Improving the catalytic efficiency of Bacillus pumilus CotA-laccase by site-directed mutagenesis

Characterization and rational engineering of a novel laccase from Geobacillus thermocatenulatus M17 for improved lignin degradation activity

Lignin, with its complex, high-molecular-weight aromatic polymer structure and stable ether or ester bonds, greatly impedes the efficient degradation of lignocellulosic waste. Bacterial laccases have gained attention for their potential in lignocellulosic waste degradation due to their resilience in extreme conditions and ability to be produced in large quantities. In this study, a novel laccase from Geobacillus thermocatenulatus M17 was identified and expressed in E. coli BL21 (DE3). The enzymatic properties of this M17 laccase, including its tolerance to pH, temperature, metal ions, inhibitors, and organic solvents, were thoroughly investigated. The M17 laccase demonstrated optimal activity at pH 3-6 and at temperatures of 50-60 °C, with Co2+ enhancing its activity over Cu2+, and exhibited strong resistance to organic solvents. Further optimization through mutagenesis led to the engineered D217K variant. The efficiency of the engineered laccase was validated with alkali lignin and various sources of plant biomass. The degradation rate of D217K variant for alkali lignin increased significantly, rising from 66.33 % to 83.27 %. Additionally, for high-lignin-content biomass, the degradation rates improved as follows: wheat stover increased from 7.63 % to 10.29 %, switchgrass from 6.02 % to 7.00 %, and corn stalk from 4.51 % to 6.59 %. In conclusion, this study identified a new bacterial laccase and further enhanced its activity through rational engineering, suggesting its promising application in plant biomass degradation.

Enhancement in the Catalytic Properties of CotA Laccase from Bacillus pumilus via High-Throughput Screening Using Malachite Green as a Pressure

Bacterial laccase exhibits substantial application potential in various fields. In this study, we constructed a mutation library of CotA laccase from Bacillus pumilus using error-prone PCR, and we performed four rounds of enrichment screening under malachite green (MG) pressure. The results demonstrated that the proportions of the four selected mutant strains were significantly increased. The enzyme activities of the four final mutants PW2, PW5, PW4G, and PW6 were 94.34, 75.74, 100.66, and 87.04 U/mg, respectively, representing a significant increase of approximately 2- to 3-fold compared to the wild-type CotA laccase. Notably, PW4 exhibited significantly improved thermal stability at 90 °C and pH tolerance at pH 12.0. Homology modeling analysis revealed that alterations in the amino acid sequence rendered the spatial structure of the enzyme's catalytic site more favorable for substrate binding. For instance, the substitution of T262A in PW2 and V426I in PW4 shortened the side chains of the amino acids, thereby enlarging the substrate-binding cavity. The G382D mutation in PW2 and PW5 may induce altered protein conformation via spatial steric hindrance or electrostatic interactions, consequently impacting enzyme activity and stability. These findings provide valuable insights for enhancing the industrial application of bacterial laccase.

Simultaneous enhancement of activity and stability of Bacillus safensis-derived laccase and its application in lignocellulose saccharification

Effective hydrolysis of lignocelluloses for producing reducing sugar is impeded by the covalent binding of hemicellulose and cellulose through lignin, which could be eliminated by laccases. This study identified a novel thermostable laccase from Bacillus safensis TCCC 111022 and created an iterative mutant E231D/Y441H, exhibiting 1.59-fold greater specific activity and a 183 % greater half-life at 80°C than the wild-type enzyme. Computational analysis revealed that the stability and activity of the E231D/Y441H could be simultaneously enhanced by increasing the flexibility of the ring around the substrate binding pocket. Additionally, the saccharification efficiency of sugarcane bagasse and corn stalks were both enhanced by 235 % in the system adding E231D/Y441H, mixed-cellulases, and mediator (1-hydroxybenzotriazole) compared to the samples treated with mixed-cellulases. The findings of this research provide a reference for the degradation of lignocellulosic substrates and contribute to the sustainable development of biomass-based industries.

