Enhancing thermal tolerance of Aspergillus niger PhyA phytase directed by structural comparison and computational simulation

Assessment of Recombinant β-Propeller Phytase of the Bacillus Species Expressed Intracellularly in Yarrowia lipolityca

Phytases of the PhyD class according to their pH optimum (7.0-7.8) and high thermal stability can claim to be used in the production of feed supplements. However, today they have no practical application in feed production because there are no suitable producers sufficient for its biotechnological production compared to the PhyA and PhyC class ones. Moreover, in most cases, the technologies with the enzymes produced in secretory form are preferable for the production of phytases, though upon microencapsulation in yeast-producing cells, the phytase thermal stability increases significantly compared to the extracellular form, which improves its compatibility with spray drying technology. In this study, we assayed the intracellular heterologous expression of PhyD phytase from Bacillus species in the Yarrowia lipolytica yeast cells. While the technology has been successfully used to synthesize PhyC phytase from Obesumbacterium proteus, PhyD phytase tends to aggregate upon intracellular accumulation. Furthermore, we evaluated the prospects for the production of encapsulated phytase of the PhyD class of high enzymatic activity when it accumulates in the cell cytoplasm of the Y. lipolytica extremophile yeast, a highly effective platform for the production of recombinant proteins.

Structural and Functional Characterization of Obesumbacterium proteus Phytase: A Comprehensive In-Silico Study

Phytate, also known as myoinositol hexakisphosphate, exhibits anti-nutritional properties and possesses a negative environmental impact. Phytase enzymes break down phytate, showing potential in various industries, necessitating thorough biochemical and computational characterizations. The present study focuses on Obesumbacterium proteus phytase (OPP), indicating its similarities with known phytases and its potential through computational analyses. Structure, functional, and docking results shed light on OPP's features, structural stability, strong and stable interaction, and dynamic conformation, with flexible sidechains that could adapt to different temperatures or specific functions. Root Mean Square fluctuation (RMSF) highlighted fluctuating regions in OPP, indicating potential sites for stability enhancement through mutagenesis. The systematic approach developed here could aid in enhancing enzyme properties via a rational engineering approach. Computational analysis expedites enzyme discovery and engineering, complementing the traditional biochemical methods to accelerate the quest for superior enzymes for industrial applications.

Achieving thermostability of a phytase with resistance up to 100 °C

The development of enzymes with high-temperature resistance up to 100 °C is of significant and practical value in advancing the sustainability of industrial production. Phytase, a crucial enzyme in feed industrial applications, encounters challenges due to its limited heat resistance. Herein, we employed rational design strategies involving the introduction of disulfide bonds, free energy calculation, and B-factor analysis based on the crystal structure of phytase APPAmut4 (1.90 Å), a variant with enhanced expression levels derived from Yersinia intermedia, to improve its thermostability. Among the 144 variants experimentally verified, 29 exhibited significantly improved thermostability with higher t1/2 values at 65 °C. Further combination and superposition led to APPAmut9 with an accumulation of five additional pairs of disulfide bonds and six single-point mutation sites, leading to an enhancement in its thermostability with a t1/2 value of 256.7 min at 65 °C, which was more than 75-fold higher than that of APPAmut4 (3.4 min). APPAmut9 exhibited a T50 value of 96 °C, representing a substantial increase of 40.9 °C compared to APPAmut4. Notably, approximately 70% of enzyme activity remained intact after exposure to boiling water at 100 °C for a holding period of 5 min. Significantly, these advantageous modifications were strategically positioned away from the catalytic pocket where enzymatic reactions occur to ensure minimal compromise on catalytic efficiency between APPAmut9 (11,500 ± 1100/mM/s) and APPAmut4 (12,300 ± 1600/mM/s). This study demonstrates the feasibility of engineering phytases with resistance to boiling using rational design strategies.

