Trends in lipase engineering for enhanced biocatalysis.

Lipases, also known as triacylglycerol hydrolases (E.C.No. 3.1.1.3), are considered as leading biocatalysts in the lipid modification business. With properties like ease of availability, capability to work in heterogeneous media, stability in organic solvents, property of catalyzing at the lipid-water interface and even in nonaqueous conditions, have made them a versatile choice for applications in the food, flavor, detergent, pharmaceutical, leather, textile, cosmetic, and paper industries [1]. The increasing alertness toward sustainable technologies, lesser waste generation and solvent usage and minimization of energy input has brought light toward the production and usage of recombinant/improved lipases. For example, Novozym 435, a broadly used recombinant lipase isolated from Candida antarctica, dominates the lipase industry and has even created a supplier bias in the market. This shows that there is a desperate need for novel, low-cost lipases with better properties. For this, mining of existing extremophilic genomes seems more rewarding. But considering the diversity of industrial requirements such as types of solvents used or carrier systems employed for enzyme immobilization, tailor-designed enzymes are an unrealized pressing priority. Therefore, protein engineering strategies in collaboration with the discovery of new lipases can serve as a vital tool to obtain tailor-made enzymes with specific characteristics.

N-terminal domain replacement changes an archaeal monoacylglycerol lipase into a triacylglycerol lipase.

BACKGROUND: Lipolytic enzymes of hyperthermophilic archaea generally prefer small carbon chain fatty acid esters (C2-C12) and are categorized as esterases. However, a few have shown activity with long-chain fatty acid esters, but none of them have been classified as a true lipase except a lipolytic enzyme AFL from Archaeglobus fulgidus. Thus, our main objective is to engineer an archaeal esterase into a true thermostable lipase for industrial applications. Lipases which hydrolyze long-chain fatty acid esters display an interfacial activation mediated by the lid domain which lies over active site and switches to open conformation at the oil-water interface. Lid domains modulate enzyme activities, substrate specificities, and stabilities which have been shown by protein engineering and mutational analyses. Here, we report engineering of an uncharacterized monoacylglycerol lipase (TON-LPL) from an archaeon Thermococcus onnurineus (strain NA1) into a triacylglycerol lipase (rc-TGL) by replacing its 61 N-terminus amino acid residues with 118 residues carrying lid domain of a thermophilic fungal lipase-Thermomyces lanuginosus (TLIP). RESULTS: TON-LPL and rc-TGL were cloned and overexpressed in E. coli, and the proteins were purified by Ni-NTA affinity chromatography for biochemical studies. Both enzymes were capable of hydrolyzing various monoglycerides and shared the same optimum pH of 7.0. However, rc-TGL showed a significant decrease of 10 °C in its optimum temperature (Topt). The far UV-CD spectrums were consistent with a well-folded α/ß-hydrolase fold for both proteins, but gel filtration chromatography revealed a change in quaternary structure from trimer (TON-LPL) to monomer (rc-TGL). Seemingly, the difference in the oligomeric state of rc-TGL may be linked to a decrease in temperature optimum. Nonetheless, rc-TGL hydrolyzed triglycerides and castor oil, while TON-LPL was not active with these substrates. CONCLUSIONS: Here, we have confirmed the predicted esterase activity of TON-LPL and also performed the lid engineering on TON-LPL which effectively expanded its substrate specificity from monoglycerides to triglycerides. This approach provides a way to engineer other hyperthermophilic esterases into industrially suitable lipases by employing N-terminal domain replacement. The immobilized preparation of rc-TGL has shown significant activity with castor oil and has a potential application in castor oil biorefinery to obtain value-added chemicals.

SGNH hydrolase-type esterase domain containing Cbes-AcXE2: a novel and thermostable acetyl xylan esterase from Caldicellulosiruptor bescii.

