Enhancing the thermal tolerance and gastric performance of a microbial phytase for use as a phosphate-mobilizing monogastric-feed supplement

Improving the thermal stability of phytase using core-shell hydrogel beads

A core-shell hydrogel bead system was designed to maintain the catalytic activity of phytase and protect its enzymatic functionality from heat treatment. The designed structure consists of a chitosan-phytase complex core and an alginate-carrageenan hydrogel shell. The core-shell hydrogel was optimized to improve phytase encapsulation efficiency and increase the thermal stability of the encapsulated phytase. After heat treatment, encapsulated phytase retained ∼ 70 % of its catalytic activity and the same secondary structure of free phytase. Fourier transform infrared spectroscopy indicated strong intermolecular interactions between chitosan and phytase in the core, but little interaction between the core and the alginate and κ-carrageenan shell, this supports the structural and functional stability of the phytase. Differential scanning calorimetry confirmed that the designed core-shell structure had a higher melting point. Encapsulating phytase in a core-shell hydrogel bead can enhance the thermal stability of phytase, which broadens the potential applications for phytase delivery.

Thermally stable and acidic pH tolerant mutant phytases with high catalytic efficiency from Yersinia intermedia for potential application in feed industries

Heat- and pH-stable phytase efficiently hydrolyzes phytic acid. In this research, heat- and pH-stable mutant phytases, T⁸³R, L²⁸⁷R, and T⁸³R/L²⁸⁷R were generated by site-directed mutagenesis from Yersinia intermedia. After the induction and expression of recombinant wild-type and mutant phytases in E. coli BL21, the enzymes were purified using nickel sepharose affinity chromatography, and characterized kinetically and thermodynamically using spectroscopy methods. The mutants showed optimum activity at pH 5.15 and 55-61 °C. The catalytic efficiencies of T⁸³R, L²⁸⁷R, T⁸³R/L²⁸⁷R, and wild-type phytases were calculated to be 2941, 29346, 4906, and 6917 mmol/L^-1s^-1, respectively. Moreover, after the incubation of T⁸³R, L²⁸⁷R, wild-type, and T⁸³R/ L²⁸⁷R phytases at 100 °C for 1 h, the enzymes retained 22, 5, 4, and 2% of their initial activities, respectively. In addition, T⁸³R, T⁸³R/L²⁸⁷R, L²⁸⁷R, and wild-type phytases retained 82, 44, 16 as well as 11% of their initial activities after 1 h at pH 5.15, respectively. Among these mutants, T⁸³R mutant showed 18% increase in thermal stability, 71% increase in pH stability, and +0.103 KJ/mole increase in ΔΔG, while the catalytic efficiency and ΔΔG value of L²⁸⁷R mutant increased by 4 times and +0.0903 KJ/mole, respectively. Thus, the mutants have the potential to be used in feed industries to increase the bioavailability of minerals while decreasing soil and water pollution.

High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering

Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype–phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward.

Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma.

Dietary Phosphorus and Calcium Utilization in Growing Pigs: Requirements and Improvements

The sustainability of animal production relies on the judicious use of phosphorus (P). Phosphate, the mined source of agricultural phosphorus supplements, is a non-renewable resource, but phosphorus is essential for animal growth, health, and well-being. P must be provided by efficient and sustainable means that minimize the phosphorus footprint of livestock production by developing precise assessment of the bioavailability of dietary P using robust models. About 60% of the phosphorus in an animal's body occurs in bone at a fixed ratio with calcium (Ca) and the rest is found in muscle. The P and Ca requirements must be estimated together; they cannot be dissociated. While precise assessment of P and Ca requirements is important for animal well-being, it can also help to mitigate the environmental effects of pig farming. These strategies refer to multicriteria approaches of modeling, efficient use of the new generations of phytase, depletion and repletion strategies to prime the animal to be more efficient, and finally combining these strategies into a precision feeding model that provides daily tailored diets for individuals. The industry will need to use strategies such as these to ensure a sustainable plant–animal–soil system and an efficient P cycle.

Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris

BACKGROUND

Phytases are widely used commercially as dietary supplements for swine and poultry to increase the digestibility of phytic acid. Enzyme development has focused on increasing thermostability to withstand the high temperatures during industrial steam pelleting. Increasing thermostability often reduces activity at gut temperatures and there remains a demand for improved phyases for a growing market.

