Abstract:Enzyme engineering combines enzymology and engineering, and is one of the major fields of modern biotechnology. To promote enzyme engineering research in China, we present in this special issue with reviews and original articles focusing on recent relevant advances reported by Chinese scientists.

Abstract:The development and application of industrial enzymes have penetrated major industrial fields. China faces a major challenge as a large country in applying enzyme but a small one in producing enzyme. Biocatalysis has become an important technology and strategy of industrial development in the world since chemical catalysis encounters the crises from resource, energy and environment. The application of efficient and clean biocatalysis is one of the important ways to realize the sustainable development of chemical industry and to modernize the fermentation industry. From perspective of the industry-university-research cooperation, we reviewed the current status and the future development of enzyme engineering from the aspects of enzyme resources, customization of enzyme molecular machine and cell factory.

Abstract:The high efficiency and stability of enzymes are the basis for industrial application. Hybrid enzyme suitable for industrial applications could be constructed by many molecular biology technologies including tandem fusion, domain insertion and post-translational protein conjugation. However, the low expression and activity of hybrid enzyme limit its application in industrial production, and multifunctional design of a specific protein domain has been becoming a new trend. With the advent of high-throughput sequencing, biologists are starting to wrestling with massive data sets. Besides, the concept of protein sectors and co-evolution provides novel insight into the relationship of protein structure and function. The residues–covariation of a protein sector displays preference, which imparts functional diversity to different enzymes in the same family. The covariation-residues in specific protein sectors can be located based on the analysis of massive data, and then these functional residues can be assembled in a new enzyme variant using the biotechnology of synthetic biology, thus completing the redesign of natural enzymes. This indicates a new stage of designing hybrid enzyme, as well as the new trend of protein design in the era of biological big data.

Abstract:Hydroxy amino acids, constituents of chiral pharmaceutical intermediates or precursors, have a variety of unique functions in the research fields of biotechnology and molecular biology, i.e. antifungal, antibacterial, antiviral and anticancer properties. Biosynthesis of hydroxy amino acids is preferred because of its high specificity and selectivity. The hydroxylation of hydrophobic amino acids is catalyzed by hydroxylase, which belongs to the mononuclear non-heme Fe(Ⅱ)/α-ketoglutarate-dependent dioxygenases (Fe/αKGDs). Fe/αKGDs utilize an (Fe(Ⅳ)=O) intermediate to activate diverse oxidative transformations with key biological roles in the process of catalytic reaction. Here, we review the physiological properties and synthesis of hydroxy amino acids, especially for the 4-HIL and hydroxyproline. The catalytic mechanism of Fe/αKGDs is elucidated, and the applications of hydroxy amino acids in industrial engineering are also discussed.

Abstract:w-Transaminase catalyzes the asymmetric reductive amination of carbonyl compounds, and has great application prospect in the preparation of chiral amines. The application in synthesis of bulky chiral amines is limited by the special structure of substrate binding region in the wild-type enzyme. Moreover, there are also some drawbacks in the stereoselectivity and stability of w-transaminase. So far, w-transaminase satisfying the industrial requirements is still rare. In this review, we first introduce the structure and catalytic mechanism of w-transaminase, and then discuss the structural differences between S-selective and R-selective enzymes. Molecular modification of w-transaminase was introduced in detail, by focusing on the structure and mechanism-based molecular modification, including substrate specificity, stereoselectivity, and stability.

Abstract:Crude glycerol is the main by-product of biodiesel production. A few microorganisms can transfer crude glycerol to 1,3-propanediol (1,3-PD) that is an important chemical material. There exist many limitations such as substrate inhibition, product inhibition when wild strains are used in 1,3-PD biosynthesis. In this review, based on the microbial transformation of 1,3-propanediol from glycerol and its limitations, some strategies using genetic engineering such as knockout or gene overexpression were summarized. The latest research progresses in biosynthesis of 1,3-propanediol from glycerol by genetically engineered strains are discussed.

Abstract:Cellulose hydrolysis to glucose requires a series of cellulase enzymes, of which β-glucosidases play a crucial role. β-glucosidase (MbmgBG1) derived from the midgut of Macrotermes barneyi has higher glucose tolerance (maintaining more than 60% enzyme activity at 1.5 mol/L glucose). However, low enzyme activity and poor thermal stability limit the applications of β-glucosidase in food industries. Point mutants (F167L, T176C, E347I, R354K, N393G and V425M) were obtained by site-directed mutagenesis of non-conserved amino acids near conserved amino acids. Among them, the specific activities against to substrate pNPG of two mutants (F167L and R354K) were about 2-fold and 4-fold higher than that of MbmgBG1. Kcat/Km values were also higher than that of the wild-type, reflecting stronger affinity to the substrate and higher catalytic ability of mutants than MbmgBG1. When the glucose concentration was 1.5 mol/L, the enzyme activity of MbmgBG1 was about 60% of the original activity. F167L and R354K kept 60% enzymatic activity when the glucose concentrations of was 2.0 mol/L and 3.0 mol/L, respectively. These results lay a foundation for further studies on the catalytic efficiency of β-glucosidase.

