK2-1C. High yielding engineered strains were obtained by using synthetic biology technology constructing carotenoid pathway in S. cerevisiae and optimizing the precursor supply after fed-batch fermentation with palmitic acid supplementation. Genome sequencing analysis and metabolite identification has enhanced the understanding of evolutionary relationships and metabolic pathways in R. glutinis X-20, while heterologous construction of carotenoid pathway has facilitated its industrial application.

Consolidated bioprocessing of lactose into lactic acid and ethanol using non-engineered cell factories

The aim of this study is the consolidated bioprocessing of lactose into lactic acid and ethanol using non-engineered Cell Factories (CFs). Therefore, two different types of composite biocatalysts (CF1-CF2) based on Saccharomyces cerevisiae with immobilized microorganism or enzyme on starch gel (SG) were prepared for 5% w/v lactose fermentation. In CF1, S. cerevisiae was covered with SG containing Lactobacillus casei, Lactobacillus bulgaricus, Kluyveromyces marxianus CF1a-c. S. cerevisiae/SG-β-galactosidase (CF1d) was also used for simultaneous saccharification and fermentation (SSF) of lactose. In CF2, S. cerevisiae immobilized on tubular cellulose (TC) was covered with SG containing the aforementioned microorganisms (CF2a-c). The wet CF1d resulted in 96% of the theoretical ethanol yield while the wet CF1b and freeze-dried CF2b resulted in 89% of the theoretical lactic acid yield. The repeated batches using the CF2a-c exhibited better results than using CF1a-c. Subsequently, the freeze-dried CF2 as preservative and more manageable were verified for future exploitation of whey.

Cellobiose dehydrogenase in biofuel cells

Enzymatic biofuel cells utilize oxidoreductases as highly specific and highly active electrocatalysts to convert a fuel and an oxidant even in complex biological matrices like hydrolysates or physiological fluids into electric energy. The hemoflavoenzyme cellobiose dehydrogenase is investigated as a versatile bioelectrocatalyst for the anode reaction of biofuel cells, because it is robust, converts a range of different carbohydrates, and can transfer electrons to the anode by direct electron transfer or via redox mediators. The versatility of cellobiose dehydrogenase has led to the development of various electrode modifications to create biofuel cells and biosupercapacitors that are capable to power small electronic devices like biosensors and connect them wireless to a receiver.

Non-conventional expression of recombinant chitinase A originated from Bacillus licheniformis DSM8785, in Saccharomyces cerevisiae INVSc1

Chitinases are glycosyl hydrolases, that cleave the ?-1,4 linkage between N-acetyl glucosamines present in chitin chains. Chitin is the second most abundant polysaccharide on Earth after cellulose, and it is produced in the exoskeleton of crustaceans and insects, and in some parts of the cell walls of fungi. Enzymatic development and the extraction of superior derivatives from chitin wastes - such as chitooligosaccharides with vast importance in the medical and biofuels industry - lead to the necessity of creating chitinases using different strains of organisms. In this paper, the chiA gene from the Bacillus licheniformis DSM8785 encoding chitinase A (ChiA) with C-terminal hexahistidine tag was cloned and expressed in the extracellular expression system pYES2 from Saccharomyces cerevisiae INVSc1 as a hyperglycosylated enzyme. The production of recombinant ChiA was successfully confirmed by dot blotting, using anti-His antibodies. The optimal time of expression was identified to be 24 h when galactose was added only at the beginning of fermentation, the chitinase activity starting to decrease after this threshold. Nevertheless, in another experiment, when galactose was added every 24 h for 72 h, the expression continued for the entire period. The purified enzyme was detected, using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), as a heterogeneous diffuse band between 80 and 180 kDa. The molecular mass of the same ChiA enzyme expressed in Pichia pastoris KM71H and Escherichia coli BL21 (DE3) was compared using SDS-PAGE with ChiA expressed in Saccharo-myces cerevisiae INVSc1. The activity of ChiA was determined using the fluorogenic substrate, 4-methylumbelliferyl ?-D-N,N,N-triacetylchitotrioside (4MUTC). Using a bioinformatics simulation, the number of the glycolsylation sites of the chiA gene sequence and the proximity of these sites to the alpha factor sequence were hypothesized to be a possible reason for which ChiA enzyme was internally expressed.

Engineering the Turnover Stability of Cellobiose Dehydrogenase toward Long-Term Bioelectronic Applications

Cellobiose dehydrogenase (CDH) is an attractive oxidoreductase for bioelectrochemical applications. Its two-domain structure allows the flavoheme enzyme to establish direct electron transfer to biosensor and biofuel cell electrodes. Yet, the application of CDH in these devices is impeded by its limited stability under turnover conditions. In this work, we aimed to improve the turnover stability of CDH by semirational, high-throughput enzyme engineering. We screened 13 736 colonies in a 96-well plate setup for improved turnover stability and selected 11 improved variants. Measures were taken to increase the reproducibility and robustness of the screening setup, and the statistical evaluation demonstrates the validity of the procedure. The selected CDH variants were expressed in shaking flasks and characterized in detail by biochemical and electrochemical methods. Two mechanisms contributing to turnover stability were found: (i) replacement of methionine side chains prone to oxidative damage and (ii) the reduction of oxygen reactivity achieved by an improved balance of the individual reaction rates in the two CDH domains. The engineered CDH variants hold promise for the application in continuous biosensors or biofuel cells, while the deduced mechanistic insights serve as a basis for future enzyme engineering approaches addressing the turnover stability of oxidoreductases in general.