RESULTS

In this work, we present a thermostable variant of the E. coli AppA phytase, ApV1, that contains an extra non-consecutive disulfide bond. Detailed biochemical characterisation of ApV1 showed similar activity to the wild type, with no statistical differences in k_cat and K_M for phytic acid or in the pH and temperature activity optima. Yet, it retained approximately 50% activity after incubations for 20 min at 65, 75 and 85 °C compared to almost full inactivation of the wild-type enzyme. Production of ApV1 in Pichia pastoris (Komagataella phaffi) was much lower than the wild-type enzyme due to the presence of the extra non-consecutive disulfide bond. Production bottlenecks were explored using bidirectional promoters for co-expression of folding chaperones. Co-expression of protein disulfide bond isomerase (Pdi) increased production of ApV1 by ~ 12-fold compared to expression without this folding catalyst and restored yields to similar levels seen with the wild-type enzyme.

CONCLUSIONS

Overall, the results show that protein engineering for enhanced enzymatic properties like thermostability may result in folding complexity and decreased production in microbial systems. Hence parallel development of improved production strains is imperative to achieve the desirable levels of recombinant protein for industrial processes.

Generating tumor-selective conditionally active biologic anti-CTLA4 antibodies via protein-associated chemical switches

Anticytotoxic T lymphocyte-associated protein 4 (CTLA4) antibodies have shown potent antitumor activity, but systemic immune activation leads to severe immune-related adverse events, limiting clinical usage. We developed novel, conditionally active biologic (CAB) anti-CTLA4 antibodies that are active only in the acidic tumor microenvironment. In healthy tissue, this binding is reversibly inhibited by a novel mechanism using physiological chemicals as protein-associated chemical switches (PaCS). No enzymes or potentially immunogenic covalent modifications to the antibody are required for activation in the tumor. The novel anti-CTLA4 antibodies show similar efficacy in animal models compared to an analog of a marketed anti-CTLA4 biologic, but have markedly reduced toxicity in nonhuman primates (in combination with an anti-PD1 checkpoint inhibitor), indicating a widened therapeutic index (TI). The PaCS encompass mechanisms that are applicable to a wide array of antibody formats (e.g., ADC, bispecifics) and antigens. Examples shown here include antibodies to EpCAM, Her2, Nectin4, CD73, and CD3. Existing antibodies can be engineered readily to be made sensitive to PaCS, and the inhibitory activity can be optimized for each antigen's varying expression level and tissue distribution. PaCS can modulate diverse physiological molecular interactions and are applicable to various pathologic conditions, enabling differential CAB antibody activities in normal versus disease microenvironments.

Synergistic optimisation of expression, folding, and secretion improves E. coli AppA phytase production in Pichia pastoris

Background

Pichia pastoris (Komagataella phaffii) is an important platform for heterologous protein production due to its growth to high cell density and outstanding secretory capabilities. Recent developments in synthetic biology have extended the toolbox for genetic engineering of P. pastoris to improve production strains. Yet, overloading the folding and secretion capacity of the cell by over-expression of recombinant proteins is still an issue and rational design of strains is critical to achieve cost-effective industrial manufacture. Several enzymes are commercially produced in P. pastoris, with phytases being one of the biggest on the global market. Phytases are ubiquitously used as a dietary supplement for swine and poultry to increase digestibility of phytic acid, the main form of phosphorous storage in grains.

Results

Potential bottlenecks for expression of E. coli AppA phytase in P. pastoris were explored by applying bidirectional promoters (BDPs) to express AppA together with folding chaperones, disulfide bond isomerases, trafficking proteins and a cytosolic redox metabolism protein. Additionally, transcriptional studies were used to provide insights into the expression profile of BDPs. A flavoprotein encoded by ERV2 that has not been characterised in P. pastoris was used to improve the expression of the phytase, indicating its role as an alternative pathway to ERO1. Subsequent AppA production increased by 2.90-fold compared to the expression from the state of the AOX1 promoter.

Discussion

The microbial production of important industrial enzymes in recombinant systems can be improved by applying newly available molecular tools. Overall, the work presented here on the optimisation of phytase production in P. pastoris contributes to the improved understanding of recombinant protein folding and secretion in this important yeast microbial production host.

Effects of a novel E. coli phytase expressed in Pseudomonas fluorescens on growth, bone mineralization, and nutrient digestibility in pigs fed corn-soybean meal diets