Caldicellulosiruptor bescii, the most thermophilic cellulolytic bacterium, is rich in hydrolytic and accessory enzymes that can degrade untreated biomass, but the precise role of many these enzymes is unknown. One of such enzymes is a predicted GDSL lipase or esterase encoded by the locus Athe_0553. In this study, this probable esterase named as Cbes-AcXE2 was overexpressed in Escherichia coli. The Ni-NTA affinity purified enzyme exhibited an optimum pH of 7.5 at an optimum temperature of 70 °C. Cbes-AcXE2 hydrolyzed p-nitrophenyl (pNP) acetate, pNP-butyrate, and phenyl acetate with approximately equal efficiency. The specific activity and K M for the most preferred substrate, phenyl acetate, were 142 U/mg and 0.85 mM, respectively. Cbes-AcXE2 removed the acetyl group of xylobiose hexaacetate and glucose pentaacetate like an acetyl xylan esterase (AcXE). Bioinformatics analyses suggested that Cbes-AcXE2, which carries an SGNH hydrolase-type esterase domain, is a member of an unclassified carbohydrate esterase (CE) family. Moreover, Cbes-AcXE2 is evolutionarily and biochemically similar to an unclassified AcXE, Axe2, of Geobacillus stearothermophilus. Thus, we proposed a novel family of carbohydrate esterase for both Cbes-AcXE2 and Axe2.

Heterologous expression and biochemical studies of a thermostable glucose tolerant ß-glucosidase from Methylococcus capsulatus (bath strain).

Glucose inhibition of ß-glucosidase (BG) is a bottleneck in biomass hydrolysis. In this study, a glucose resistant GH1 ß-glucosidase gene- Mbgl from Methylococcus capsulatus (bath strain) was cloned and overexpressed in E.coli. The Ni-NTA affinity purified Mbgl displayed an optimum temperature of 70°C and optimum pH was 6.0. The calculated KM of the enzyme was 48.6mM and 0.12mM for cellobiose and 4-Nitrophenyl ß-d-glucopyranoside (PNPG) respectively. PNPG hydrolysis in presence of various glucose concentrations showed that the enzyme was stimulated by ∼2.2 fold at 50mM glucose and was not inhibited up to 450-500mM glucose. Homology modeling and structural comparisons of Mbgl with a glucose tolerant ß-glucosidase of Humicola insolens (HiBG) revealed that the Mbgl has a much broader active site unlike to a deep and narrow active site pocket of HiBG. The difference in active site shape reflects on an alternative mechanism of glucose tolerance in Mbgl. Supplementing a commercial cellulase enzyme mixture CTec with Mbgl in the hydrolysis of the pretreated rice straw enhanced the glucose yield by 10-15%. In addition, Mbgl was also stable in organic solvents, detergents and oxidative conditions which would be advantageous for biotechnological applications.

Dataset of gene cloning and gel filtration chromatography of R-est6.

The data presented in this article are connected to the research article entitled "Expression, purification and biochemical characterization of a family 6 carboxylesterase from Methylococcus capsulatus (bath)" (Soni et al., 2016 [1]). The family 6 carboxylesterases are the smallest and display broad substrate specificity. The 1 kb gene encoding, a family 6 carboxylesterase - R-est6, was amplified from the genome of M. capsulatus (bath strain), and showed in the agarose gel. The corresponding purified protein, after overexpression in Escherichia coli, was biochemically studied in the research article (Soni et al., 2016 [1]). R-est6 has hydrophobic patches on the surface so, it is expected to show oligimeric forms. Here, we have confirmed the presence of oligomers by gel filtration chromatography data and the proteins belonging to the different peaks are shown on a SDS-PAGE.

Expression, purification and biochemical characterization of a family 6 carboxylesterase from Methylococcus capsulatus (bath).

The genome of Methylococcus capsulatus (bath) encodes a protein R-est6 that is annotated as a lipase family 3 protein. The phylogenetic and the sequence analyses linked this protein to the family 6 carboxylesterase. The gene encoding R-est6 was cloned and overexpressed in Escherichia coli and the recombinant 6x-His tagged protein was purified by Ni-NTA affinity chromatography. The buffers used in the purification were modified by adding 1% glycerol instead of the salt to prevent the protein aggregation. Far UV-CD spectrum and gel filtration chromatography of the purified R-est6 confirmed that the protein was well folded like a typical α/ß hydrolase and had the quaternary structure of a tetramer, in addition to a compact monomer. The optimum pH was in the range of 7.0-9.0 and the optimum temperature was at 55 °C for the hydrolysis of pNP-butyrate. As expected, being a member of the family 6 carboxylesterase, R-est6 hydrolyzed triglycerides, pNP esters of the small and the medium fatty acid chain esters and an aryl ester-phenyl acetate. However, R-est6 was also found to hydrolyze the long-chain fatty acid ester which had never been reported for the family 6 carboxylesterase. Additionally, R-est6 was stable and active in the different water-miscible organic solvents. Therefore, the broad substrate range and the structural stability of R-est6 would be advantageous for its application in industrial processes.