Tailoring CotA Laccase Substrate Specificity by Rationally Reshaping Pocket Edge

CotA is a bacterial multicopper oxidase, capable of oxidizing lots of substrates. In previous work, small size lignin phenol derivates were found to lie only in the partially covered part of pocket. However, big size substate would occupy the whole pocket to react. In this work, five residues sitting at the edge of the pocket were selected to study their roles in regulating activities against different size substrates. All mutants showed impaired activities against small size sinapic acid, however, A227E, G321F and G321P showed around 25 % increase of activities against big size ditaurobilirubin compared to wild type (WT). T262F/G321F showed moderate increased activity to alazin red S. kcat/Kms against ditaurobilirubin of A227E, T262F and G321F are around 1.5, 3 and 1.5 folds of WT's. Unexpectedly, heterologous expression yields of T262F, T262F/G321F and T262F/G321P in Escherichia coli greatly increased by around 5, 7 and 21 folds compared to WT, respectively. It is speculated positive mutants would provide a beneficial orientation for big size substrates. Substituting semi-buried residue T262 by a hydrophobic amino acid might enhance expression yields mainly by increasing van der waals and hydrophobic interaction. This work exemplified rationally regulating specific activities of laccase and is valuable for industrial application.

Combined Strategies for Improving Aflatoxin B1 Degradation Ability and Yield of a Bacillus licheniformis CotA-Laccase

Aflatoxin B1 (AFB1) contamination is a serious threat to nutritional safety and public health. The CotA-laccase from Bacillus licheniformis ANSB821 previously reported by our laboratory showed great potential to degrade AFB1 without redox mediators. However, the use of this CotA-laccase to remove AFB1 in animal feed is limited because of its low catalytic efficiency and low expression level. In order to make better use of this excellent enzyme to effectively degrade AFB1, twelve mutants of CotA-laccase were constructed by site-directed mutagenesis. Among these mutants, E186A and E186R showed the best degradation ability of AFB1, with degradation ratios of 82.2% and 91.8% within 12 h, which were 1.6- and 1.8-times higher than those of the wild-type CotA-laccase, respectively. The catalytic efficiencies (kcat/Km) of E186A and E186R were found to be 1.8- and 3.2-times higher, respectively, than those of the wild-type CotA-laccase. Then the expression vectors pPICZαA-N-E186A and pPICZαA-N-E186R with an optimized signal peptide were constructed and transformed into Pichia pastoris GS115. The optimized signal peptide improved the secretory expressions of E186A and E186R in P. pastoris GS115. Collectively, the current study provided ideal candidate CotA-laccase mutants for AFB1 detoxification in food and animal feed and a feasible protocol, which was desperately needed for the industrial production of CotA-laccases.

Study of alkali-soluble curdlan/bacterial cellulose/cinnamon essential oil blend films with enhanced mechanical properties

In response to the growing demand for biodegraded film with high mechanical properties for complex preservation application scenarios, we developed a curdlan (CD) blended films with exceptional mechanical strength through an alkali dissolution method. Notably, the alkali-soluble CD film exhibited five-fold increase in tensile strength (TS) when compared to its water-soluble counterpart. Furthermore, the inclusion of 2 % bacterial cellulose (BC) resulted in a significant 41.1 % augmentation of the film's TS. Thermal stability improvements were observed through differential scanning calorimetry (DSC) analysis and thermogravimetric analysis (TGA). X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR) results provided insights into alterations in film crystallinity and intermolecular interactions. Specifically, the incorporation of 10 % CEO led to an additional improvement in TS. Our experimental investigations involving the packaging of chilled fresh meat with these blended films unveiled their capacity to effectively inhibit microorganism growth, maintain meat color stability, delay protein decomposition and fat oxidation, and extend the storage time up to 9 days. Our study offers a promising solution for food packaging, emphasizing the development of a high-strength degradable CD/BC/CEO blended film, which holds potential for extending the shelf life of food products.