Two studies were conducted to determine the effects of a novel Escherichia coli phytase expressed in Pseudomonas fluorescens on growth performance, bone mineralization, and nutrient digestibility in pigs fed corn-soybean meal diets. In experiment 1, 160 nursery pigs (9.79 ± 1.22 kg) were randomly allotted to one of four treatments with 10 pens per treatment and four pigs per pen. Phase I and phase II diets were provided from d 0 to d 14 and d 14 to d 28, respectively. Treatments included: positive control (PC) with all nutrients meeting requirements; negative control (NC) with standardized total tract digestible (STTD) P reduced by 0.15% and 0.14% compared with PC in phase I and phase II, respectively; and NC diets containing 250 or 500 units of phytase (FTU) per kilogram. Results demonstrated that pigs fed PC had greater (P < 0.01) ADG and G:F for the overall experimental period, and greater (P < 0.01) bone ash and P concentrations, compared with pigs fed NC or diets with phytase supplementation. Pigs fed diets containing phytase had greater (P < 0.01) ADG and G:F for the overall experimental period compared with pigs fed the NC diet without phytase, and bone ash and P weights were increased (P < 0.01) as well. In experiment 2, 63 growing barrows (56.25 ± 2.54 kg) were blocked by BW and randomly allotted to one of seven treatments with nine pens per treatment and one pig per pen. A basal corn–soybean meal diet was formulated to meet nutrient requirements for growing pigs with the exception that STTD P was reduced by 0.18% compared with the requirement, and Ca was included to achieve a Ca:STTD P ratio of 2.15. Six additional diets were formulated by adding 250, 500, 750, 1,000, 1,500, or 2,000 FTU/kg of phytase to the basal diet. Pigs were fed experimental diets for 12 d with 7 d of adaptation and 5 d of fecal sample collection. Results indicated that there was a linear (P < 0.01) increase in apparent total tract digestibility of ash and ether extract, and STTD of Ca and P also increased (linear, P < 0.05) in response to increasing doses of phytase. Increasing phytase levels in the diets resulted in increase (quadratic, P < 0.05) in apparent ileal digestibility of Arg, His, Ile, Lys, Trp, Asp, and Glu. In conclusion, the novel E. coli phytase was effective in increasing growth performance, bone mineralization, and Ca and P digestibility in pigs fed corn–soybean meal-based diets. Results also indicated that this phytase had the potential to enhance the digestibility of fat and certain AA.

Characterization of a thermostable phytase from Bacillus licheniformis WHU and further stabilization of the enzyme through disulfide bond engineering

Phytases are important industrial enzymes widely used as feed additives to hydrolyze phytate and release inorganic phosphate. In this study, a phytase gene PhyBL isolated from Bacillus licheniformis WHU was cloned and expressed in Escherichia coli. PhyBL showed the highest activity at pH 7.0 and retained more than 40 % of its activity at a wide temperature range from 35 to 65 °C. Ca²⁺ significantly affected the stability and activity of the enzyme. We further improved the stability of PhyBL through extensively disulfide engineering. After constructing and screening a series of variants, an enhanced stable G197C/A358C variant was obtained. The G197C/A358C variant had a half-life at 60℃ roughly 3.8-fold longer than the wild type. In addition, the G197C/A358C variant also showed enhanced proteolytic resistance to pepsin and trypsin. The potential mechanism underlying these improvements was investigated by molecular dynamics analysis. Our results suggest that the G197C/A358C variant may have potential application as an additive enzyme in aquaculture feed.

Effect of Xylanase and Phytase Supplementation on Goat's Performance in Early Lactation

BACKGROUND AND OBJECTIVES

Supplementing diets of dairy animals with phytase and xylanase can enhance phosphorus availability and fiber degradation in the rumen and positively affect animal's health and productivity. In vitro and in vivo trials have been conducted to define the optimal addition level of xylanase and phytase to lactating Baldi goat's rations and investigate effects of these enzymes on animal's nutrients digestibility, blood chemistry, milk production and milk composition.

MATERIALS AND METHODS

In vitro batch culture technique was used to evaluate the effect of phytase and xylanase supplementation at different levels (0, 1, 2 and 3 g kg-1 DM) on rumen fermentation characteristics. Eighteen early lactating Baldi goats were randomly assigned into three groups and fed 4% dry matter according to their body weight. The first group was fed control ration (35% yellow corn, 20% corn stalks, 20% berseem hay, 12.5% soybean meal and 12.5% wheat bran), the second group fed control ration+Penizyme at 2 g kg-1 DM (R1), while the third group fed control ration+Phtase-Plus® at 1 g kg-1 DM (R2).

RESULTS

Xylanase and phytase supplementation increased the in vitro DM and OM degradability and ruminal NH3-N and total volatile fatty acids (TVFA) concentrations, with no effect on total gas production (TGP) volume. All nutrients digestibility (except CP), blood serum glucose concentration, milk production and milk components yields were increased for enzymes supplemented goats than control.

CONCLUSION

Inclusion of xylanase and phytase in lactating goat's rations improved their productive performance with no deleterious effects on their health.