Review on Desirable Microbial Phytases as a Poultry Feed Additive: Their Sources, Production, Enzymatic Evaluation, Market Size, and Regulation

Poultry's digestive tract lacks hydrolytic phytase enzymes, which results in chelation of dietary minerals, vital amino acids, proteins, and carbohydrates, phytate-phosphate unavailability, and contamination of the environment due to phosphorus. Therefore, it is necessary to use exogenous microbial phytases as feed additive to chicken feed to catalyze the hydrolysis of dietary phytate. Potential sources of microbial isolates that produce desired phytases for chicken feed supplementation have been isolated from agricultural croplands. It is achievable to isolate phytase-producing bacteria isolates using both broth and agar phytase screening media. Potential substrates for submerged fermentation (SmF) for bacterial phytase production and solid-state fermentation (SSF) for fungal phytase production include rice and wheat bran. Following fermentation, saturated ammonium sulphate precipitation is typically used to partially purify microbial culture filtrate. The precipitate is then desalted. Measurements of the pH optimum and stability, temperature optimum and stability, metal ions stability, specificity and affinity to target substrate, proteolysis resistance, storage stability, and in vitro feed dephosphorylation are used to perform an enzymatic evaluation of phytase as an additive for poultry feed. The growth of the feed phytase market is primarily due to the expansion of chicken farms to meet the demand for meat and eggs from humans. The Food and Drug Administration in the USA and the European Food and Safety Authority are primarily in charge of putting rules pertaining to feed phytase use in chicken feed into effect. Conclusively, important components of the production of phytase additives for poultry feed include identifying a reliable source for potential microbe isolation, selecting an economical method of phytase production, thoroughly characterizing the biochemical properties of phytase, and comprehending the size and regulation of the current feed phytase market.

Powerful cell wall biomass degradation enzymatic system from saprotrophic Aspergillus fumigatus

Cell wall biomass, Earth's most abundant natural resource, holds significant potential for sustainable biofuel production. Composed of cellulose, hemicellulose, lignin, pectin, and other polymers, the plant cell wall provides essential structural support to diverse organisms in nature. In contrast, non-plant species like insects, crustaceans, and fungi rely on chitin as their primary structural polysaccharide. The saprophytic fungus Aspergillus fumigatus has been widely recognized for its adaptability to various environmental conditions. It achieves this by secreting different cell wall biomass degradation enzymes to obtain essential nutrients. This review compiles a comprehensive collection of cell wall degradation enzymes derived from A. fumigatus, including cellulases, hemicellulases, various chitin degradation enzymes, and other polymer degradation enzymes. Notably, these enzymes exhibit biochemical characteristics such as temperature tolerance or acid adaptability, indicating their potential applications across a spectrum of industries.

Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification

Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.

Bioinformatic Studies, Experimental Validation of Phytase Production and Optimization of Fermentation Conditions for Enhancing Phytase Enzyme Production by Different Microorganisms under Solid-State Fermentation

Background:

Phytase is an essential enzyme necessary for the digestive process. It is a natural enzyme found in plant materials. It prevents bad effect of phytic acid on protein and energy utilization. Phytase frees the bound minerals such as phosphorus, calcium, zinc, iron, magnesium and manganese from the phytic acid molecule providing essential minerals available for healthy nutrition. This study depends on converting food processing waste into highly valuable products. Optimizing the fermentation conditions for enhancing high phytase production with low cost was the objective of this research.

Methods:

A bibliographical survey was carried out to select the most fungul producers of phytase from fungal species deposited in NCBI database. Phytases of the selected organisms were analyzed in the UNIPROT database and their protein sequences were submitted to multiple sequence alignments using Clustal Omega and visualized using Jalview program. Experimental studies using five fungal strains of Aspergillus.ssp on wheat bran under Solid-State Fermentation carried out. Comparisons were made for phytase production. A. awamori NRC- F18 as the best phytase producer-strain cultured on different types of treated wastes followed by optimizing the fermentation conditions for enhancing phytase production using rice straw as the best substrate, which provides the highest phytase production. Thermostability of crude enzyme was studied. Statistical analyses were performed using SPSS at P < 0.05 or P < 0.01.

Results:

Bioinformatic studies predicted the most producer species and explained the difference in activity of phytases produced from different species, although they have the same function. All phytases of the selected fungal species from the database NCBI have highly conserved amino acid sequences; there are 88 identical positions; 135 similar positions, but the identity percentage was 16.858%. Experimental studies using five fungal strains of Aspergillus ssp. on wheat bran revealed optimum conditions for phytase production by A. awamori NRC- F18, which cultured on different types of treated wastes. A considerably higher phytase production was obtained using rice straw as substrate 424.66± 2.92 IU /g at pH 6 (371.883± 0.822 IU /g), after 144 hrs of incubation at 30°C. The maximum enzyme activity observed when solid: moisture was 1:4; Inoculum concentration 2mg/5g (418.363± 16.709 IU /g) and substrate concentration 4.5% (277.39± 12.05 IU /g). Glucose and Ammonium acetate were the best carbon and nitrogen sources that enhanced phytase production from A. awamori NRC- F18. The obtained phytase was found to be thermostable and the maximum temperature at which phytase still active was 80°C.

