Fusion of an oligopeptide to the N terminus of an alkaline α-amylase from Alkalimonas amylolytica simultaneously improves the enzyme's catalytic efficiency, thermal stability, and resistance to oxidation

The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents

Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.

Modification of Flexible Regions for Enhanced Thermal Stability of Alkaline Amylase

Alkali-stable amylases offer potential for integrating textile desizing and scouring processes. To meet industrial requirements, molecular engineering strategies were employed to enhance oxidative stability and catalytic efficiency of alkaline amylase. In this study, alkali-stable amylase Amy I from Bacillus halodurans was engineered by modifying multiple highly flexible regions. The sequential truncation of HFR I's N-terminal 40 residues yielded mutant T-40 with 77% higher residual activity than Amy I after incubation at 70 °C for 1 h. Saturation mutagenesis of HFR II/III generated mutant M4, showing 38.9% activity enhancement. CBM-25 substitution in HFR IV further increased activity by 7%. Finally, the integrated mutant Amy I-ML demonstrated exceptional performance with 14.5-fold higher specific activity and 29.6-fold extended half-life (29.4 min at 100 °C) compared to wild-type Amy I. These engineered features-combining thermostability reinforcement with catalytic optimization-establish Amy I-ML as a promising biocatalyst for industrial textile processing. The multiregion engineering approach provided a strategic framework for developing robust industrial enzymes through rational flexibility modulation.

Biochemical characterization and molecular modification of a zearalenone hydrolyzing enzyme Zhd11D from Phialophora attinorum

ZEN lactone hydrolase (ZHD) can hydrolyze zearalenone (ZEN) to less or non-toxic product, providing an environment-friendly way for food or feeds-containing ZENs detoxification. Here, a newly identified ZHD from Phialophora attinorum, annotated as Zhd11D, was characterized to exhibit highest activity against ZEN at pH 8.0 and 35 ℃ with a specific activity of 304.7 U/mg, which was far higher than most of the reported ZHDs. A nonspecific protein engineering method was introduced through fusing a segment of amphiphilic short peptide S1 at the N-terminus of Zhd11D, resulting in both improved activity (1.5-fold) and thermostability (2-fold at 40 ℃). Biochemical analysis demonstrated that self-aggregation caused by intermolecular interactions between S1 contributed to the improvement of the enzymatic properties of Zhd11D. Additionally, S1-Zhd11D showed a higher hydrolysis rate of ZEN than Zhd11D in peanut oil.

Fusion of Oligopeptide to the C Terminus of α-Glucuronidase from Thermotoga maritima Improves the Catalytic Efficiency for Hemicellulose Biotransformation

Fusion protein combined the oligopeptide (HQAFFHA) with the C terminus of α-glucuronidase from Thermotoga maritima was produced in E. coli and purified for characterization and applications of glucuronic and glucaric acid production. The fusion protein with oligopeptide exhibited a 2.97-fold higher specific activity than individual protein. Their catalytic efficiency k_cat/K_m and k_cat increased from 469.3 ± 2.6 s^-1 (g mL^-1)^-1 and 62.4 ± 0.9 s^-1 to 2209.5 ± 26.3 s^-1 (g mL^-1)^-1 and 293.9 ± 4.9 s^-1, respectively. Fusion protein had similar temperature and pH profiles to those without oligopeptide, but the thermal stability decreases and the pH stability shifts to alkaline. Using beech xylan hydrolysate as a substrate, the glucuronic acid yield of fusion enzyme increased by 9.94% compared with its parent at 65 °C pH 8.5 for 10 h, and can hydrolyze corn cob xylan with xylanase to obtain glucuronic acid, and can be combined with uronate dehydrogenase to obtain high-added value glucaric acid. Homologous modeling analysis revealed the factors contributing to the high catalytic efficiency of fusion enzyme. These results show that the peptide fusion strategy described here may be useful for improving the catalytic efficiency and stability of other industrial enzymes, and has great potential for producing high value-added products from agricultural waste.

Enhancing heterologous expression of a key enzyme for the biosynthesis of 2'-fucosyllactose

BACKGROUND

2'-Fucosyllactose (2'-FL) is the most abundant human milk oligosaccharide (HMO) in human milk and has important physiological functions. The market demand of 2'-FL is continuing to grow, but high production cost has limited its availability. To solve the dilemma, biosynthesis of 2'-FL has been proposed and is considered the most promising pathway for massive production. α-1,2-Fucosyltransferase is one of the key elements involved in its biosynthesis, but the limited intracellular accumulation and unstable properties of α-1,2-fucosyltransferases when expressed in host strains have become a major hurdle for the effective biosynthesis of 2'-FL.

