A novel thermophilic and halophilic esterase from Janibacter sp. R02, the first member of a new lipase family (Family XVII)

AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer

A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.

Characterization of a novel carboxylesterase from Streptomyces lividans TK24 and site-directed mutagenesis for its thermostability

As an industrial enzyme that catalyzes the formation and cleavage of ester bonds, carboxylesterase has attracted attention in fine chemistry, pharmaceutical, biological energy and bioremediation fields. However, the weak thermostability limits their further developments in industrial applications. In this work, a novel carboxylesterase (EstF) from Streptomyces lividans TK24, belonging to family XVII, was acquired by successfully heterologous expressed and biochemically identified. The EstF exhibited optimal activity at 55 °C, pH 9.0 and excellent catalytic performances (Km = 0.263 mM, kcat/Km = 562.3 s-1 mM-1 for p-nitrophenyl acetate (pNPA2) hydrolysis). Besides, the EstF presented exceptionally high thermostability with a half-life of 387.23 h at 55 °C and 2.86 h at 100 °C. Furthermore, the EstF was modified to obtain EstFP144G using the site-directed mutation technique to investigate the effect of single glycine on thermostability. Remarkably, the mutant EstFP144G displayed a 5.10-fold increase of half-life at 100 °C versus wild-type without affecting catalytic performance. Structural analysis implied that the glycine introduction could release a steric strain and induce cooperative effects between distal residues to increase the thermostability. Therefore, the thermostable EstF and EstFP144G with prominently catalytic characteristics have potential industrial applications and the introduction of a single glycine strategy opens up alternative avenues for the thermostability engineering of other enzymes.

Solvent tolerant enzymes in extremophiles: Adaptations and applications

Non-aqueous enzymology has always drawn attention due to the wide range of unique possibilities in biocatalysis. In general, the enzymes do not or insignificantly catalyze substrate in the presence of solvents. This is due to the interfering interactions of the solvents between enzyme and water molecules at the interface. Therefore, information about solvent-stable enzymes is scarce. Yet, solvent-stable enzymes prove quite valuable in the present day biotechnology. The enzymatic hydrolysis of the substrates in solvents synthesizes commercially valuable products, such as peptides, esters, and other transesterification products. Extremophiles, the most valuable yet not extensively explored candidates, can be an excellent source to investigate this avenue. Due to inherent structural attributes, many extremozymes can catalyze and maintain stability in organic solvents. In the present review, we aim to consolidate information about the solvent-stable enzymes from various extremophilic microorganisms. Further, it would be interesting to learn about the mechanism adapted by these microorganisms to sustain solvent stress. Various approaches to protein engineering are used to enhance catalytic flexibility and stability and broaden biocatalysis's prospects under non-aqueous conditions. It also describes strategies to achieve optimal immobilization with minimum inhibition of the catalysis. The proposed review would significantly aid our understanding of non-aqueous enzymology.

Biochemical characterization, substrate and stereoselectivity of an outer surface putative α/β hydrolase from the pathogenic Leptospira

The genome of pathogenic leptospira encodes a plethora of outer surface and secretory proteins. The outer surface or secreted α/β hydrolases in a few pathogenic organisms are crucial virulent factors. They hydrolyze host immune factors and pathogen's immune-activating ligands, which help pathogens to evade the host's innate immunity. In this study, we report biochemical characterizations, substrate and stereoselectivity of one of the leptospiral outer surface putative α/β hydrolases, IQB77_09235 (LABH). Purified LABH displayed better kinetic parameters towards small water-soluble esters such as p-nitrophenyl acetate and p-nitrophenyl butyrate. The LABH exhibited moderate thermostability and displayed a pH optimum of 8.5. Remarkably, a phylogenetic study suggested that LABH does not cluster with other characterized bacterial esterases or lipases. Protein structural modeling revealed that some structural features are closely associated with Staphylococcus hycus lipase (SAH), a triacylglycerol hydrolase. The hydrolytic activity of the protein was found to be inhibited by a lipase inhibitor, orlistat. Biocatalytic application of the protein in the kinetic resolution of racemic 1-phenylethyl acetate reveals excellent enantioselectivity (E > 500) in the production of (R)-1-phenylethanol, a valuable chiral synthon in several industries. To our knowledge, this is the first detailed characterization of outer surface α/β hydrolases from leptospiral spp.

Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins

Microbial lipases are very prominent biocatalysts because of their ability to catalyze a wide variety of reactions in aqueous and non-aqueous media. Here microbial lipases from different origins (psychrophiles, mesophiles, and thermophiles) have been reviewed. This review emphasizes an update of structural diversity in temperature adaptation and industrial applications, of psychrophilic, mesophilic, and thermophilic lipases. The microbial origins of lipases are logically dynamic, proficient, and also have an extensive range of industrial uses with the manufacturing of altered molecules. It is therefore of interest to understand the molecular mechanisms of adaptation to temperature in occurring lipases. However, lipases from extremophiles (psychrophiles, and thermophiles) are widely used to design biotransformation reactions with higher yields, fewer byproducts, or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. Lipases as a multipurpose biological catalyst have given a favorable vision in meeting the needs of several industries such as biodiesel, foods, and drinks, leather, textile, detergents, pharmaceuticals, and medicals.

Recent Advances in the Enzymatic Synthesis of Polyester

Polyester is a kind of polymer composed of ester bond-linked polybasic acids and polyol. This type of polymer has a wide range of applications in various industries, such as automotive, furniture, coatings, packaging, and biomedical. The traditional process of synthesizing polyester mainly uses metal catalyst polymerization under high-temperature. This condition may have problems with metal residue and undesired side reactions. As an alternative, enzyme-catalyzed polymerization is evolving rapidly due to the metal-free residue, satisfactory biocompatibility, and mild reaction conditions. This article presented the reaction modes of enzyme-catalyzed ring-opening polymerization and enzyme-catalyzed polycondensation and their combinations, respectively. In addition, the article also summarized how lipase-catalyzed the polymerization of polyester, which includes (i) the distinctive features of lipase, (ii) the lipase-catalyzed polymerization and its mechanism, and (iii) the lipase stability under organic solvent and high-temperature conditions. In addition, this article also focused on the advantages and disadvantages of enzyme-catalyzed polyester synthesis under different solvent systems, including organic solvent systems, solvent-free systems, and green solvent systems. The challenges of enzyme optimization and process equipment innovation for further industrialization of enzyme-catalyzed polyester synthesis were also discussed in this article.

An overview of mammalian and microbial hormone-sensitive lipases (lipolytic family IV): biochemical properties and industrial applications

In mammals, hormone-sensitive lipase (EC 3.1.1.79) is an intracellular lipase that significantly regulates lipid metabolism. Mammalian HSL is more active towards diacylglycerol but lacks a lid covering the active site. Dyslipidemia, hepatic steatosis, cancer, and cancer-associated cachexia are symptoms of HSL pathophysiology. Certain microbial proteins show a sequence homologous to the catalytic domain of mammalian HSL, hence called microbial HSL. They possess a funnel-shaped substrate-binding pocket and restricted length of acyl chain esters, thus known as esterases. These enzymes have broad substrate specificities and are capable of stereo, regio, and enantioselective, making them attractive biocatalysts in a wide range of industrial applications in the production of flavors, pharmaceuticals, biosensors, and fine chemicals. This review will provide insight into mammalian and microbial HSLs, their sources, structural features related to substrate specificity, thermal stability, and their applications.

Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

Application of Hierarchical Clustering to Analyze Solvent-Accessible Surface Area Patterns in Amycolatopsis lipases

Simple Summary

Solvent-Accessible Surface Area (SASA) as the one dimensional structure property of the protein considers as the measuring the exposure of an amino acid residue to the solvent in one protein. It is an important structural property as the active sites of proteins are mostly located on the protein surfaces. The aim of this paper is to provide the clear information on different Amycolatopsis eburnea lipases based on the SASA patterns. This information could help in recognizing the structural stability and conformation as well as precise clustering them for revealing lipase evolution.