Mutational analysis of a catalytically important loop containing active site and substrate-binding site in Escherichia coli phytase AppA

A phytase from Escherichia coli, AppA, has been the target of protein engineering to reduce the amount of undigested phosphates from livestock manure by making phosphorous from phytic acid available as a nutrient. To understand the contribution of each amino acid in the active site loop to the AppA activity, alanine and glycine scanning mutagenesis was undertaken. The results of phytase activity assay demonstrated loss of activity by mutations at charged residues within the conserved motif, supporting their importance in catalytic activity. In contrast, both conserved, non-polar residues and non-conserved residues tended to be tolerant to Ala and/or Gly mutations. Correlation analyses of chemical/structural characteristics of each mutation site against mutant activity revealed that the loop residues located closer to the substrate have greater contribution to the activity of AppA. These results may be useful in efficiently engineering AppA to improve its catalytic activity.

Abbreviations: AppA: pH 2.5 acid phosphatase; CSU: contacts of structural units; HAPs: histidine acid phosphatases; SASA: solvent accessible surface area; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SSM: site-saturation mutagenesis; WT: wild type

Low digestibility of phytate phosphorus, their impacts on the environment, and phytase opportunity in the poultry industry

Phosphorus is an essential macro-mineral nutrient for poultry, needed for the body growth, development of bones, genomic function, good quality flesh, and eggs production. The imbalance of organic phosphorus sources in the diet mostly affect the phosphorus digestibility, reduces the poultry performance and health, and increases the environmental pollution burden. A study was reviewed to estimate the low phytate phosphorus digestibility of ingredients in poultry diet and their impacts on environmental ecosystem and opportunity of phytase supplementation. Plant ingredients mostly used in poultry diets are rich in phytate phosphorus. The phytate phosphorus digestibility and utilization is low in the gut of birds which leads to decrease other nutrients digestibility and increase excessive excretion of phosphorus with additional nutrients in the manure. When that manure applied to the lands containing excessive residual phosphorus and additional nutrients which pollute soil, groundwater disturbed the entire ecosystem. This issue is developed by poultry due to lack of digestive enzyme phytase which promotes the phytate phosphorus during digestion and reduces the excessive losses of phosphorus in excreta. To overcome this matter, the addition of mostly exogenous phospho-hydrolytic phytase enzymes in the diet, i.e. Escherichia coli, Peniophora lycii, Aspergillus niger, and Ficum, are the possible ways to increase the digestibility and utilization of phytate phosphorus and promote the stepwise release of phosphorus from phytate and significantly decrease phosphorus excretion. The aim of this review is to highlight the role of phytase supplementation in the poultry feeding, improvement of phytate phosphorus digestibility with performance, and reduction of phosphorus pollution from the environment.

Effect of phytase enzyme on growth performance, serum biochemical alteration, immune response and gene expression in Nile tilapia

The present study aimed to investigate the effect of low phosphorus diet with or without different levels of phytase enzyme supplementation on growth performance, body composition, nutrient retention efficiency, gene expression, and health status of A. hydrophila challenged fish. A total of 240 monosex males of Nile tilapia (Oreochromis niloticus) with an average body weight of 23.19 ± 0.15 g/fish were used. Fish were randomly chosen and divided into 4 equal groups (60 fish per group), with 3 subgroups containing 20 fish as a replicate. Group 1, was fed on a diet containing 100% P, group 2, was fed on a diet containing 50% P, group 3 and 4, were fed on low P with 500 or 1000 units of phytase/Kg respectively. It was observed that the 50% phosphorus diet significantly reduced body weight, feed intake, feed conversion ratio (FCR), and protein efficiency ratio (PER) compared to Nile tilapia fish fed on the diet containing 100% phosphorus. In contrast, fish fed on the diet containing 50% phosphorus supplemented by 500 or 1000 phytase units/kg significantly (P ≤ 0.05) increased final body weight (FBW), total body gain (TBG), average daily gain (ADG), and weight gain compared to Nile tilapia fed on the same diet or fed on the diet containing normal phosphorus without phytase supplementation. Different phosphorus and phytase supplementation levels had no significant effect on serum total protein, albumin, and globulin concentrations, meanwhile, phytase supplementation increased serum calcium and phosphorus levels. Nile tilapia fed on phytase supplementation had an increase in body protein, lipid content, and nutrient utilization efficiency compared to Nile tilapia fed on the diet containing 100% phosphorus. Nile tilapia fed on low dietary phosphorus showed an increase in mortality after infection and a decrease in phagocytosis and neutrophil compared to fish fed on normal phosphorus. Phytase supplementation, made immune response parameters return to its normal values and the pathological lesions of liver, spleen, stomach, and intestine were reduced. Moreover, normal phosphorus significantly up-regulated lipoprotein lipase (LPL) mRNA expression and down-regulated fatty acid synthase (FAS) mRNA in Nile tilapia's liver while low phosphorus with or without phytase supplementation reduced LPL expression and relatively up-regulated FAS.