RESULTS

A combinatorial engineering strategy of synergic modification of ribosome binding site, fusion peptide and enzyme gene was leveraged to enhance the soluble expression of α-1,2-fucosyltransferases and promote enzyme activity. The preferable combination was to employ an optimized ribosome binding site region to drive 3 × FLAG as a fusion partner along with the α-1,2-fucosyltransferase for expression in Escherichia coli (DE3) PlySs, and protein yield and enzyme activity were remarkably improved by 11.51-fold and 13.72-fold, respectively.

CONCLUSION

After finely tuning the synergy among different elements, the abundant protein yield and high enzyme activity confirmed that the drawbacks of heterologous expression in α-1,2-fucosyltransferase had been properly addressed. A suitable external environment further drives the efficient synthesis of α-1,2-fucosyltransferases. To our knowledge, this is the first report of a systematic and effective modification of α-1,2-fucosyltransferase expression, which could potentially serve as a guideline for industrial application. © 2022 Society of Chemical Industry.

Native to designed: microbial -amylases for industrial applications

Background

-amylases catalyze the endo-hydrolysis of -1,4-D-glycosidic bonds in starch into smaller moieties. While industrial processes are usually performed at harsh conditions, -amylases from mainly the bacteria, fungi and yeasts are preferred for their stabilities (thermal, pH and oxidative) and specificities (substrate and product). Microbial -amylases can be purified and characterized for industrial applications. While exploring novel enzymes with these properties in the nature is time-costly, the advancements in protein engineering techniques including rational design, directed evolution and others have privileged their modifications to exhibit industrially ideal traits. However, the commentary on the strategies and preferably mutated residues are lacking, hindering the design of new mutants especially for enhanced substrate specificity and oxidative stability. Thus, our review ensures wider accessibility of the previously reported experimental findings to facilitate the future engineering work.

Survey methodology and objectives

A traditional review approach was taken to focus on the engineering of microbial -amylases to enhance industrially favoured characteristics. The action mechanisms of - and -amylases were compared to avoid any bias in the research background. This review aimed to discuss the advances in modifying microbial -amylases via protein engineering to achieve longer half-life in high temperature, improved resistance (acidic, alkaline and oxidative) and enhanced specificities (substrate and product). Captivating results were discussed in depth, including the extended half-life at 100C, pH 3.5 and 10, 1.8 M hydrogen peroxide as well as enhanced substrate (65.3%) and product (42.4%) specificities. These shed light to the future microbial -amylase engineering in achieving paramount biochemical traits ameliorations to apt in the industries.

Conclusions

Microbial -amylases can be tailored for specific industrial applications through protein engineering (rational design and directed evolution). While the critical mutation points are dependent on respective enzymes, formation of disulfide bridge between cysteine residues after mutations is crucial for elevated thermostability. Amino acids conversion to basic residues was reported for enhanced acidic resistance while hydrophobic interaction resulted from mutated hydrophobic residues in carbohydrate-binding module or surface-binding sites is pivotal for improved substrate specificity. Substitution of oxidation-prone methionine residues with non-polar residues increases the enzyme oxidative stability. Hence, this review provides conceptual advances for the future microbial -amylases designs to exhibit industrially significant characteristics. However, more attention is needed to enhance substrate specificity and oxidative stability since they are least reported.

Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology

Biocatalysts have wider applications in various industries. Biocatalysts are generating bigger attention among researchers due to their unique catalytic properties like activity, specificity and stability. However the industrial use of many enzymes is hindered by low catalytic efficiency and stability during industrial processes. Properties of enzymes can be altered by protein engineering. Protein engineers are increasingly study the structure-function characteristics, engineering attributes, design of computational tools for enzyme engineering, and functional screening processes to improve the design and applications of enzymes. The potent and innovative techniques of enzyme engineering deliver outstanding opportunities for tailoring industrially important enzymes for the versatile production of biochemicals. An overview of the current trends in enzyme engineering is explored with important representative examples.

An efficient expression tag library based on self-assembling amphipathic peptides

Background

Self-assembling amphipathic peptides (SAPs) may improve protein production or induce the formation of inclusion bodies by fusing them to the N-terminus of proteins. However, they do not function uniformly well with all target enzymes and systematic research on how the composition of SAPs influence the production of fusion protein is still limited.

