Thermal and pH inactivation of an immobilized thermostable β-galactosidase from Thermus sp. strain T2: Comparison to the free enzyme

Quantifying microbial guilds

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

Laccase multi-point covalent immobilization: characterization, kinetics, and its hydrophobicity applications

Laccase from Myceliophthora thermophila was immobilized using one-point and multi-point covalent attachment on both a native and a modified new commercial epoxy carrier (Immobead 150P). After 10 cycles of operation at pH 3.0 and temperature 70 °C, the multi-point covalently immobilized laccase on the modified Immobead 150P performed best in terms of immobilization characteristics, retaining 95% of its initial activity. Thermodynamic parameters of thermal inactivation emphasized the positive impact of the immobilization procedure. At 50 °C, the immobilized and free enzyme activity levels dropped by 27 and 73%, respectively, after 48 h of incubation. The immobilized enzyme enhanced its stability in alkaline conditions, resuming 95% of its original activity after 3 h at pH 9.0. Immobilization reduced substrate affinity because the free laccase's K_m value was lower than that of the immobilized laccase. Finally, the application of immobilized laccase in an innovative wood treatment process was tested by grafting lauryl gallate (LG) in order to provide hydrophobic properties to the wood. The results showed a relative water contact angle of 85.7% for treated wood, whereas the control showed only 26.6%, after 4 min of contact between water and beechwood surface. KEY POINTS: • Multi-point covalent immobilization of a commercial laccase on a commercial support. • Enzymatic parameters generally improved by immobilization process. • New application of immobilized laccase: enzymatic-assisted wood hydrophobization.

Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy

Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t_1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t_1/2 at 35 °C and a 5.7 °C increase in melting temperature (T_m). Unexpectedly, its specific activity and catalytic efficiency (k_cat/K_m) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.

Aliivibrio fischeri L-Asparaginase production by engineered Bacillus subtilis: a potential new biopharmaceutical

L-Asparaginase (L-ASNase) is an enzyme applied in the treatment of lymphoid malignancies. However, an innovative L-ASNase with high yield and lower side effects than the commercially available preparations are still a market requirement. Here, a new-engineered Bacillus subtilis strain was evaluated for Aliivibrio fischeri L-ASNase II production, being the bioprocess development and the enzyme characterization studied. The pBS0E plasmid replicative in Bacillus sp and containing PxylA promoter inducible by xylose and its repressive molecule sequence (XylR) was used for the genetic modification. Initially, cultivations were carried out in orbital shaker, and then the process was scaled up to stirred tank bioreactor (STB). After the bioprocess, the cells were recovered and submitted to ultrasound sonication for cells disruption and intracellular enzyme recovery. The enzymatic extract was characterized to assess its biochemical, kinetic and thermal properties using L-Asparagine and L-Glutamine as substrates. The results indicated the potential enzyme production in STB achieving L-ASNase activity up to 1.539 U mL^-1. The enzymatic extract showed an optimum pH of 7.5, high L-Asparagine affinity (K_m = 1.2275 mmol L^-1) and low L-Glutaminase activity (0.568-0.738 U mL^-1). In addition, thermal inactivation was analyzed by two different Kinect models to elucidate inactivation mechanisms, low kinetic thermal inactivation constants for 25 ºC and 37 ºC (0.128 and 0.148 h^-1, respectively) indicate an elevated stability. The findings herein show that the produced recombinant L-ASNase has potential to be applied for pharmaceutical purposes.

Simultaneous improvement of the thermostability and activity of lactic dehydrogenase from Lactobacillus rossiae through rational design

d-Phenyllactic acid, is a versatile organic acid with wide application prospects in the food, pharmaceutical and material industries. Wild-type lactate dehydrogenase LrLDH from Lactobacillus rossiae exhibits a high catalytic performance in the production of d-phenyllactic acid from phenylpyruvic acid or sodium phenylpyruvate, but its industrial application is hampered by poor thermostability. Here, computer aided rational design was applied to improve the thermostability of LrLDH. By using HotSpot Wizard 3.0, five hotspot residues (N218, L237, T247, D249 and S301) were identified, after which site-saturation mutagenesis and combined mutagenesis were performed. The double mutant D249A/T247I was screen out as the best variant, with optimum temperature, t_1/2, and T¹⁰₅₀ that were 12 °C, 17.96 min and 19 °C higher than that of wild-type LrLDH, respectively. At the same time, the k_cat/K_m of D249A/T247I was 1.47 s⁻¹ mM⁻¹, which was 3.4 times higher than that of the wild-type enzyme. Thus rational design was successfully applied to simultaneously improve the thermostability and catalytic activity of LrLDH to a significant extent. The results of molecular dynamics simulations and molecular structure analysis could explain the mechanisms for the improved performance of the double mutant. This study shows that computer-aided rational design can greatly improve the thermostability of d-lactate dehydrogenase, offering a reference for the modification of other enzymes.