Abstract:The catalytic activity of Aspergillus terreus lipase (ATL) was improved by rational design. According to the sequence analysis and homologous modeling, several amino acids involved in the lid domain and substrate binding pocket domains of the acidic lipase ATL were mutated by site-directed mutagenesis, and eight mutants were constructed. These mutants and the wild type lipase ATL were expressed in Pichia pastoris GS115 and the enzymatic properties were characterized. The mutants ATLLid and ATLV218W exhibited higher hydrolytic activity than ATL towards p-nitrophenyl laurate. The kcat values of ATLLid and ATLV218W towards p-nitrophenyl laurate were 39.37- and 50.79-fold higher, and the kcat/Km values were 2.85- and 8.48-fold higher than the wild type, respectively. Although thermostability of these mutants decreased slightly, ATLLid and ATLV218W still exhibited the maximum activity at pH 5.0 and high stability in a broad range of pH (4.0–8.0), which were similar to the wild type. Using homologous modeling and molecular docking technology the mechanism for the improvement of catalytic activity was analyzed. These findings not only shed light on the relationship between the lid domain/substrate binding pocket domain and catalytic activity but also provided comprehensive scheme for further engineering to gain more efficient lipases.

Abstract:Glucose oxidase catalyzes the oxidation of β-D-glucose to gluconic acid and its derivatives, thus shows a great potential in the development of antibiotic-free feed. However, its production and processing still have the problem of poor thermal stability of enzyme activity. In this study, fusion of amphiphilic peptide technology was used to improve the stability of glucose oxidase. Herein, eight self-assembling peptides with different amino acid lengths and Linkers were fused to the N terminus of the glucose oxidase, yielding eight chimeric fusions SAP1-GS-GOD, SAP1-PT-GOD, SAP2-PT-GOD, SAP3-PT-GOD, SAP4-PT-GOD, SAP5-PT-GOD, SAP6-PT-GOD and SAP7-PT-GOD. Then, the 8 recombinant proteins were expressed in P. pastoris GS115. After separation and purification, the stability of glucose oxidase at 60 ℃was determined. The relative enzyme activities of the PT Linker-linked fusion enzyme incubated at 60 ℃ for 60 min were higher than those of the original enzyme, and the relative activity of SAP5-PT-GOD was 67% at 60 ℃ for 30 min, which was 10.9 times higher than that of the initial enzyme with the same treatment. Among them, the Kcat/Km value of SAP1-PT-GOD, SAP2-PT-GOD, SAP3-PT-GOD and SAP5-PT-GOD of the fusion enzyme was further improved than that of the initial enzyme. Through the analysis of the intramolecular force of the fusion enzyme, the increase of the thermal stability of the fusion enzyme is mainly due to the increase of the hydrogen bond. In summary, the study indicates that translational fusion of self-assembling peptides with PT Linker was able to augment the thermo-stability of glucose oxidase, which has certain potential in the production and application of glucose oxidase. The glucose oxidase with improved thermostability obtained in the above study and the related mechanism will play an important role in improving the activity of related enzymes in the proceeding of processing and application.

Abstract:Fungal α-amylases are widely used in the production of maltose syrup, while additional production costs may be required in the syrup production process due to the loss of enzyme activity, because of the poor thermostability exhibited in this type of enzyme. After deeply studying the importance of thermostability of fungal α-amylases applied in industrial production, with attempt to improve the thermostability of Rhizopus oryzae α-amylase (ROAmy), single-point mutations and combined mutations that based on analysis of B-factor values and molecular dynamics simulations were carried out for amino acid residues G128, K269 and G393 of ROAmy by overlapping PCR. The results showed that all the 7 mutants obtained presented better thermostability than the wild-type enzyme, and the best mutant was G128L/K269L/G393P which showed a 5.63-fold increase in half-life at 55 ℃ compared with the wild-type enzyme. Meanwhile, its optimum temperature increased from 50 ℃ to 65 ℃, the maximum reaction rate (Vmax) and catalytic efficiency (kcat/Km) increased by 65.38% and 99.86%. By comparing and analyzing the protein structure and function between the mutants and the wild-type enzyme, it was found that the increase of the number of hydrogen bonds or the introduction of proline in special position may be the main reasons for the improved thermostability that found in the mutants.