Improvement of aflatoxin B1 degradation ability by Bacillus licheniformis CotA-laccase Q441A mutant

Aflatoxin B1 (AFB1) contamination seriously threatens nutritional safety and common health. Bacterial CotA-laccases have great potential to degrade AFB1 without redox mediators. However, CotA-laccases are limited because of the low catalytic activity as the spore-bound nature. The AFB1 degradation ability of CotA-laccase from Bacillus licheniformis ANSB821 has been reported by a previous study in our laboratory. In this study, a Q441A mutant was constructed to enhance the activity of CotA-laccase to degrade AFB1. After the site-directed mutation, the mutant Q441A showed a 1.73-fold higher catalytic efficiency (kcat/Km) towards AFB1 than the wild-type CotA-laccase did. The degradation rate of AFB1 by Q441A mutant was higher than that by wild-type CotA-laccase in the pH range from 5.0 to 9.0. In addition, the thermostability was improved after mutation. Based on the structure analysis of CotA-laccase, the higher catalytic efficiency of Q441A for AFB1 may be due to the smaller steric hindrance of Ala441 than Gln441. This is the first research to enhance the degradation efficiency of AFB1 by CotA-laccase with site-directed mutagenesis. In summary, the mutant Q441A will be a suitable candidate for highly effective detoxification of AFB1 in the future.

Laccase Engineering: Redox Potential Is Not the Only Activity-Determining Feature in the Metalloproteins

Laccase, one of the metalloproteins, belongs to the multicopper oxidase family. It oxidizes a wide range of substrates and generates water as a sole by-product. The engineering of laccase is important to broaden their industrial and environmental applications. The general assumption is that the low redox potential of laccases is the principal obstacle, as evidenced by their low activity towards certain substrates. Therefore, the primary goal of engineering laccases is to improve their oxidation capability, thereby increasing their redox potential. Even though some of the determinants of laccase are known, it is still not entirely clear how to enhance its redox potential. However, the laccase active site has additional characteristics that regulate the enzymes' activity and specificity. These include the electrostatic and hydrophobic environment of the substrate binding pocket, the steric effect at the substrate binding site, and the orientation of the binding substrate with respect to the T1 site of the laccase. In this review, these features of the substrate binding site will be discussed to highlight their importance as a target for future laccase engineering.

Deciphering the alkaline stable mechanism of bacterial laccase from Bacillus pumilus by molecular dynamics simulation can improve the decolorization of textile dyes

Laccases are considered promising tools for removing synthetic dyes from textile and tannery effluents. However, the alkaline pH in the effluents causes laccase instability, inactivation, and difficulty in its bioremediation. Based on a Bacillus pumilus ZB1 (BpLac) derived alkaline stable laccase, this study aimed to elucidate its alkaline stable mechanism at molecular level using molecular dynamics simulation. The effects of metal ions, organic solvents, and inhibitors on BpLac activity were assessed. BpLac formed more salt bridges and negatively charged surface in alkaline environment. Thereafter, pH-induced conformation changes were analyzed using GROMACS at pH 5.0 and 10.0. Among the identified residues with high fluctuation, the distance between Pro359 and Thr414 was stable at pH 10.0 but highly variable at pH 5.0. DSSP analysis suggested that BpLac formed more β-sheet and less coil at pH 10.0. Principal component analysis and free energy landscape indicated that irregular coils formed at pH 5.0 benefit for activity, while rigid α-helix and β-sheet structures formed at pH 10.0 contributed to alkaline stability. Breaking the α-helix near T1 copper center would not reduce alkaline stability but could improve dye decolorization by BpLac. Overall, these findings would advance the potential application of bacterial laccase in alkaline effluent treatment.

Improvement of thermoalkaliphilic laccase (CtLac) by a directed evolution and application to lignin degradation