Improved microscale cultivation of Pichia pastoris for clonal screening

Background

Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed during screenings and early phases of bioprocess development, although major drawbacks such as low oxygen transfer rates are well documented. In recent years, miniaturization and parallelization of stirred and shaken bioreactor concepts have led to the development of novel microbioreactor concepts. They combine high cultivation throughput with reproducibility and scalability, and represent promising tools for bioprocess development.

Results

Parallelized microplate cultivation of the eukaryotic protein production host Pichia pastoris was applied effectively to support miniaturized phenotyping of clonal libraries in batch as well as fed-batch mode. By tailoring a chemically defined growth medium, we show that growth conditions are scalable from microliter to 0.8 L lab-scale bioreactor batch cultivation with different carbon sources. Thus, the set-up allows for a rapid physiological comparison and preselection of promising clones based on online data and simple offline analytics. This is exemplified by screening a clonal library of P. pastoris constitutively expressing AppA phytase from Escherichia coli. The protocol was further modified to establish carbon-limited conditions by employing enzymatic substrate-release to achieve screening conditions relevant for later protein production processes in fed-batch mode.

Conclusion

The comparison of clonal rankings under batch and fed-batch-like conditions emphasizes the necessity to perform screenings under process-relevant conditions. Increased biomass and product concentrations achieved after fed-batch microscale cultivation facilitates the selection of top producers. By reducing the demand to conduct laborious and cost-intensive lab-scale bioreactor cultivations during process development, this study will contribute to an accelerated development of protein production processes.

Electronic supplementary material

The online version of this article (10.1186/s40694-018-0053-6) contains supplementary material, which is available to authorized users.

Directed Evolution of Proteins Based on Mutational Scanning

Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.

Microbial phytase: Impact of advances in genetic engineering in revolutionizing its properties and applications

Phytases are enzymes that increase the availability of phosphorous in monogastric diet and reduces the anti-nutrition effect of phytate. This review highlights contributions of recombinant technology to phytase research during the last decade with specific emphasis on new generation phytases. Application of modern molecular tools and genetic engineering have aided the discovery of novel phytase genes, facilitated its commercial production and expanded its applications. In future, by adopting most recent gene improvement techniques, more efficient next generation phytases can be developed for specific applications.

GigaMatrix™: An Ultra High-Throughput Tool for Accessing Biodiversity

Recombinant approaches for tapping into the biodiversity present in nature for the discovery of novel enzymes and biosynthetic pathways can result in large gene libraries. Likewise, laboratory evolution techniques can result in large but potentially valuable libraries. Thorough screening of these libraries requires ultra high-throughput methods. The GigaMatrix™ screening platform addresses this opportunity using reusable high-density plates with 100,000 to 1,000,000 through-hole wells in a microplate footprint. In addition to throughputs of over 107 wells per day, the platform offers a significant reduction in reagent use and waste, has fully integrated automated “cherry picking,” and uses no complicated dispensing equipment. Wells containing putative hits from targeted fluorescent liquid phase assays are revealed by a fluorescent imaging system. Vision-guided robotics are utilized to recover hits by accessing individual 200 μm and smaller wells with a disposable sterile needle. The GigaMatrix platform has proven to be an effective and efficient tool for screening gene libraries for both discovery and evolution applications.

Evaluation of increasing levels of a microbial phytase in phosphorus deficient broiler diets via live broiler performance, tibia bone ash, apparent metabolizable energy, and amino acid digestibility

The objective was to investigate increasing concentrations of an evolved microbial phytase on male broiler performance, tibia bone ash, AME, and amino acid digestibility when fed diets deficient in available phosphorus (aP). Experiment 1 evaluated the effects of phytase during a 21 d battery cage study and Experiment 2 was a 42 d grow-out. Experiment 1 included six treatments; negative control (NC) with an aP level of 0.23% (starter) and 0.19% (grower), two positive controls (PC) consisting of an additional 0.12% and 0.22% aP (PC 1 and PC 2), and the NC supplemented with three levels of phytase (250, 500, and 2,000 U/kg). The NC diet reduced (P < 0.05) FC, BW, and bone ash. Phytase increased (P < 0.05) BW with 2,000 U/kg phytase yielding similar results to the PC2, and improved FCR and increased bone ash was observed at all phytase levels. Amino acid digestibility coefficients were increased (P < 0.05) with phytase at 250 U/kg. Phytase at all rates increased (P < 0.05) AME to levels similar level as PC diets. Linear regression analysis indicated average P equivalency values for BW and bone ash of 0.137, 0.147, and 0.226 for phytase inclusion of 250, 500, and 2000 U/kg, respectively. Experiment 2 included a PC consisting of 0.45%, 0.41%, and 0.38% aP for the starter, grower, and finisher, respectively; NC with reduced aP of 0.17%; and phytase at 500 and 2,000 U/kg. Phytase increased BW (P < 0.05) compared to the NC as 2,000 U/kg phytase resulted in further BW increases compared to the PC (starter and grower). Phytase improved FCR to levels comparable to the PC, with supplementation at 2,000 U/kg resulting in improvements beyond the PC in the starter phase. Amino acid digestibility coefficients were increased with phytase at 2,000 U/kg to levels comparable to that of the PC. These data confirm that the inclusion of phytase improves broiler performance and bone mineralization in aP reduced diets and levels beyond the traditional 500 U/kg can result in further improvements.