The d-LDH was engineered using computationally-assisted rational mutagenesis. The two mutants D249A and D249A/T247I showed significantly enhanced thermostability and catalytic activity to sodium phenylpyruvate compared with the wild-type enzyme.

Enhanced Thermostability of D-Psicose 3-Epimerase from Clostridium bolteae through Rational Design and Engineering of New Disulfide Bridges

D-psicose 3-epimerase (DPEase) catalyzes the isomerization of D-fructose to D-psicose (aka D-allulose, a low-calorie sweetener), but its industrial application has been restricted by the poor thermostability of the naturally available enzymes. Computational rational design of disulfide bridges was used to select potential sites in the protein structure of DPEase from Clostridium bolteae to engineer new disulfide bridges. Three mutants were engineered successfully with new disulfide bridges in different locations, increasing their optimum catalytic temperature from 55 to 65 °C, greatly improving their thermal stability and extending their half-lives (t_1/2) at 55 °C from 0.37 h to 4−4.5 h, thereby greatly enhancing their potential for industrial application. Molecular dynamics simulation and spatial configuration analysis revealed that introduction of a disulfide bridge modified the protein hydrogen–bond network, rigidified both the local and overall structures of the mutants and decreased the entropy of unfolded protein, thereby enhancing the thermostability of DPEase.

Kinetic and thermodynamic study of laccase cross-linked onto glyoxyl Immobead 150P carrier: Characterization and application for beechwood biografting

In this study, we cross-linked aminated Thermothelomyces thermophilus laccase onto Immobead 150P epoxy carrier, and achieved an immobilization yield of 99.84 %. The optimum temperature and pH values for the oxidation of ABTS by laccase were determined to be 70 °C and pH 3.0. After 6 h at 50 °C, laccase activity was diminished by about 13 % in the free form and 28 %, in the immobilized form. K_m values for both free and cross-linked laccase were 0.051 and 0.567 mM, whereas V_max values were 2.027 and 0.854 μmol. min^-1, respectively. The immobilized laccase was able to preserve its full activity for 6 weeks, retaining approximately 95 % and 78 % of its initial activity after 8 and 20 weeks, respectively. The contact angles were two-fold higher when the laccase enzyme was occupied in the biografting reaction, revealing that the hydrophobic compound bonded stably onto beechwood samples.

Remediation and improvement of 2,4-dichlorophenol contaminated soil by biochar-immobilized laccase

In this paper, laccase was immobilized with the adsorption-crosslinking method in which biochar was used as the carrier and glutaraldehyde was used as the crosslinking agent. Firstly, the optimal immobilization conditions and optimal operating conditions were investigated, and then the stability of both free laccase and immobilized laccase was compared. Finally, the 2,4-dichlorophenol contaminated soil was remedied with both free laccase and immobilized laccase, and the improvement on the remediation of the contaminated soil by immobilized laccase was analysed through the ecological evaluation. The results showed that in the optimal immobilization condition, the biochar with a particle size of 30 mesh should be selected, and glutaraldehyde with a volume fraction of 4% and 20 mL of laccase solution should be added to complete the 6-hour adsorption operation and 4-hour crosslinking operation. The stability of immobilized laccase was better than that of free laccase, and the thermal deactivation kinetic equation for the free laccase was lnA = -0.7657t + 0.4344 and the thermal deactivation kinetic equation for the immobilized laccase was lnA = -0.1048t + 0.0608, respectively. The degradation ability of immobilized laccase for 2-4 dichlorophenol was better than that of free laccase. The degradation rate of 2,4-dichlorophenol was 44.4% in the free laccase group and 64.6% in the immobilized laccase group. The ecological evaluation showed that the biochar-immobilized laccase had a positive effect on the soil ecological environment in the remediation process of the soil and can improve the remediation of the contaminated soil to some extent.