Conclusion:

Bioinformatic studies predicted the most producer species. Experimental study revealed that A.awamori NRC- F18 was the best Phytase -producer strain. Solid state fermentation was a good method; pretreatment of agriculture residues as rice straw was useful for less expensive phytase production, which was thermostable. A. awamori NRC- F18 can be used in the industrial production of phytase.

Conditioning of Feed Material Prior to Feeding: Approaches for a Sustainable Phosphorus Utilization

A circular phosphorus (P) bioeconomy is not only worthwhile for conserving limited mineral P reservoirs, but also for minimizing negative environmental impacts caused by human-made alterations. Although P is an essential nutrient, most of the P in concentrates based on cereals, legumes and oilseed byproducts is organically bound to phytate. The latter cannot be efficiently utilized by monogastric animals and is therefore diluted into the environment through the manure pathway. This review examines various strategies for improved P utilization in animals and reflects the respective limitations. The strategies considered include feeding of debranned feedstuffs, pre-germinated feed, co-feeding of phytase and feeding material with high native phytase activity. All these approaches contribute to an improved P bioavailability. However, about half of the organic P content continues to be excreted and therefore remains unused by the animals. Nevertheless, technologies for an efficient utilization of P from cereal-based feed already exist; however, these are not industrially established. Conditioning feed material prior to feeding fosters P-reduced feed; meanwhile, P bound to phytate can be recovered. Based on known techniques for P separation and solubilisation from cereal products and phytate conversion, potential designs for feed material conditioning processes are proposed and evaluated.

Fungal phytases: from genes to applications

Phytic acid stores 60-90% of the inorganic phosphorus in legumes, oil seeds, and cereals, making it inaccessible for metabolic processes in living systems. In addition, given its negative charge, phytic acid complexes with divalent cations, starch, and proteins. Inorganic phosphorous can be released from phytic acid upon the action of phytases. Phytases are phosphatases produced by animals, plants, and microorganisms, notably Aspergillus niger, and are employed as animal feed additive, in chemical industry and for ethanol production. Given the industrial relevance of phytases produced by filamentous fungi, this work discusses the functional characterization of fungal phytase-coding genes/proteins, highlighting the physicochemical parameters that govern the enzymatic activity, the development of phytase super-producing strains, and key features for industrial applications.

Integrative Structural and Computational Biology of Phytases for the Animal Feed Industry

Resistance to high temperature, acidic pH and proteolytic degradation during the pelleting process and in the digestive tract are important features of phytases as animal feed. The integration of insights from structural and in silico analyses into factors affecting thermostability, acid stability, proteolytic stability, catalytic efficiency and specific activity, as well as N-glycosylation, could improve the limitations of marginal stable biocatalysts with trade-offs between stability and activity. Synergistic mutations give additional benefits to single substitutions. Rigidifying the flexible loops or inter-molecular interactions by reinforcing non-bonded interactions or disulfide bonds, based on structural and roof mean square fluctuation (RMSF) analyses, are contributing factors to thermostability. Acid stability is normally achieved by targeting the vicinity residue at the active site or at the neighboring active site loop or the pocket edge adjacent to the active site. Extending the positively charged surface, altering protease cleavage sites and reducing the affinity of protease towards phytase are among the reported contributing factors to improving proteolytic stability. Remodeling the active site and removing steric hindrance could enhance phytase activity. N-glycosylation conferred improved thermostability, proteases degradation and pH activity. Hence, the integration of structural and computational biology paves the way to phytase tailoring to overcome the limitations of marginally stable phytases to be used in animal feeds.

Transcriptomic Analysis of Pichia pastoris (Komagataella phaffii) GS115 During Heterologous Protein Production Using a High-Cell-Density Fed-Batch Cultivation Strategy