Abstract:Xylulose as a metabolic intermediate is the precursor of rare sugars, and its unique pattern of biological activity plays an important role in the fields of food, health, medicine and so on. The aim of this study was to design a new pathway for xylulose synthesis from formaldehyde, which is one of the most simple and basic organic substrate. The pathway was comprised of 3 steps: (1) formaldehyde was converted to glycolaldehyde by benzoylformate decarboxylase mutant BFD-M3 (from Pseudomonas putida); (2) formaldehyde and glycolaldehyde were converted to dihydroxyacetone by BFD-M3 as well; (3) glycolaldehyde and dihydroxyacetone were converted to xylulose by transaldolase mutant TalB-F178Y (from Escherichia coli). By adding formaldehyde (5 g/L), BFD-M3 and TalB-F178Y in one pot, xylulose was produced at a conversion rate of 0.4%. Through optimizing the concentration of formaldehyde, the conversion rate of xylulose was increased to 4.6% (20 g/L formaldehyde), which is 11.5 folds higher than the initial value. In order to further improve the xylulose conversion rate, we employed Scaffold Self-Assembly technique to co-immobilize BFD-M3 and TalB-F178Y. Finally, the xylulose conversion rate reached 14.02%. This study provides a new scheme for the biosynthesis of rare sugars.

Abstract:As a novel fungal type Ⅲ polyketide synthase, CsyB from Aspergillus oryzae can sequentially accept one molecular short chain fatty acyl CoA as start unit, one molecular malonyl-CoA and one molecular acetoacetyl-CoA as extend unit to produce the short chain csypyrone B1-3. On the basis of crystal structure of CsyB, a fatty acyl CoA binding tunnel of a length of about 16 ? is located in its active center that is proposed to accept diversified start units. In order to examine the substrate diversity of CsyB, CsyB gene was introduced and expressed in Escherichia coli that contained a number of precursors of long chain fatty acyl CoA in vivo. The results of HPLC revealed that a series of long chain csypyrone derivatives were detected in the recombinant strain in comparison with the control strain. These new csypyrone compounds were preliminarily analyzed by UV-visible spectroscopy and LC-HRMS. Three hydroxylated csypyrones were intensively determined by 1D and 2D NMR experiments, especially the position of the hydroxyl group in these compounds. These results demonstrate that CsyB exhibits a broad substrate specificity, which not only can accept the long chain saturated or unsaturated fatty acyl CoA as substrate, but also accept hydroxylated long chain fatty acyl CoA.

Abstract:Urate oxidase (Uox), an enzyme catalyzing oxidation of uric acid to allantoin, is widely used as diagnostic reagents and for treatments of uarthritis and hyperuricemia diseases. In our study, a higher Uox producer, bacterial strain OUC-1, was isolated from soil samples. The 16S rRNA gene sequence of strain OUC-1 showed 99% identity to the homologous fragments of Bacillus fastidiosus. After purification, Uox showed the optimal pH and temperature was 10.0 and 40 °C. The Km value of Uox was (0.15±0.04) mmol/L (n=5) with uric acid as the substrate. Uox activity was enhanced by Mg2+, and seriously inhibited by Zn2+ and SDS. Then the uox gene of B. fastidiosus OUC-1 was amplified and sequenced. The 3D structures of Uox, predicted with SWISS-MODEL, showed a homotetramer structure with a subunit molecular weight of 35.38 kDa. Finally, the gene coding for the B. fastidiosus Uox was successfully cloned and heterologously expressed in E. coli, which provides theoretical basis and technical support for improvement of Uox in the future.