Abstract

The wealth of biological databases provides a valuable asset to understand evolution at a molecular level. This research presents the machine learning approach, an unsupervised agglomerative hierarchical clustering analysis of invariant solvent accessible surface areas and conserved structural features of Amycolatopsis eburnea lipases to exploit the enzyme stability and evolution. Amycolatopsis eburnea lipase sequences were retrieved from biological database. Six structural conserved regions and their residues were identified. Total Solvent Accessible Surface Area (SASA) and structural conserved-SASA with unsupervised agglomerative hierarchical algorithm were clustered lipases in three distinct groups (99/96%). The minimum SASA of nucleus residues was related to Lipase-4. It is clearly shown that the overall side chain of SASA was higher than the backbone in all enzymes. The SASA pattern of conserved regions clearly showed the evolutionary conservation areas that stabilized Amycolatopsis eburnea lipase structures. This research can bring new insight in protein design based on structurally conserved SASA in lipases with the help of a machine learning approach.

Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus

Esterases are a class of enzymes that split esters into an acid and an alcohol in a chemical reaction with water, having high potential in pharmaceutical, food and biofuel industrial applications. To advance the understanding of esterases, we have identified and characterized E53, an alkalophilic esterase from a marine bacterium Erythrobacter longus. The crystal structures of wild type E53 and three variants were solved successfully using the X-ray diffraction method. Phylogenetic analysis classified E53 as a member of the family IV esterase. The enzyme showed highest activity against p-nitrophenyl butyrate substrate at pH 8.5-9.5 and 40°C. Based on the structural feature, the catalytic pocket was defined as R1 (catalytic center), R2 (pocket entrance), and R3 (end area of pocket) regions. Nine variants were generated spanning R1-R3 and thorough functional studies were performed. Detailed structural analysis and the results obtained from the mutagenesis study revealed that mutations in the R1 region could regulate the catalytic reaction in both positive and negative directions; expanding the bottleneck in R2 region has improved the enzymatic activity; and R3 region was associated with the determination of the pH pattern of E53. N166A in R3 region showed reduced activity only under alkaline conditions, and structural analysis indicated the role of N166 in stabilizing the loop by forming a hydrogen bond with L193 and G233. In summary, the systematic studies on E53 performed in this work provide structural and functional insights into alkaliphilic esterases and further our knowledge of these enzymes.

Janibacter endophyticus sp. nov., an Endophytic Actinobacterium Isolated from the Root of Paris polyphylla Smith var. Yunnanensis

A novel endophytic actinobacterium, designated as strain YIM B02568^T, was isolated from the root of Paris polyphylla Smith var. Yunnanensis obtained from Yunnan Province, southwest China. Strain YIM B02568^T was characterized using a polyphasic approach. Phylogenetic analysis indicated that this isolate belonged to the genus Janibacter. The 16S rRNA gene sequence similarity values of strain YIM B02568^T to the type strains of members of this genus ranged from 95.8 to 98.6%. However, overall genome relatedness indices were significantly lower than the widely accepted species-defined threshold. The cell wall of strain YIM B02568^T contained meso-diaminopimelic acid. The major menaquinone was MK-8(H₄). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The major cellular fatty acids were comprised of iso-C_16:0 and C_18:1 ω9c. The DNA G + C content was 71.6 mol%. Based on the data from the polyphasic studies, we propose that strain YIM B02568^T represents a novel species within the genus Janibacter, Janibacter endophyticus sp. nov. The type strain is YIM B02568^T (= JCM 34639^T = CGMCC 1.18658^T).