Abstract

Thermoalkaliphilic laccase (CtLac) from the Caldalkalibacillus thermarum strain TA2.A1 has advantageous properties with potential industrial applications, such as high enzyme activity and stability at 70 °C and pH 8.0. In the present study, a directed evolution approach using a combination of random and site-directed mutagenesis was adopted to enhance the laccase activity of CtLac. Spectrophotometric assay and real-time oxygen measurement techniques were employed to compare and evaluate the enzyme activity among mutants. V243 was targeted for site-directed mutagenesis based on library screening. V243D showed a 25–35% higher laccase activity than wild-type CtLac in the spectrophotometric assay and oxygen consumption measurement results. V243D also showed higher catalytic efficiency than wild-type CtLac with decreased Km and increased kcat values. In addition, V243D enhanced oxidative degradation of the lignin model compound, guaiacylglycerol-β-guaiacyl ether (GGGE), by 10% and produced a 5–30% increase in high-value aldehydes than wild-type CtLac under optimal enzymatic conditions (i.e., 70 °C and pH 8.0). Considering the lack of protein structural information, we used the directed evolution approach to predict Val at the 243 position of CtLac as one of the critical amino acids contributing to the catalytic efficiency of the enzyme. Moreover, it found that the real-time oxygen measurement technique could overcome the limitations of the spectrophotometric assay, and apply to evaluate oxidase activity in mutagenesis research.

Key points

• CtLac was engineered for enhanced laccase activity through directed evolution approach

• V243D showed higher catalytic efficiency (kcat/Km) than wild-type CtLac

• V243D produced higher amounts of high-value aldehydes from rice straw than wild-type CtLac

Biological oxidation methods for the removal of organic and inorganic contaminants from wastewater: A comprehensive review

Enzyme-based bioremediation is a simple, cost-effective, and environmentally friendly method for isolating and removing a wide range of environmental pollutants. This study is a comprehensive review of recent studies on the oxidation of pollutants by biological oxidation methods, performed individually or in combination with other methods. The main bio-oxidants capable of removing all types of pollutants, such as organic and inorganic molecules, from fungi, bacteria, algae, and plants, and different types of enzymes, as well as the removal mechanisms, were investigated. The use of mediators and modification methods to improve the performance of microorganisms and their resistance under harsh real wastewater conditions was discussed, and numerous case studies were presented and compared. The advantages and disadvantages of conventional and novel immobilization methods, and the development of enzyme engineering to adjust the content and properties of the desired enzymes, were also explained. The optimal operating parameters such as temperature and pH, which usually lead to the best performance, were presented. A detailed overview of the different combination processes was also given, including bio-oxidation in coincident or consecutive combination with adsorption, advanced oxidation processes, and membrane separation. One of the most important issues that this study has addressed is the removal of both organic and inorganic contaminants, taking into account the actual wastewaters and the economic aspect.

Thermostability Improvement of L-Asparaginase from Acinetobacter soli via Consensus-Designed Cysteine Residue Substitution

To extend the application range of L-asparaginase in food pre-processing, the thermostability improvement of the enzyme is essential. Herein, two non-conserved cysteine residues with easily oxidized free sulfhydryl groups, Cys8 and Cys283, of Acinetobacter soli L-asparaginase (AsA) were screened out via consensus design. After saturation mutagenesis and combinatorial mutation, the mutant C8Y/C283Q with highly improved thermostability was obtained with a half-life of 361.6 min at 40 °C, an over 34-fold increase compared with that of the wild-type. Its melting temperature (T_m) value reaches 62.3 °C, which is 7.1 °C higher than that of the wild-type. Molecular dynamics simulation and structure analysis revealed the formation of new hydrogen bonds of Gln283 and the aromatic interaction of Tyr8 formed with adjacent residues, resulting in enhanced thermostability. The improvement in the thermostability of L-asparaginase could efficiently enhance its effect on acrylamide inhibition; the contents of acrylamide in potato chips were efficiently reduced by 86.50% after a mutant C8Y/C283Q treatment, which was significantly higher than the 59.05% reduction after the AsA wild-type treatment. In addition, the investigation of the mechanism behind the enhanced thermostability of AsA could further direct the modification of L-asparaginases for expanding their clinical and industrial applications.