Study on improving the stability of adsorption-encapsulation immobilized Laccase@ZIF-67

Laccase (Trametes versicolor) was immobilized onto/into zeolite imidazolate framework-67 (ZIF-67) for the first time, materials were performed by assisting one-pot synthesis strategy in aqueous solution at room temperature. The resulting laccase@ZIF-67 composite was characterized by powder X-ray diffraction (PXRD), fourier transform infrared (FT-IR) spectroscopies, field emission scanning electron microscopy (FE-SEM) and energy dispersive X-ray (EDX), thermal gravimetric analyses (TGA). The results showed that laccase could be well immobilized on ZIF-67 materials. Laccase@ZIF-67 was stable on storage stability and reuseablility, retaining 88 % (15 days at 4 °C) and 59 % (five reaction cycles) of residual enzyme activity. Laccase@ZIF-67 exhibited relatively stable activity at pH 3-5. In addition, the thermal deactivation kinetic studies of laccase@ZIF-67 showed a lower k value, higher t1/2 and ΔG values along with the enhancement of thermodynamic parameters than that of free laccase, and laccase@ZIF-67 had excellent level of thermostability.

Enhancing thermostability of Yarrowia lipolytica lipase 2 through engineering multiple disulfide bonds and mitigating reduced lipase production associated with disulfide bonds

The limited thermostability of Yarrowia lipolytica lipase 2 (Lip2) hampers its industrial application. To improve its thermostability, we combined single disulfide bonds which our group identified previously. In this study, combining different regional disulfide bonds had greater effect than combining same regional disulfide bonds. Furthermore, mutants with 4, 5, and 6 disulfide bonds exhibited dramatically enhanced thermostability. Compared with the wild-type, sextuple mutant 6s displayed a 22.53 and 31.23 ℃ increase in the melting temperature (T_m) and the half loss temperature at 15 min (T15 50), respectively, with greater pH stability and a wider reaction pH range. Molecular dynamics simulation revealed that multiple disulfide bonds resulted in more rigid structures of mutants 4s, 5s and 6s, and prolonged enzyme unfolding times. Moreover, secretions of mutants 5s and 6s were significantly increased by 60% and 80% by co-expressing with the chaperone protein disulfide isomerase (PDI), which mitigated the reduced production issue caused by multiple disulfide bonds. Results of this study indicated that enhanced heat endurance giving more potential for industrial application.

Thermal inactivation kinetics of Aspergillus oryzae β-galactosidase in concentrated lactose solution

Thermal inactivation of a commercial β-galactosidase from Aspergillus oryzae in a 300 g/L lactose solution was studied in the temperature range of 65–75 °C. Lactose exhibited a stabilisation effect when similar inactivation rates as those in lactose solution were observed in a lactose-free solution at temperatures lower by 5°C. Inactivation process in the lactose solution was biphasic. A kinetic model based on the Lumry-Eyring mechanism was proposed and successfully verified. Estimated activation energy values were very different. Rather high activation energy values of the forward reactions were responsible for both the significant change of rate constants and the rate-controlling reaction with temperature. For these two reasons, an increase of the operational lifetime of the enzyme from 7 days at 60 °C to 580 days at 55 °C was predicted.

Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identity

Biomass deconstruction to small simple sugars is a potential approach to biofuels production; however, the highly recalcitrant nature of biomass limits the economic viability of this approach. Thus, research on efficient biomass degradation is necessary to achieve large-scale production of biofuels. Enhancement of cellulolytic activity by increasing synergism between cellulase enzymes holds promise in achieving high-yield biofuels production. Here we have inserted cellulase pairs from extremophiles into hyperstable α-helical consensus ankyrin repeat domain scaffolds. Such chimeric constructs allowed us to optimize arrays of enzyme pairs against a variety of cellulolytic substrates. We found that endocellulolytic domains CelA (CA) and Cel12A (C12A) act synergistically in the context of ankyrin repeats, with both three and four repeat spacing. The extent of synergy differs for different substrates. Also, having C12A N-terminal to CA provides greater synergy than the reverse construct, especially against filter paper. In contrast, we do not see synergy for these enzymes in tandem with CelK (CK) catalytic domain, a larger exocellulase, demonstrating the importance of enzyme identity in synergistic enhancement. Furthermore, we found endocellulases CelD and CA with three repeat spacing to act synergistically against filter paper. Importantly, connecting CA and C12A with a disordered linker of similar contour length shows no synergistic enhancement, indicating that synergism results from connecting these domains with folded ankyrin repeats. These results show that ankyrin arrays can be used to vary spacing and orientation between enzymes, helping to design and optimize artificial cellulosomes, providing a novel architecture for synergistic enhancement of enzymatic cellulose degradation. Proteins 2016; 84:1043-1054. © 2016 Wiley Periodicals, Inc.