A Novel Phytase Derived from an Acidic Peat-Soil Microbiome Showing High Stability under Acidic Plus Pepsin Conditions

Four novel phytases of the histidine acid phosphatase family were identified in two publicly available metagenomic datasets of an acidic peat-soil microbiome in northeastern Bavaria, Germany. These enzymes have low similarity to all the reported phytases. They were overexpressed in <i>Escherichia coli</i> and purified. Catalytic efficacy in simulated gastric fluid was measured and compared among the four candidates. The phytase named rPhyPt4 was selected for its high activity. It is the first phytase identified from unculturable Acidobacteria. The phytase showed a longer half-life than all the gastric-stable phytases that have been reported to date, suggesting a strong resistance to low pH and pepsin. A wide pH profile was observed between pH 1.5 and 5.0. At the optimum pH (2.5) the activity was 2,790 μmol/min/mg at the physiological temperature of 37°C and 3,989 μmol/min/mg at the optimum temperature of 60°C. Due to the competent activity level as well as the high gastric stability, the phytase could be a potential candidate for practical use in livestock and poultry feeding

Phytases from Enterobacter and Serratia species with desirable characteristics for food and feed applications

Phytases are enzymes of great industrial importance with wide range of applications in animal and human nutrition. These catalyze the hydrolysis of phosphomonoester bonds in phytate, thereby releasing lower forms of myo-inositol phosphates and inorganic phosphate. Addition of phytase to plant-based foods can improve its nutritional value and increase mineral bioavailability by decreasing nutritional effect of phytate. In the present investigation, 43 phytase positive bacteria on PSM plates were isolated from different sources and characterized for phytase activity. On the basis of phytase activity and zone of hydrolysis, two bacterial isolates (PSB-15 and PSB-45) were selected for further characterization studies, i.e., pH and temperature optima and stability, kinetic properties and effect of modulators. The phytases from both isolates were optimally active at the pH value from 3 to 8 and in the temperature range of 50-70 °C. Further, the stability of isolates was good in the pH range of 3.0-8.0. Much variation was observed in temperature and storage stability, responses of phytases to metal ions and modulators. The K m and V max values for PSB-15 phytase were 0.48 mM and 0.157 μM/min, while for PSB-45 these were 1.25 mM and 0.140 μM/min, respectively. Based on 16S rDNA gene sequence, the isolates were identified as Serratia sp. PSB-15 (GenBank Accession No. KR133277) and Enterobacter cloacae strain PSB-45 (GenBank Accession No. KR133282). The novel phytases from these isolates have multiple characteristics of high thermostability and good phytase activity at desirable range of pH and temperature for their efficient use in food and feed to facilitate hydrolysis of phytate-metal ion complex and in turn, increased bioavailability of important metal ions to monogastric animals.

Identification and characterization of a mesophilic phytase highly resilient to high-temperatures from a fungus-garden associated metagenome

Phytases are enzymes degrading phytic acid and thereby releasing inorganic phosphate. While the phytases reported to date are majorly from culturable microorganisms, the fast-growing quantity of publicly available metagenomic data generated in the last decade has enabled bioinformatic mining of phytases in numerous data mines derived from a variety of ecosystems throughout the world. In this study, we are interested in the histidine acid phosphatase (HAP) family phytases present in insect-cultivated fungus gardens. Using bioinformatic approaches, 11 putative HAP phytase genes were initially screened from 18 publicly available metagenomes of fungus gardens and were further overexpressed in Escherichia coli. One phytase from a south pine beetle fungus garden showed the highest activity and was then chosen for further study. Biochemical characterization showed that the phytase is mesophilic but possesses strong ability to withstand high temperatures. To our knowledge, it has the longest half-life time at 100 °C (27 min) and at 80 °C (2.1 h) as compared to all the thermostable phytases publicly reported to date. After 100 °C incubation for 15 min, more than 93 % of the activity was retained. The activity was 3102 μmol P/min/mg at 37 °C and 4135 μmol P/min/mg at 52.5 °C, which is higher than all the known thermostable phytases. For the high activity level demonstrated at mesophilic temperatures as well as the high resilience to high temperatures, the phytase might be promising for potential application as an additive enzyme in animal feed.