Results

To improve the efficiency of SAPs, we studied factors that might be involved in SAP-mediated protein production using S1 (AEAEAKAK)₂ as the original SAP and green fluorescent protein (GFP) as the reporter. The results indicate that hydrophobicity and net charges of SAPs play a key role in protein expression. As hydrophobicity regulation tend to cause the formation of insoluble inclusion bodies of protein, an expression tag library composed of SAPs, which varied in net charge (from + 1 to + 20), was constructed based on the random amplification of S1nv1 (ANANARAR)₁₀. The efficiency of the library was validated by polygalacturonate lyase (PGL), lipoxygenase (LOX), l-asparaginase (ASN) and transglutaminase (MTG). To accelerate preliminary screening, each enzyme was fused at the C-terminus with GFP. Among the four enzyme fusions, the SAPs with + 2 – + 6 net charges were optimal for protein expression. Finally, application of the library improved the expression of PGL, LOX, ASN, and MTG by 8.3, 3.5, 2.64, and 3.68-fold relative to that of the corresponding wild-type enzyme, respectively.

Conclusions

This is the first report to study key factors of SAPs as an expression tag to enhance recombinant enzyme production. The SAP library could be used as a novel plug-and-play protein-engineering method to screen for enzymes or proteins with enhanced production.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1142-9) contains supplementary material, which is available to authorized users.

Combinatorial pathway enzyme engineering and host engineering overcomes pyruvate overflow and enhances overproduction of N-acetylglucosamine in Bacillus subtilis

BACKGROUND

Glucosamine-6-phosphate N-acetyltransferase (GNA1) is the key enzyme that causes overproduction of N-acetylglucosamine in Bacillus subtilis. Previously, we increased GlcNAc production by promoting the expression of GNA1 from Caenorhabditis elegans (CeGNA1) in an engineered B. subtilis strain BSGN12. In this strain overflow metabolism to by-products acetoin and acetate had been blocked by mutations, however pyruvate accumulated as an overflow metabolite. Although overexpression of CeGNA1 drove carbon flux from pyruvate to the GlcNAc synthesis pathway and decreased pyruvate accumulation, the residual pyruvate reduced the intracellular pH, resulting in inhibited CeGNA1 activity and limited GlcNAc production.

RESULTS

In this study, we attempted to further overcome pyruvate overflow by enzyme engineering and host engineering for enhanced GlcNAc production. To this end, the key enzyme CeGNA1 was evolved through error-prone PCR under pyruvate stress to enhance its catalytic activity. Then, the urease from Bacillus paralicheniformis was expressed intracellularly to neutralize the intracellular pH, making it more robust in growth and more efficient in GlcNAc production. It was found that the activity of mutant CeGNA1 increased by 11.5% at pH 6.5-7.5, with the catalytic efficiency increasing by 27.5% to 1.25 s^-1 µM^-1. Modulated expression of urease increased the intracellular pH from 6.0 to 6.8. The final engineered strain BSGN13 overcame pyruvate overflow, produced 25.6 g/L GlcNAc with a yield of 0.43 g GlcNAc/g glucose in a shake flask fermentation and produced 82.5 g/L GlcNAc with a yield of 0.39 g GlcNAc/g glucose by fed-batch fermentation, which was 1.7- and 1.2-times, respectively, of the yield achieved previously.

CONCLUSIONS

This study highlights a strategy that combines pathway enzyme engineering and host engineering to resolve overflow metabolism in B. subtilis for the overproduction of GlcNAc. By means of modulated expression of urease reduced pyruvate burden, conferred bacterial survival fitness, and enhanced GlcNAc production, all of which improved our understanding of co-regulation of cell growth and metabolism to construct more efficient B. subtilis cell factories.

Enzymatic characterization of a soluble aggregate induced by N-terminal extension to a lipolytic enzyme

A self-assembling peptide (27PEP) was isolated from an open reading frame (ORF). The ORF consisted of an unknown functional domain and a catalytic (lipolytic and phospholipolytic) domain (MPlaG) on metagenomic fosmid clone. This extension of 27 amino acids prior to the N-terminus of the catalytic domain (27PEP-MPlaG), starting at Met₂₆₁, produced an aggregate of high molecular weight (> 700 kDa). Compared with MPlaG, 27PEP-MPlaG showed the same temperature and pH effect for maximum activity but was stable in the presence of inhibitors such as EDTA and PMSF. The 27PEP-MPlaG exhibited lower specific activity than that of MPlaG, but when pre-incubated for 30 min at temperatures between 4 and 100 °C, its activity increased at temperatures greater than 40 °C under alkaline conditions and eventually reached the specific activity level of MPlaG at 60 °C. We experimentally determined that the aggregate caused by 27PEP was dissociated at elevated temperatures resulting in an active catalytic monomer. The 27PEP-indued aggregation may be attractive as application tool for improving or engineering of biocatalysts and biomaterials.