Immobilization of laccase on functionalized multiwalled carbon nanotube membranes and application for dye decolorization

Myceliophthora thermophilalaccase was covalently immobilized on functionalized multiwalled carbon nanotubes (MWNT) arranged over a supporting membrane to obtain a permeable bio-barrier that could be applied in multibatch or continuous processes.

Immobilization of laccase on modified silica: stabilization, thermal inactivation and kinetic behaviour in 1-ethyl-3-methylimidazolium ethylsulfate ionic liquid

Laccase was immobilized on modified silica carrier. The immobilization conditions, pH and enzyme concentration were optimized. Operational stability of 10 reaction cycles showed that immobilized laccase in buffer was stable, presenting an activity loss <30%. Nevertheless, a high decrease >80% was obtained in ionic liquid (IL) solution. Activity of immobilized laccase was maintained when incubated in IL. After 7days of incubation, immobilized laccase lost 30-50% of its initial activity. Immobilization also improved thermal stability of laccase in the presence of IL. Enzyme kinetics was modelled with Michaelis-Menten model. The Km value for free laccase increases significantly with the IL concentration. Slight differences were found in Vm for free enzyme. Unusual kinetic behaviour was obtained for immobilized laccase in IL: Both Vm and Km increased with IL concentration, resulting in increased catalytic efficiency of the immobilized enzyme in presence of IL.

Effect of the inducers veratryl alcohol, Xylidine, and ligninosulphonates on activity and thermal stability and inactivation kinetics of laccase from Trametes versicolor

Laccase production from Trametes versicolor was improved in the presence of the inducers ligninosulphonates, veratryl alcohol, and xylidine respectively two-, four-, and eightfold. The thermal inactivation of the produced laccase, after partial purification with ammonium sulfate was kinetically investigated at various temperatures (60-70 °C) and pH values (3.5, 4.5, and 5.5). The inactivation process followed first-order kinetics for all conditions tested, except for veratryl alcohol, for which a constant activity level was observed at the end of the inactivation, also after first-order decay. Enzyme thermostability was affected by the type of inducer used in the culture medium for the production of laccase and also by the pH of incubation mixture. Generally, laccase stability increased with pH increment, being more stable at pH 5.5, except with xylidine. At pHs 4.5 and 5.5, the three inducers significantly increased laccase thermal stability, with the higher effect being observed for pH 5.5 and ligninosulphonates, where increment of half-life times ranged from 3- to 20-fold, depending on the temperature.

Enhancing the functional properties of thermophilic enzymes by chemical modification and immobilization

The immobilization of proteins (mostly typically enzymes) onto solid supports is mature technology and has been used successfully to enhance biocatalytic processes in a wide range of industrial applications. However, continued developments in immobilization technology have led to more sophisticated and specialized applications of the process. A combination of targeted chemistries, for both the support and the protein, sometimes in combination with additional chemical and/or genetic engineering, has led to the development of methods for the modification of protein functional properties, for enhancing protein stability and for the recovery of specific proteins from complex mixtures. In particular, the development of effective methods for immobilizing large multi-subunit proteins with multiple covalent linkages (multi-point immobilization) has been effective in stabilizing proteins where subunit dissociation is the initial step in enzyme inactivation. In some instances, multiple benefits are achievable in a single process. Here we comprehensively review the literature pertaining to immobilization and chemical modification of different enzyme classes from thermophiles, with emphasis on the chemistries involved and their implications for modification of the enzyme functional properties. We also highlight the potential for synergies in the combined use of immobilization and other chemical modifications.

Hyperthermophilic enzymes − stability, activity and implementation strategies for high temperature applications

Current theories agree that there appears to be no unique feature responsible for the remarkable heat stability properties of hyperthermostable proteins. A concerted action of structural, dynamic and other physicochemical attributes are utilized to ensure the delicate balance between stability and functionality of proteins at high temperatures. We have thoroughly screened the literature for hyperthermostable enzymes with optimal temperatures exceeding 100 degrees C that can potentially be employed in multiple biotechnological and industrial applications and to substitute traditionally used, high-cost engineered mesophilic/thermophilic enzymes that operate at lower temperatures. Furthermore, we discuss general methods of enzyme immobilization and suggest specific strategies to improve thermal stability, activity and durability of hyperthermophilic enzymes.