Abstract:Trametes versicolor has strong ability to degrade environmental organic pollutants. NADPH-cytochrome P450 reductase (CPR) of T. versicolor transfers electron to cytochrome P450s (CYPs) and participates in the degradation process of organic pollutants. Sequence analysis showed that the genome of T. versicolor contains 1 potential CPR and multiple potential CYP sequences. To further study the molecular mechanism for the involvement of T. versicolor CPR in the cellular degradation of organic pollutants, a CPR gene from T. versicolor was cloned and heterologously expressed in Escherichia coli. Subsequently, the main properties of the recombinant enzyme were investigated. A truncated CPR protein lacking the predicted membrane anchor region (residues 1-24), named CPRΔ24, was overexpressed as a soluble form in E. coli. The recombinant CPRΔ24 protein showed a molecular weight consistent with the theoretical value of 78 kDa. Recombinant CPRΔ24 was purified using a Ni2+-chelating column followed by size exclusion chromatography. The specific activity of the purified CPRΔ24 was 5.82 U/mg. The CPRΔ24 enzyme displayed the maximum activity at 35 ℃ and pH 8.0. It has different degrees of tolerance against several types of metal ions and organic solvents. The apparent Km and kcat values of recombinant CPRΔ24 for NADPH were 19.7 μmol/L and 3.31/s, respectively, and those for the substrate cytochrome c were 25.9 μmol/L and 10.2/s, respectively, under conditions of 35 ℃ and pH 8.0. The above research provides the basis for exploring the functional mechanism of T. versicolor CPR in the degradation pathway of environmental organic pollutants.

Abstract:α-Amino acid ester acyltransferase (Aet) catalyzes the L-alanyl-L-glutamine forming reaction from L-alaine methylester hydrochloride and L-glutamine. In this study, the recombinant Escherichia coli saet-QC01 was used to express the α-amino acid acyltransferase, and its expression conditions were optimized. The recombinant protein was separated and purified by Ni-NTA affinity chromatography, and its enzymatic properties and catalytic applications were studied. The induction conditions suitable for enzyme production optimized were as follows: The temperature was 20 ℃, the induction stage (OD600=2.0?2.5), IPTG concentration was 0.6 mmol/L, induction time was 12 h. The optimal reaction conditions of α-amino acid acyltransferase were 27 ℃, pH 8.5, it was most stable between pH 7.0 and 8.0 and relatively stable in an acidic environment, and low concentration of Co2+ or EDTA could promote the enzyme activity. Under optimal reaction conditions, 600 mmol/L of L-alaine methylester hydrochloride and 480 mmol/L of L-glutamine, the yield of L-alanyl-L-glutamine reached 78.2 g/L and productivity of 1.955 g/L/min, the conversion rate reached 75.0%. α-Amino acid ester acyltransferase has excellent acid-basei resistance, high catalytic efficiency. These characteristics suggest its application prospects in the industrial production.

Abstract:With the discovery of the significant medicinal value of alginate oligosaccharides and bioethanol produced by microalgae, alginate lyase has been the focus of research in all fields. Five alginate lyase genes in cluster from Vibrio alginolyticus were cloned and expressed in Escherichia coli. SDS-PAGE and enzyme activity showed that four of the five genes have the activity to degrade alginate. Optimization of the induction conditions, protein purification and enzyme properties of rAlgV3 with the highest enzyme activity were studied. The results showed that the enzyme activity of recombinant enzyme rAlgV3 increased from 2.34×104 U/L to 1.68×105 U/L, which was 7.3 times higher than before. The optimal reaction temperature was 40 °C, and the enzyme was relatively stable between 4 °C and 20 °C. The enzyme had a higher activity between pH 6.5 and 9.0, with the optimum pH 8.0. It showed a wide range of pH that the alginate lyase can exist stably between pH 4.5 and 9.5. Appropriate concentrations of NaCl and Fe2+, Fe3+ ions promoted enzyme activity. SDS and Cu2+ ions inhibited the enzyme activity. The enzyme degraded Poly-M fragments and Poly-G fragments, with a wide range of substrate properties. The degraded product of sodium alginate of rAlgV3 analyzed by ESI-MS mainly was oligosaccharides with a polymerization degree of 2 to 3, which means that rAlgV3 was an endo-type alginate lyase. This enzyme has the potential in the development of third-generation bioethanol and the production of alginate oligosaccharides.

Abstract:Displaying Candida antarctica lipase B (CALB) on the cell surface of Aspergillus niger is effectively applied for the industries of food, cosmetics, pharmaceutical and so on. Displaying CALB using induced promoter of glucoamylase on the cell surface of A. niger SH-1 has some problems such as inhibiting its expression under high concentration of glucose, mycelium cleavage and decreasing enzyme activity in the later period of fermentation process. Displaying CALB manipulated by constitutive promoter from glyceraldehyde-3-phosphate dehydrogenase instead of glucoamylase on the cell surface of A. niger SH-1, called AN-GpdA, could solve the above problems effectively. Furthermore, it can not only use glucose, but also xylose as a sole carbon source. Enzyme activity of AN-GpdA using xylose for fermentation reached 1 100.28 U/g of dry cell. We also used lignocellulose such as the hydrolysate of bagasse for fermentation with good performance. The result would provide a novel strategy for the utilization of bagasse.