Efficient production of d-amino acid oxidase in Escherichia coli by a trade-off between its expression and biomass using N-terminal modification

Native d-amino acid oxidase (DAAO) that is expressed mostly as inclusion body and its toxicity for E. coli hamper efficient heterologous expression. In this study, the soluble expression of DAAO from Rhodosporidium toruloides (RtDAAO) was improved in E. coli through N-terminal modification, but the cell biomass was decreased. Then a trade-off between DAAO expression and biomass was achieved to obtain the highest volumetric activity of DAAO through regulated the number of N-terminus histidine residues. When variant ²H³G was fused with three N-terminus histidine residues, the volumetric activity was increased by 3.1 times and the biomass was not significant change compared with the wild type. Finally, the N-terminus disordered region of RtDAAO (HSQK) was replaced with HHHG and the variant enzyme activity reached 80.7U/mL (with a 40 percent of inactive DAAO reduced) in a 7.5L fermenter in 24h.

Oligomerization triggered by foldon: a simple method to enhance the catalytic efficiency of lichenase and xylanase

BACKGROUND

Effective and simple methods that lead to higher enzymatic efficiencies are highly sough. Here we proposed a foldon-triggered trimerization of the target enzymes with significantly improved catalytic performances by fusing a foldon domain at the C-terminus of the enzymes via elastin-like polypeptides (ELPs). The foldon domain comprises 27 residues and can forms trimers with high stability.

RESULTS

Lichenase and xylanase can hydrolyze lichenan and xylan to produce value added products and biofuels, and they have great potentials as biotechnological tools in various industrial applications. We took them as the examples and compared the kinetic parameters of the engineered trimeric enzymes to those of the monomeric and wild type ones. When compared with the monomeric ones, the catalytic efficiency (k _cat /K _m ) of the trimeric lichenase and xylanase increased 4.2- and 3.9- fold. The catalytic constant (k _cat ) of the trimeric lichenase and xylanase increased 1.8- fold and 5.0- fold than their corresponding wild-type counterparts. Also, the specific activities of trimeric lichenase and xylanase increased by 149% and 94% than those of the monomeric ones. Besides, the recovery of the lichenase and xylanase activities increased by 12.4% and 6.1% during the purification process using ELPs as the non-chromatographic tag. The possible reason is the foldon domain can reduce the transition temperature of the ELPs.

CONCLUSION

The trimeric lichenase and xylanase induced by foldon have advantages in the catalytic performances. Besides, they were easier to purify with increased purification fold and decreased the loss of activities compared to their corresponding monomeric ones. Trimerizing of the target enzymes triggered by the foldon domain could improve their activities and facilitate the purification, which represents a simple and effective enzyme-engineering tool. It should have exciting potentials both in industrial and laboratory scales.

The promises and challenges of fusion constructs in protein biochemistry and enzymology

Fusion constructs are used to improve the properties of or impart novel functionality to proteins for biotechnological applications. The biochemical characteristics of enzymes or functional proteins optimized by fusion include catalytic efficiency, stability, activity, expression, secretion, and solubility. In this review, we summarize the parameters of enzymes or functional proteins that can be modified by fusion constructs. For each parameter, fusion strategies and molecular partners are examined using examples from recent studies. Future prospects in this field are also discussed. This review is expected to increase interest in and advance fusion strategies for optimization of enzymes and other functional proteins.

Improvement of proteolytic and oxidative stability of Chondroitinase ABC I by cosolvents

Recently, utilization of the enzyme Chondroitinase ABC I (cABC I) has received considerable attention in treatment of spinal cord injury. cABC I removes chondroitin sulfate proteoglycans which are inhibitory to axon growth and enhances nerve regeneration. Therefore, determination of cABC I resistance to proteolysis and oxidation provides valuable information for optimizing its clinical application. In this work, proteolytic stability of cABC I to trypsin and chymotrypsin as well as its oxidative resistance to H2O2 was measured. Moreover, the effect of cosolvents glycerol, sorbitol and trehalose on cABC I proteolytic and oxidative stability was determined. The results indicated that cABC I is highly susceptible to proteolysis and oxidation. Comparison of proteolytic patterns demonstrated a high degree of similarity which confirmed the exposure of specific regions of cABC I to proteolysis. However, proteolytic degradation was significantly reduced in the presence of cosolvents. In addition, cosolvents decreased the rate of both cABC I proteolytic and oxidative inactivation. Notably, the degree of stabilization provided by these cosolvents varied greatly. These findings indicated the high potential of cosolvents in protein stabilization to proteolysis and oxidative inactivation.