Significant Improvement of Both Catalytic Efficiency and Stability of Fructosyltransferase from Aspergillus niger by Structure-Guided Engineering of Key Residues in the Conserved Sequence of the Catalytic Domain

Fructosyltransferase is a key enzyme in fructo-oligosaccharide production, while the highly demanding conditions of industrial processes may reduce its stability and activity. This study employs sequence alignment and structural analysis to target three potential residues (Gln38, Ile39, and Cys43) around the active center of FruSG from Aspergillus niger, and mutants with greatly improved activity and stability were obtained through site-directed mutagenesis. The K_m values of C43N and Q38Y were, respectively, reduced to 60.8 and 93.1% compared to those of WT. Meanwhile, the k_cat of C43N was increased by 21.2-fold compared to that of WT. These imply that both the affinity and catalytic efficiency of C43N were significantly enhanced compared to WT. The Glide docking score of sucrose inside C43N was calculated to be -5.980, which was lower than that of WT (-4.887). What is more, the proposed general acid/base catalyst Glu273 with a lower pK_a value of C43N calculated by PROPKA might contribute to an easier catalytic reaction compared to that of WT. The thermal stability and pH stability of the mutant C43N were significantly enhanced compared to those of WT, and more hydrogen bonds formed during molecular dynamics simulations might contribute to the improved stability of C43N.

Improving the catalytic efficiency and dimeric stability of Cu,Zn superoxide dismutase by combining structure-guided consensus approach with site-directed mutagenesis

Superoxide dismutase (SOD) leads the front line of defense against injuries mediated by the reactive oxygen species (ROS). The SOD from a high-altitude plant Potentilla atrosanguinea is a unique thermostable enzyme. In this study, we applied a structure-guided consensus approach on Cu,Zn SOD from Potentilla atrosanguinea plant, to improve its enzymatic properties. The polar uncharged amino acid (threonine) at position 97 of wild-type (WT) SOD was selected as a target residue for substitution by aspartate (T97D) through site-directed mutagenesis. The WT and T97D were examined by a combinative approach consisting of robust computational and experimental tools. The in-silico analysis indicated improved dimeric stability in T97D as compared to the WT. The strong interactions between the monomers were related to improved dimerization and enhanced catalytic efficiency of T97D. These results were validated by in-vitro assays showing improved dimer stability and catalytic efficiency in T97D than WT. Moreover, the mutation also improved the thermostability of the enzyme. The combined structural and functional data described the basis for improved specific activity and thermostability. This study could expand the scope of interface residue to be explored as targets for designing of SODs with improved kinetics.

Improving the decolorization activity of Bacillus pumilus W3 CotA-laccase to Congo Red by rational modification

Congo Red (CR) is a typical azo dye with highly toxic and carcinogenic properties. This study aimed to improve the decolorization activity of Bacillus pumilus W3 CotA-laccase for azo dye CR. This work analyzed the interaction between CotA-laccase and CR based on homology modeling and molecular docking. The three amino acids (Gly323, Thr377, Thr418) in the substrate-binding pocket were rationally modified through saturation mutation. Finally, the obtained multi-site mutants T377I/T418G and G323S/T377I/T418G decolorized 76.59% and 59.37% of CR within 24 h at pH 8.0 without a mediator, which were 3.15- and 2.44-fold higher than the wild-type CotA. The catalytic efficiency of the multi-site mutants T377I/T418G and G323S/T377I/T418G to CR were increased by 2.21- and 2.01-fold compared with the wild-type CotA, respectively. The mechanism of activity enhancement of mutants was proposed by structural analysis. This evidence suggests that the mutants T377I/T418G and G323S/T377I/T418G could be used as novel bioremediation tools.

Chemically induced oxidative stress improved bacterial laccase-mediated degradation and detoxification of the synthetic dyes

To alleviate the risk of textile effluent, the development of highly effective bioremediation strategies for synthetic dye removal is needed. Herein, we aimed to assess whether intensified bioactivity of Bacillus pumilus ZB1 by oxidative stress could improve the removal of textile dyes. Methyl methanesulfonate (MMS) induced oxidative stress significantly promoted laccase expression of B. pumilus ZB1. Both the level of hydrogen dioxide and superoxide anion showed a significant positive correlation with laccase activity (RSQ = 0.963 and 0.916, respectively) along with the change of MMS concentration. The regulation of laccase expression was closely related to oxidative stress. The overexpressed laccase in the supernatant improved the decolorization of synthetic dyes (16.43% for Congo Red, 54.05% for Crystal Violet, and 41.61% for Reactive Blue 4). Laccase was subsequently expressed in E. coli. Investigation of the potential of bacterial laccase in dye remediation using Congo Red showed that an effective degradation of azo dye could be achieved with laccase treatment. Laccase remediation alleviated the cytotoxicity of Congo Red to human hepatocytes. In silico study identified eight amino acid residues of laccase involved in binding with Congo Red. Overall, regulation of oxidative stress towards bacterium can be used as a promising approach for the improvement of bacterial bioactivity in synthetic dye remediation.

