Modifying Thermostability of appA from Escherichia coli

High-Throughput Screening Techniques for the Selection of Thermostable Enzymes

The acquisition of a thermostable enzyme is an indispensable prerequisite for its successful implementation in industrial applications and the development of novel functionalities. Various protein engineering approaches, including rational design, semirational design, and directed evolution, have been employed to enhance thermostability. However, all of these approaches require sensitive and reliable high-throughput screening (HTS) technologies to efficiently and rapidly identify variants with improved properties. While numerous reviews focus on modification strategies for enhancing enzyme thermostability, there is a dearth of literature reviewing HTS methods specifically aimed at this objective. Herein, we present a comprehensive overview of various HTS methods utilized for modifying enzyme thermostability across different screening platforms. Additionally, we highlight significant recent examples that demonstrate the successful application of these methods. Furthermore, we address the technical challenges associated with HTS technologies used for screening thermostable enzyme variants and discuss valuable perspectives to promote further advancements in this field. This review serves as an authoritative reference source offering theoretical support for selecting appropriate screening strategies tailored to specific enzymes with the aim of improving their thermostability.

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

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.

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.

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).

A multi-factors rational design strategy for enhancing the thermostability of Escherichia coli AppA phytase

Despite recent advances in our understanding of the importance of protein surface properties for protein thermostability,there are seldom studies on multi-factors rational design strategy, so a more scientific, simple and effective rational strategy is urgent for protein engineering. Here, we first attempted to use a three-factors rational design strategy combining three common structural features, protein flexibility, protein surface, and salt bridges. Escherichia coli AppA phytase was used as a model enzyme to improve its thermostability. Moreover, the structure and enzyme features of the thermostable mutants designed by our strategy were analyzed roundly. For the single mutants, two (Q206E and Y311K), in five exhibited thermostable property with a higher success rate of prediction (40 %). For the multiple mutants, the themostable sites were combined with another site, I427L, we obtained by directed evolution, Q206E/I427L, Y311K/I427L, and Q206E/Y311K/I427L, all exhibited thermostable property. The Y311K/I427L doubled thermostability (61.7 %, and was compared to 30.97 % after being heated at 80 °C for 10 min) and catalytic efficiency (4.46 was compared to 2.37) improved more than the wild-type AppA phytase almost without hampering catalytic activity. These multi-factors of rational design strategy can be applied practically as a thermostabilization strategy instead of the conventional single-factor approach.

Relationship between Escherichia coli AppA phytase's thermostability and salt bridges

In order to study on the relationship between Escherichia coli AppA phytase's thermostability and salt bridges, and indicate an effective technical route of which factor to think about and where to modify at AppA for enhancing its thermostability, a salt bridge subtraction mutant E31Q and a salt bridge addition mutant Q307D were constructed by site-directed mutagenesis. The residual activities of the wild-type AppA phytase, E31Q and Q307D were 31.42%, 17.46%, and 40.57%, respectively, after being heated at 80°C for 10 min. The salt bridge subtraction mutant E31Q showed 13.96% thermostability decreasement, and the salt bridge addition mutant Q307D showed 9.15% thermostability enhancement than the wild-type both without the pH and temperature optimum changed. It proved salt bridges play a key role in E. coli AppA phytase's thermostability and the α/β-domain of AppA may be sensitive to heat. Salt bridges and the α/β-domain of AppA should have high priority to think about to enhance AppA's thermostability for commercial application. Besides, molecular dynamics simulation was used for salt bridges analysis.