Iterative key-residues interrogation of a phytase with thermostability increasing substitutions identified in directed evolution

Bacterial phytases have attracted industrial interest as animal feed supplement due to their high activity and sufficient thermostability (required for feed pelleting). We devised an approach named KeySIDE,  an iterative Key-residues interrogation of the wild type with Substitutions Identified in Directed Evolution for improving Yersinia mollaretii phytase (Ymphytase) thermostability by combining key beneficial substitutions and elucidating their individual roles. Directed evolution yielded in a discovery of nine positions in Ymphytase and combined iteratively to identify key positions. The "best" combination (M6: T77K, Q154H, G187S, and K289Q) resulted in significantly improved thermal resistance; the residual activity improved from 35 % (wild type) to 89 % (M6) at 58 °C and 20-min incubation. Melting temperature increased by 3 °C in M6 without a loss of specific activity. Molecular dynamics simulation studies revealed reduced flexibility in the loops located next to helices (B, F, and K) which possess substitutions (Helix-B: T77K, Helix-F: G187S, and Helix-K: K289E/Q). Reduced flexibility in the loops might be caused by strengthened hydrogen bonding network (e.g., G187S and K289E/K289Q) and a salt bridge (T77K). Our results demonstrate a promising approach to design phytases in food research, and we hope that the KeySIDE might become an attractive approach for understanding of structure-function relationships of enzymes.

Performance of microbial phytases for gastric inositol phosphate degradation

Microbial phytases catalyze dephosphorylation of phytic acid, thereby potentially releasing chelated iron and improving human iron absorption from cereal-based diets. For this catalysis to take place in vivo, the phytase must be robust to low pH and proteolysis in the gastric ventricle. This study compares the robustness of five different microbial phytases, evaluating thermal stability, activity retention, and extent of dephosphorylation of phytic acid in a simulated low-pH/pepsin gastric environment and examines secondary protein structural changes at low pH via circular dichroism. The Peniophora lycii phytase was found to be the most thermostable, but the least robust enzyme in gastric conditions, whereas the Aspergillus niger and Escherichia coli phytases proved to be most resistant to gastric conditions. The phytase from Citrobacter braakii showed intermediate robustness. The extent of loss of secondary structure at low pH correlated positively with the extent of activity loss at low pH.

Hydrolysis of phytate and formation of inositol phosphate isomers without or with supplemented phytases in different segments of the digestive tract of broilers

The objective was to characterise degradation of myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (InsP₆) and formation of inositol phosphate (InsP) isomers in different segments of the broiler digestive tract. Influence of an Aspergillus niger (PhyA) and two Escherichia coli-derived (PhyE1 and PhyE2) phytases was also investigated. A total of 600 16-d-old broilers were allocated to forty floor pens (ten pens per treatment). Low-P (5·2 g/kg DM) maize–soyabean meal-based diets were fed without (basal diet; BD) or with a phytase added. On day 25, digesta from different digestive tract segments were pooled per segment on a pen-basis, freeze-dried and analysed for P, InsP isomers and the marker TiO₂. InsP₆ degradation until the lower ileum (74 %) in BD-fed birds showed a high potential of broilers and their gut microbiota to hydrolyse InsP₆ in low-P diets. Different InsP patterns in different gut segments suggested the involvement of phosphatases of different origin. Supplemented phytases increased InsP₆ hydrolysis in the crop (P < 0·01) but not in the lower ileum. Measurements in the crop and proventriculus/gizzard confirmed published in vitro degradation pathways of 3- and 6-phytases for the first time. In the intestinal segments, specifically formed InsP_4–5 isomers of supplemented phytases were still present, indicating further activity of these enzymes. Myo-inositol tetrakisphosphate (InsP₄) accumulation differed between PhyE1 and PhyE2 compared with PhyA in the anterior segments of the gut (P < 0·01). Thus, the hydrolytic cleavage of the first phosphate group is not the only limiting step in phytate degradation in broilers.

Enzymology and thermal stability of phytase appA mutants

(A) The comparison of different melting temperature (T_m) of appA (), appAM8 () and appAM10 (). TheT_mvalues were 60 °C for appA, 64.1 °C for appAM8, and 67.5 °C for appAM10. (B) Titration curves of the addition TNS to appAM10 (a) and appA (b).