An alkaline thermostable laccase from termite gut associated strain of Bacillus stratosphericus

Laccase, an important oxidoreductase, is widely distributed in various organisms. Termites are known to decompose lignocellulose efficiently with the aid of gut microorganisms. However, few laccases have been characterized from termite or its gut microbes. We aimed to screen the strain capable of degrading lignocellulose from fungus-growing termites. In this study, Bacillus stratosphericus BCMC2 with lignocellulolytic activity was firstly isolated from the hindgut of fungus-growing termite Macrotermes barneyi. The laccase gene (BaCotA) was cloned both from the BCMC2 strain and termite intestinal metagenomic DNA. BaCotA was overexpressed in E. coli, and the recombinant BaCotA showed high specific activity (554.1 U/mg). BaCotA was thermostable with an optimum temperature of 70 °C, pH 5.0. Furthermore, BaCotA was resistant to alkali and organic solvents. The enzyme remained more than 70% residual activity at pH 8.0 for 120 min; and the organic solvents such as methanol, ethanol and acetone (10%) had no inhibitory effect on laccase activity. Additionally, BaCotA exhibited efficient decolorization ability towards indigo and crystal violet. The multiple enzymatic properties suggested the presented laccase as a potential candidate for industrial applications. Moreover, this study highlighted that termite intestine is a good resource for either new strains or enzymes.

The catalytic properties of Thermus thermophilus SG0.5JP17-16 laccase were regulated by the conformational dynamics of pocket loop 6

BACKGROUND

Laccase is one member of the blue multicopper oxidase family. It can catalyze the oxidation of various substrates. The Thermus thermophilus SG0.5JP17-16 laccase (lacTT) is thermostable, pH-stable, and high tolerance to halides, and can decolorize the synthetic dyes. In lacTT, the function of the loop 6 constructing the substrate-binding pocket wasn't clear.

METHODS

The residues Asp394 and Asp396 located in loop 6, and were used to probe how the loop 6 influenced catalytic properties of the laccase. Site-directed mutagenesis was performed for two amino acids. Kinetic assay was utilized to characterize the catalytic efficiency of mutants. Mutants with different catalytic activities were used to decolorize the synthetic dyes to clarify the relationship between the catalytic efficiency and dye decolorization. Redox potential, structural and spectral analyses were performed to explain the differences in laccase activity between wild type and mutant enzymes.

RESULTS

D394M, D394E and D394R mutants with the lower laccase activity displayed a decreased decolorization efficiency, while D396A, D396M and D396E mutant enzymes with higher catalytic efficiency decolorized the synthetic dye more efficiently than the wild type enzyme.

CONCLUSIONS

The pocket loop 6 might experience a conformational dynamics. The D394 residue controlled this conformation change by amino acid interaction networks containing the D396 residue at the entrance of substrate channel.

GENERAL SIGNIFICANCES

These studies may provide clues to improve the activity of the laccase for the better use in industrial applications, and/or contribute to further understanding the mechanism of laccase oxidation on the substrate.

Improving decolorization of dyes by laccase from Bacillus licheniformis by random and site-directed mutagenesis

BACKGROUND

Dye wastewater increases cancer risk in humans. For the treatment of dyestuffs, biodegradation has the advantages of economy, high efficiency, and environmental protection compared with traditional physical and chemical methods. Laccase is the best candidate for dye degradation because of its multiple substrates and pollution-free products.