A High-Throughput Screening System Based on Fluorescence-Activated Cell Sorting for the Directed Evolution of Chitinase A

Chitinases catalyze the degradation of chitin, a polymer of N-acetylglucosamine found in crustacean shells, insect cuticles, and fungal cell walls. There is great interest in the development of improved chitinases to address the environmental burden of chitin waste from the food processing industry as well as the potential medical, agricultural, and industrial uses of partially deacetylated chitin (chitosan) and its products (chito-oligosaccharides). The depolymerization of chitin can be achieved using chemical and physical treatments, but an enzymatic process would be more environmentally friendly and more sustainable. However, chitinases are slow-acting enzymes, limiting their biotechnological exploitation, although this can be overcome by molecular evolution approaches to enhance the features required for specific applications. The two main goals of this study were the development of a high-throughput screening system for chitinase activity (which could be extrapolated to other hydrolytic enzymes), and the deployment of this new method to select improved chitinase variants. We therefore cloned and expressed the Bacillus licheniformis DSM8785 chitinase A (chiA) gene in Escherichia coli BL21 (DE3) cells and generated a mutant library by error-prone PCR. We then developed a screening method based on fluorescence-activated cell sorting (FACS) using the model substrate 4-methylumbelliferyl β-d-N,N′,N″-triacetyl chitotrioside to identify improved enzymes. We prevented cross-talk between emulsion compartments caused by the hydrophobicity of 4-methylumbelliferone, the fluorescent product of the enzymatic reaction, by incorporating cyclodextrins into the aqueous phases. We also addressed the toxicity of long-term chiA expression in E. coli by limiting the reaction time. We identified 12 mutants containing 2–8 mutations per gene resulting in up to twofold higher activity than wild-type ChiA.

Cell factory models of non-engineered S. cerevisiae containing lactase in a second layer for lactose fermentation in one batch

The objective of this project was to ferment lactose and whey to ethanol in one-step process. Models of cell factory of non-engineered S.cerevisiae have been proposed to ferment lactose. The cell factory of non-engineered S. cerevisiae/SG-lactase was prepared by the addition, of a starch gel solution containing lactase on non-engineered S. cerevisiae, and freeze drying of it. The 2-layer non engineered S.cerevisiae-TC/SG-lactase factory was prepared by immobilizing S. cerevisiae on the internal layer of tubular cellulose (TC), and the lactase enzyme was contained in the upper layer of starch gel (SG) covering cells of S. cerevisiae. Using such cell factory for the fermentation of lactose, alcohol yield of 23-32 mL/L at lactose conversion of 71-100%. The improvement in alcohol yield by cell factory versus co-immobilization of lactase enzyme and S. cerevisiae on alginates, was found in the range of 28-78%. Likewise, the cell factories are more effective than engineered S. cerevisiae. The fermentation of whey instead of lactose resulted in a significant reduction of the fermentation time. Freeze-dried cell factories led to improved results as compared with non-freeze dried. When lactase was substituted with L. casei, ethanol and lactic acid were produced simultaneously at high concentrations, but in a much longer fermentation time. The cell factories can be considered as models for white biotechnology using lactose containing raw materials. This suggested cell factory model can be applied for other bioconversions using the appropriate enzymes and cells, in the frame of White Biotechnology without genetic modification.

Semi-rational design of cellobiose dehydrogenase for increased stability in the presence of peroxide

Cellobiose dehydrogenase (CDH, EC 1.1.99.18) from white rot fungi Phanerochaete chrysosporium can be used for constructing biosensors and biofuel cells, for bleaching cotton in textile industry, and recently, the enzyme has found an important application in biomedicine as an antimicrobial and antibiofilm agent. Stability and activity of the wild-type (wt) CDH and mutants at methionine residues in the presence of hydrogen peroxide were investigated. Saturation mutagenesis libraries were made at the only methionine in heme domain M65 and two methionines M685 and M738 in the flavin domain that were closest to the active site. After screening the libraries, three mutants with increased activity and stability in the presence of peroxide were found, M65F with 70% of residual activity after 6 h of incubation in 0.3 M hydrogen peroxide, M738S with 80% of residual activity and M685Y with over 90% of residual activity compared to wild-type CDH that retained 40% of original activity. Combined mutants showed no activity. The most stable mutant M685Y with 5.8 times increased half-life in the presence of peroxide showed also 2.5 times increased k_cat for lactose compared to wtCDH and could be good candidate for applications in biofuel cells and biocatalysis for lactobionic acid production.