In vitro engineering of microbial enzymes with multifarious applications: prospects and perspectives

The discovery of a novel enzyme from a microbial source takes anywhere between months to years, and therefore, there has been an immense interest in modifying the existing microbial enzymes to suit the present day needs of the industry. The redesigning of industrially useful enzymes for improving their performance has become a challenge because bioinformatics databases have been revealing new facts on a day-to-day basis. Modification of the existing enzymes has become a trend for fine tuning of biocatalysts in the biotech industry. Hydrolases are employed in pharmaceutical, biofuel, detergent, food and feed industries that significantly contribute to the global annual revenue, and therefore, the emphasis has been on engineering them. Although a large data is accumulating on making alterations in microbial enzymes, there is a lack of definite information on redesigning industrial enzymes. This review focuses on the recent developments in improving the characteristics of various biotechnologically important enzymes.

Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis

Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.

Phytase, a New Life for an “Old” Enzyme

Phytases are phosphohydrolytic enzymes that initiate stepwise removal of phosphate from phytate. Simple-stomached species such as swine, poultry, and fish require extrinsic phytase to digest phytate, the major form of phosphorus in plant-based feeds. Consequently, this enzyme is supplemented in these species’ diets to decrease their phosphorus excretion, and it has emerged as one of the most effective and lucrative feed additives. This chapter provides a comprehensive review of the evolving course of phytase science and technology. It gives realistic estimates of the versatile roles of phytase in animal feeding, environmental protection, rock phosphorus preservation, human nutrition and health, and industrial applications. It elaborates on new biotechnology and existing issues related to developing novel microbial phytases as well as phytase-transgenic plants and animals. And it targets critical and integrated analyses on the global impact, novel application, and future demand of phytase in promoting animal agriculture, human health, and societal sustainability.

MAP(2.0)3D: a sequence/structure based server for protein engineering

The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.

Directed evolution of a highly active Yersinia mollaretii phytase

Phytase improves as a feed supplement the nutritional quality of phytate-rich diets (e.g., cereal grains, legumes, and oilseeds) by hydrolyzing indigestible phytate (myo-inositol 1,2,3,4,5,6-hexakis dihydrogen phosphate) and increasing abdominal absorption of inorganic phosphates, minerals, and trace elements. Directed phytase evolution was reported for improving industrial relevant properties such as thermostability (pelleting process) or activity. In this study, we report the cloning, characterization, and directed evolution of the Yersinia mollaretii phytase (Ymphytase). Ymphytase has a tetrameric structure with positive cooperativity (Hill coefficient was 2.3) and a specific activity of 1,073 U/mg which is ∼10 times higher than widely used fungal phytases. High-throughput prescreening methods using filter papers or 384-well microtiter plates were developed. Precise subsequent screening for thermostable and active phytase variants was performed by combining absorbance and fluorescence-based detection system in 96-well microtiter plates. Directed evolution yielded after mutant library generation (SeSaM method) and two-step screening (in total ∼8,400 clones) a phytase variant with ∼20% improved thermostability (58°C for 20 min; residual activity wild type ∼34%; variant ∼53%) and increased melting temperature (1.5°C) with a slight loss of specific activity (993 U/mg).

Production of phytase under solid-state fermentation using Rhizopus oryzae: novel strain improvement approach and studies on purification and characterization

Present study introduces linseed oil cake as a novel substrate for phytase production by Rhizopus oryzae. Statistical approach was employed to optimize various medium components under solid state fermentation (SSF). An overall 8.41-fold increase in phytase production was achieved at the optimum concentrations (w/w, mannitol, 2.05%; ammonium sulfate, 2.84% and phosphate, 0.38%). Further enhancement by 59% was observed due to a novel strain improvement approach. Purified phytase (∼34 kDa) showed optimal temperature of 45 °C, dual pH optima at 1.5 and 5.5 and possesses high catalytic efficiency (2.38×10(6) M(-1) s(-1)). Characterization study demonstrates the phytase as highly thermostable and resistant to proteolysis, heavy metal ions, etc. Furthermore, an improved HPLC method was introduced to confirm the ability of phytase to degrade phytic acid completely and was found to be an efficient method.

OmniChange: the sequence independent method for simultaneous site-saturation of five codons

Focused mutant library generation methods have been developed to improve mainly "localizable" enzyme properties such as activity and selectivity. Current multi-site saturation methods are restricted by the gene sequence, require subsequent PCR steps and/or additional enzymatic modifications. Here we report, a multiple site saturation mutagenesis method, OmniChange, which simultaneously and efficiently saturates five independent codons. As proof of principle, five chemically cleaved DNA fragments, each carrying one NNK-degenerated codon, were generated and assembled to full gene length in a one-pot-reaction without additional PCR-amplification or use of restriction enzymes or ligases. Sequencing revealed the presence of up to 27 different codons at individual positions, corresponding to 84.4% of the theoretical diversity offered by NNK-degeneration. OmniChange is absolutely sequence independent, does not require a minimal distance between mutated codons and can be accomplished within a day.