Improving the thermostability and stress tolerance of an archaeon hyperthermophilic superoxide dismutase by fusion with a unique N-terminal domain

The superoxide dismutase from the archaeon Sulfolobus solfataricus (SOD Ss ) is a well-studied hyperthermophilic SOD with crystal structure and possible thermostability factors characterized. Previously, we discovered an N-terminal domain (NTD) in a thermophilic SOD from Geobacillus thermodenitrificans NG80-2 which confers heat resistance on homologous mesophilic SODs. The present study therefore aimed to further improve the thermostability and stress tolerance of SOD Ss via fusion with this NTD. The recombinant protein, rSOD Ss , exhibited improved thermophilicity, higher working temperature, improved thermostability, broader pH stability, and enhanced tolerance to inhibitors and organic media than SOD Ss without any alterations in its oligomerization state. These results suggest that the NTD is an excellent candidate for improving stability of both mesophilic and thermophilic SOD from either bacteria or archaea via simple genetic manipulation. Therefore, this study provides a general, feasible and highly useful strategy for generating extremely thermostable SODs for industrial applications.

Fusion of self-assembling amphipathic oligopeptides with cyclodextrin glycosyltransferase improves 2-O-D-glucopyranosyl-L-ascorbic acid synthesis with soluble starch as the glycosyl donor

In this study, we fused six self-assembling amphipathic peptides (SAPs) with cyclodextrin glycosyltransferase (CGTase) from Paenibacillus macerans to catalyze 2-O-D-glucopyranosyl-L-ascorbic acid (AA-2G) production with cheap substrates, including maltose, maltodextrin, and soluble starch as glycosyl donors. The results showed that two fusion enzymes, SAP5-CGTase and SAP6-CGTase, increased AA-2G yields to 2.33- and 3.36-fold that of wild-type CGTase when soluble starch was used as a substrate. The cyclization activities of these enzymes decreased, while disproportionation activities increased. Enzymatic characterization of the two fusion enzymes was performed, and kinetics analysis of AA-2G synthesis confirmed the enhanced soluble starch specificity of SAP5-CGTase and SAP6-CGTase compared to that in the wild-type CGTase. As revealed by structure modeling of the fusion and wild-type CGTases, enhanced substrate-binding capacity may result from the increased number of hydrogen bonds present after fusion. This study demonstrates an effective protein fusion approach to improving the substrate specificity of CGTase for AA-2G synthesis. Fusion enzymes, especially SAP6-CGTase, are promising starting points for further development through protein engineering.

A C-terminal proline-rich sequence simultaneously broadens the optimal temperature and pH ranges and improves the catalytic efficiency of glycosyl hydrolase family 10 ruminal xylanases

Efficient degradation of plant polysaccharides in rumen requires xylanolytic enzymes with a high catalytic capacity. In this study, a full-length xylanase gene (xynA) was retrieved from the sheep rumen. The deduced XynA sequence contains a putative signal peptide, a catalytic motif of glycoside hydrolase family 10 (GH10), and an extra C-terminal proline-rich sequence without a homolog. To determine its function, both mature XynA and its C terminus-truncated mutant, XynA-Tr, were expressed in Escherichia coli. The C-terminal oligopeptide had significant effects on the function and structure of XynA. Compared with XynA-Tr, XynA exhibited improved specific activity (12-fold) and catalytic efficiency (14-fold), a higher temperature optimum (50°C versus 45°C), and broader ranges of temperature and pH optima (pH 5.0 to 7.5 and 40 to 60°C versus pH 5.5 to 6.5 and 40 to 50°C). Moreover, XynA released more xylose than XynA-Tr when using beech wood xylan and wheat arabinoxylan as the substrate. The underlying mechanisms responsible for these changes were analyzed by substrate binding assay, circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), and xylooligosaccharide hydrolysis. XynA had no ability to bind to any of the tested soluble and insoluble polysaccharides. However, it contained more α helices and had a greater affinity and catalytic efficiency toward xylooligosaccharides, which benefited complete substrate degradation. Similar results were obtained when the C-terminal sequence was fused to another GH10 xylanase from sheep rumen. This study reveals an engineering strategy to improve the catalytic performance of enzymes.