METHODS

Here, we modified the laccase gene of Bacillus licheniformis by error-prone PCR and site-directed mutagenesis and expressed in E. coli. The protein was purified by His-tagged protein purification kit. We tested the enzymatic properties of wild type and mutant laccase by single factor test, and further evaluated the decolorization ability of laccase to acid violet, alphazurine A, and methyl orange by spectrophotometry.

RESULTS

Mutant laccase Lacep69and D500G were superior to wild type laccase in enzyme activity, stability, and decolorization ability. Moreover, the laccase D500G obtained by site-directed mutagenesis had higher enzyme activity in both, and the specific activity of the purified enzyme was as high as 426.13 U/mg. Also, D500G has a higher optimum temperature of 70 °C and temperature stability, while it has a more neutral pH 4.5 and pH stability. D500G had the maximum enzyme activity at a copper ion concentration of 12 mM. The results of decolorization experiments showed that D500G had a strong overall decolorization ability, with a lower decolorization rate of 18% for methyl orange and a higher decolorization rate of 78% for acid violet.

CONCLUSION

Compared with the wild type laccase, the enzyme activity of D500G was significantly increased. At the same time, it has obvious advantages in the decolorization effect of different dyes. Also, the advantages of temperature and pH stability increase its tolerance to the environment of dye wastewater.

Enhancing the decolorization activity of Bacillus pumilus W3 CotA-laccase to Reactive Black 5 by site-saturation mutagenesis

Reactive Black 5 (RB5) is a typical refractory azo dye. Widespread utilization of RB5 has caused a variety of environmental and health problems. The enzymatic degradation of RB5 can be a promising solution due to its superiority as an eco-friendly and cost-competitive process. Bacterial CotA-laccase shows great application prospect to eliminate hazardous dyes from wastewater. However, efficient decolorization of RB5 CotA-laccase generally requires the participation of costly, toxic mediators. In the present study, we modified the amino acids Thr415 and Thr418 near the type 1 copper site and the amino acid Gln442 at the entrance of the substrate-binding pocket of Bacillus pumilus W3 CotA-laccase to boost its RB5 decolorization activity based on molecular docking analysis and site-saturation mutagenesis. Through the strategies, two double site mutants T415D/Q442A and T418K/Q442A obtained demonstrated 43.94 and 52.64% RB5 decolorization rates in the absence of a mediator at pH 10.0, respectively, which were about 3.70- and 4.43-fold higher compared with the wild-type CotA-laccase. Unexpectedly, the catalytic efficiency of the T418K/Q442A to ABTS was enhanced by 5.33-fold compared with the wild-type CotA-laccase. The mechanisms of conferring enhanced activity to the mutants were proposed by structural analysis. In summary, the mutants T415D/Q442A and T418K/Q442A have good application potentials for the biodegradation of RB5. KEY POINTS: • Three amino acids of CotA-laccase were manipulated by site-saturation mutagenesis. • Decolorization rate of two mutants to RB5 was enhanced 3.70- and 4.43-fold, respectively. • The mechanisms of awarding enhanced activity to the mutants were supposed.

Enhanced catalytic efficiency of CotA-laccase by DNA shuffling

Bacterial CotA-laccases exhibit higher activity in alkaline pH and salt concentration conditions compared to laccases from white-rot fungi. They are considered as green catalysts in decolorizing of industrial dyes. However, CotA-laccases are limited due to the low yield and catalytic efficiency as the spore-bound nature of CotA. A DNA shuffling strategy was applied to generate a random mutation library. To improve laccase activities, a mutant (T232P/Q367R 5E29) with two amino acid substitutions was identified. The catalytic efficiency of mutant 5E29 was 1.21 fold higher compared with that of the wild-type. The Km and k_cat values of 5E29 for SGZ were of 20.3 ± 1.3 µM and 7.6 ± 2.7 s^-1. The thermal stability was a slight enhancement. Indigo Carmine and Congo red were efficiently decolorized by using this mutant at pH 9.0. These results provide that 5E29 CotA-laccase is a good candidate for biotechnology applications under alkaline condition, with an effective decolorization capability.