Pichia pastoris (Komagataella phaffii) is a methylotrophic yeast that is widely used in industry as a host system for heterologous protein expression. Heterologous gene expression is typically facilitated by strongly inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters. However, protein production is usually accomplished by a fed-batch induction process, which is known to negatively affect cell physiology, resulting in limited protein yields and quality. To assess how yields of exogenous proteins can be increased and to further understand the physiological response of P. pastoris to the carbon conversion of glycerol and methanol, as well as the continuous induction of methanol, we analyzed recombinant protein production in a 10,000-L fed-batch culture. Furthermore, we investigated gene expression during the yeast cell culture phase, glycerol feed phase, glycerol-methanol mixture feed (GM) phase, and at different time points following methanol induction using RNA-Seq. We report that the addition of the GM phase may help to alleviate the adverse effects of methanol addition (alone) on P. pastoris cells. Secondly, enhanced upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway was observed in P. pastoris following methanol induction. The MAPK signaling pathway may be related to P. pastoris cell growth and may regulate the alcohol oxidase1 (AOX1) promoter via regulatory factors activated by methanol-mediated stimulation. Thirdly, the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways were not significantly upregulated during the methanol induction period. These results imply that the presence of unfolded or misfolded phytase protein did not represent a serious problem in our study. Finally, the upregulation of the autophagy pathway during the methanol induction phase may be related to the degradation of damaged peroxisomes but not to the production of phytase. This work describes the metabolic characteristics of P. pastoris during heterologous protein production under high-cell-density fed-batch cultivation. We believe that the results of this study will aid further in-depth studies of P. pastoris heterologous protein expression, regulation, and secretory mechanisms.

Multivariate Information Fusion With Fast Kernel Learning to Kernel Ridge Regression in Predicting LncRNA-Protein Interactions

Long non-coding RNAs (lncRNAs) constitute a large class of transcribed RNA molecules. They have a characteristic length of more than 200 nucleotides which do not encode proteins. They play an important role in regulating gene expression by interacting with the homologous RNA-binding proteins. Due to the laborious and time-consuming nature of wet experimental methods, more researchers should pay great attention to computational approaches for the prediction of lncRNA-protein interaction (LPI). An in-depth literature review in the state-of-the-art in silico investigations, leads to the conclusion that there is still room for improving the accuracy and velocity. This paper propose a novel method for identifying LPI by employing Kernel Ridge Regression, based on Fast Kernel Learning (LPI-FKLKRR). This approach, uses four distinct similarity measures for lncRNA and protein space, respectively. It is remarkable, that we extract Gene Ontology (GO) with proteins, in order to improve the quality of information in protein space. The process of heterogeneous kernels integration, applies Fast Kernel Learning (FastKL) to deal with weight optimization. The extrapolation model is obtained by gaining the ultimate prediction associations, after using Kernel Ridge Regression (KRR). Experimental outcomes show that the ability of modeling with LPI-FKLKRR has extraordinary performance compared with LPI prediction schemes. On benchmark dataset, it has been observed that the best Area Under Precision Recall Curve (AUPR) of 0.6950 is obtained by our proposed model LPI-FKLKRR, which outperforms the integrated LPLNP (AUPR: 0.4584), RWR (AUPR: 0.2827), CF (AUPR: 0.2357), LPIHN (AUPR: 0.2299), and LPBNI (AUPR: 0.3302). Also, combined with the experimental results of a case study on a novel dataset, it is anticipated that LPI-FKLKRR will be a useful tool for LPI prediction.

Expression and Biochemical Characterization of a Yersinia intermedia Phytase Expressed in Escherichia coli

BACKGROUND

Phytases are enzymes capable of degrading phytic acid and used in animal feed supplementation in order to improve digestibility through the release of minerals such as phosphorus.

OBJECTIVE

The main goal of this study was to express and characterize a Yersinia intermedia phytase expressed in Escherichia coli cells.

METHODS

The Y. intermedia phytase gene was synthesized and overexpressed in Escherichia coli cells. The phytase recombinante (rPHY) was purified to homogeneity using a Ni-NTA column. The biochemical and biophysical properties of the rPHY were measured in order to fully characterize the recombinant enzyme. The following patents database were consulted: Espacenet, USPTO, LATIPAT, Patent Scope, WIPO and Google Patents.

RESULTS

The results showed that the rPHY is active at 37-40ºC and presented an optimal pH and temperature of 8.0 and 40°C, respectively. The phytase rPHY was activated by Cu2+ ion and showed resistance to trypsin and pepsin, retaining 55% of the activity at the ratio of 0.02. Furthermore, the dissociation constant (Kd = 1.1150 ± 0.0087 mM), as estimated by a fluorescence binding assay, suggests a medium affinity of the enzyme with the substrate.

CONCLUSION

The results of this article can be considered as innovative and for this reason, they were protected by Intellectual Property Law in Brazil. Take together, the biochemical properties of the rPHY could be useful in future for its industrial application of this enzyme as an additive in the monogastric feed.