Structure-based engineering of alkaline α-amylase from alkaliphilic Alkalimonas amylolytica for improved thermostability

This study aimed to improve the thermostability of alkaline α-amylase from Alkalimonas amylolytica through structure-based rational design and systems engineering of its catalytic domain. Separate engineering strategies were used to increase alkaline α-amylase thermostability: (1) replace histidine residues with leucine to stabilize the least similar region in domain B, (2) change residues (glycine, proline, and glutamine) to stabilize the highly conserved α-helices in domain A, and (3) decrease the free energy of folding predicted by the PoPMuSiC program to stabilize the overall protein structure. A total of 15 single-site mutants were obtained, and four mutants - H209L, Q226V, N302W, and P477V - showed enhanced thermostability. Combinational mutations were subsequently introduced, and the best mutant was triple mutant H209L/Q226V/P477V. Its half-life at 60 °C was 3.8-fold of that of the wild type and displayed a 3.2 °C increase in melting temperature compared with that of the wild type. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50 °C to 55 °C, the optimum pH shifted from 9.5 to 10.0, the stable pH range expanded from 7.0-11.0 to 6.0-12.0, the specific activity increased by 24 %, and the catalytic efficiency (k cat/K m) increased from 1.8×10(4) to 3.5 × 10(4) l/(g min). Finally, the mechanisms responsible for the increased thermostability were analyzed through comparative analysis of structure models. The structure-based rational design and systems engineering strategies in this study may also improve the thermostability of other industrial enzymes.

In silico rational design and systems engineering of disulfide bridges in the catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica to improve thermostability

High thermostability is required for alkaline α-amylases to maintain high catalytic activity under the harsh conditions used in textile production. In this study, we attempted to improve the thermostability of an alkaline α-amylase from Alkalimonas amylolytica through in silico rational design and systems engineering of disulfide bridges in the catalytic domain. Specifically, 7 residue pairs (P35-G426, Q107-G167, G116-Q120, A147-W160, G233-V265, A332-G370, and R436-M480) were chosen as engineering targets for disulfide bridge formation, and the respective residues were replaced with cysteines. Three single disulfide bridge mutants-P35C-G426C, G116C-Q120C, and R436C-M480C-of the 7 showed significantly enhanced thermostability. Combinational mutations were subsequently assessed, and the triple mutant P35C-G426C/G116C-Q120C/R436C-M480C showed a 6-fold increase in half-life at 60°C and a 5.2°C increase in melting temperature compared with the wild-type enzyme. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50°C to 55°C, the optimum pH shifted from 9.5 to 10.0, the stable pH range extended from 7.0 to 11.0 to 6.0 to 12.0, and the catalytic efficiency (kcat/Km) increased from 1.8 × 10(4) to 2.4 × 10(4) liters/g · min. The possible mechanism responsible for these improvements was explored through comparative analysis of the model structures of wild-type and mutant enzymes. The disulfide bridge engineering strategy used in this work may be applied to improve the thermostability of other industrial enzymes.

Integrating terminal truncation and oligopeptide fusion for a novel protein engineering strategy to improve specific activity and catalytic efficiency: alkaline α-amylase as a case study

In this work, we integrated terminal truncation and N-terminal oligopeptide fusion as a novel protein engineering strategy to improve specific activity and catalytic efficiency of alkaline α-amylase (AmyK) from Alkalimonas amylolytica. First, the C terminus or N terminus of AmyK was partially truncated, yielding 12 truncated mutants, and then an oligopeptide (AEAEAKAKAEAEAKAK) was fused at the N terminus of the truncated AmyK, yielding another 12 truncation-fusion mutants. The specific activities of the truncation-fusion mutants AmyKΔC500-587::OP and AmyKΔC492-587::OP were 25.5- and 18.5-fold that of AmyK, respectively. The kcat/Km was increased from 1.0 × 10(5) liters · mol(-1) · s(-1) for AmyK to 30.6 × and 23.2 × 10(5) liters · mol(-1) · s(-1) for AmyKΔC500-587::OP and AmyKΔC492-587::OP, respectively. Comparative analysis of structure models indicated that the higher flexibility around the active site may be the main reason for the improved catalytic efficiency. The proposed terminal truncation and oligopeptide fusion strategy may be effective to engineer other enzymes to improve specific activity and catalytic efficiency.