Enhancement in catalytic activity of CotA-laccase from Bacillus pumilus W3 via site-directed mutagenesis

CotA-laccases are potential enzymes that are widely used in decolorization of dyes and degradation of toxic substances. In this study, a novel CotA-laccase gene from Bacillus pumilus W3 was applied for rational design. After a series of site-directed genetic mutations, the mutant S208G/F227A showed a 5.1-fold higher catalytic efficiency (k_cat/K_m) than the wild-type CotA-laccase did. The optimal pH of S208G/F227A was 3.5 with ABTS as substrate. The residual activity of mutant S208G/F227A was more than 80% after incubated for 10 h at pH 7-11. Mutant S208G/F227A showed optimal temperature at 80°C with ABTS as substrate. The thermal stability of mutant laccase S208G/F227A was lower than that of wild-type CotA-laccase. This study showed that Gly208 and Ala227 play key roles in catalytic efficiency and it is possible to improve catalytic efficiency of CotA-laccase through site-directed mutagenesis.

Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives

Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.

Enhanced hydrolysis of lignocellulosic biomass with doping of a highly thermostable recombinant laccase

A highly thermostable laccase from Geobacillus sp. strain WSUCF1 was cloned into Escherichia coli (E. coli) using pRham N-His SUMO expression system. The thermostable laccase with a molecular weight ~30 kDa had a t_1/2 (pH 6.0) of 120 h at 50 °C. The homology modelling for laccase structure showed the presence of Cu active centers with His and Cys residues involved in the active site and ligand binding activity of the enzyme, respectively. The K_m, V_max, K_cat and K_cat/K_m values of the purified enzyme with ABTS were found to be 0.146 mM, 1.52 U/mg, 1037 s^-1 and 7102.7 s^-1 mM^-1, respectively. The doping of recombinant WSUCF1 laccase to commercial enzyme cocktails Accellerase® 1500 and Cellic CTec2 improved the hydrolysis of untreated, alkali and acid treated corn stover by 1.31-2.28 times and bagasse by 1.32-2.02 times. Further, in-house enzyme cocktails with laccase hydrolyzed untreated, alkali and acid treated bagasse and gave 1.44, 1.1, and 0.92 folds higher sugar, respectively, when compared with Accellerase 1500. The results suggested that thermostable laccase can aid in the improved hydrolysis of lignocellulosic biomass.

Engineered microbial host selection for value-added bioproducts from lignocellulose

Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.

Bacterial laccases: promising biological green tools for industrial applications

Multicopper oxidases (MCOs) are a pervasive family of enzymes that oxidize a wide range of phenolic and nonphenolic aromatic substrates, concomitantly with the reduction of dioxygen to water. MCOs are usually divided into two functional classes: metalloxidases and laccases. Given their broad substrate specificity and eco-friendliness (molecular oxygen from air as is used as the final electron acceptor and they only release water as byproduct), laccases are regarded as promising biological green tools for an array of applications. Among these laccases, those of bacterial origin have attracted research attention because of their notable advantages, including broad substrate spectrum, wide pH range, high thermostability, and tolerance to alkaline environments. This review aims to summarize the significant research efforts on the properties, mechanisms and structures, laccase-mediator systems, genetic engineering, immobilization, and biotechnological applications of the bacteria-source laccases and laccase-like enzymes, which principally include Bacillus laccases, actinomycetic laccases and some other species of bacterial laccases. In addition, these enzymes may offer tremendous potential for environmental and industrial applications.

Establishment of a markerless multiple-gene deletion method based on Cre/loxP mutant system for Bacillus pumilus

In this study, we established a Cre/loxP mutant recombination system (Cre/lox71-66 system) for markerless gene deletion to facilitate our follow-up rational genetic engineering to the strain Bacillus pumilus W3. This modified method uses two mutant loxP sites, which after recombination creates a double-mutant loxP site that is poorly recognized by Cre recombinase, facilitating multiple gene deletions in a single genetic background. Two selected genes, cotA and sigF, were continuously knocked out and verified at different levels using this method. This method is simple and efficient and can be easily implemented for multiple gene deletions in B. pumilus.