Ancestral Sequence Reconstruction of Ancient Lipase from Family I.3 Bacterial Lipolytic Enzymes

Family I.3 lipase is distinguished from other families by the amino acid sequence and secretion mechanism. Little is known about the evolutionary process driving these differences. This study attempt to understand how the diverse temperature stabilities of bacterial lipases from family I.3 evolved. To achieve that, eighty-three protein sequences sharing a minimum 30% sequence identity with Antarctic Pseudomonas sp. AMS8 lipase were used to infer phylogenetic tree. Using ancestral sequence reconstruction (ASR) technique, the last universal common ancestor (LUCA) sequence of family I.3 was reconstructed. A gene encoding LUCA was synthesized, cloned and expressed as inclusion bodies in E. coli system. Insoluble form of LUCA was refolded using urea dilution method and then purified using affinity chromatography. The purified LUCA exhibited an optimum temperature and pH at 70℃ and 10 respectively. Various metal ions increased or retained the activity of LUCA. LUCA also demonstrated tolerance towards various organic solvents in 25% v/v concentration. The finding from this study could support the understanding on temperature and environment during ancient time. In overall, reconstructed ancestral enzymes have improved physicochemical properties that make them suitable for industrial applications and ASR technique can be employed as a general technique for enzyme engineering.

Investigation of Lipolytic-Secreting Bacteria from an Artificially Polluted Soil Using a Modified Culture Method and Optimization of Their Lipase Production

Compared to lipases from plants or animals, microbial lipases play a vital role in different industrial applications and biotechnological perspectives due to their high stability and cost-effectiveness. Therefore, numerous lipase producers have been investigated in a variety of environments in the presence of lipidic carbon and organic nitrogen sources. As a step in the development of cultivating the unculturable functional bacteria in this study, the forest soil collected from the surrounding plant roots was used to create an artificially contaminated environment for lipase-producing bacterial isolation. The ten strongest active bacterial strains were tested in an enzyme assay supplemented with metal ions such as Ca2+, Zn2+, Cu2+, Fe2+, Mg2+, K+, Co2+, Mn2+, and Sn2+ to determine bacterial tolerance and the effect of these metal ions on enzyme activity. Lipolytic bacteria in this study tended to grow and achieved a high lipase activity at temperatures of 35-40 °C and at pH 6-7, reaching a peak of 480 U/mL and 420 U/mL produced by Lysinibacillus PL33 and Lysinibacillus PL35, respectively. These potential lipase-producing bacteria are excellent candidates for large-scale applications in the future.

An encapsulated report on enzyme-assisted transesterification with an allusion to lipase

Biodiesel is a renewable, sulfur-free, toxic-free, and low carbon fuel which possesses enhanced lubricity. Transesterification is the easiest method employed for the production of biodiesel, in which the oil is transformed into biodiesel. Biocatalyst-mediated transesterification is more advantageous than chemical process because of its non-toxic nature, the requirement of mild reaction conditions, absence of saponification, easy product recovery, and production of high-quality biodiesel. Lipases are found to be the primary enzymes in enzyme-mediated transesterification process. Currently, researchers are using lipases as biocatalyst for transesterification. Lipases are extracted from various sources such as plants, microbes, and animals. Biocatalyst-based biodiesel production is not yet commercialized due to high-cost of purified enzymes and higher reaction time for the production process. However, research works are growing in the area of various cost-effective techniques for immobilizing lipase to improve its reusability. And further reduction in the production cost of lipases can be achieved by genetic engineering techniques. The reduction in reaction time can be achieved through ultrasonic-assisted biocatalytic transesterification. Biodiesel production by enzymatic transesterification is affected by many factors. Various methods have been developed to control these factors and improve biodiesel production. This report summarizes the various sources of lipase, various production strategies for lipase and the lipase-mediated transesterification. It is fully focused on the lipase enzyme and its role in biodiesel production. It also covers the detailed explanation of various influencing factors, which affect the lipase-mediated transesterification along with the limitations and scope of lipase in biodiesel production.

A Valuable Product of Microbial Cell Factories: Microbial Lipase

As a powerful factory, microbial cells produce a variety of enzymes, such as lipase. Lipase has a wide range of actions and participates in multiple reactions, and they can catalyze the hydrolysis of triacylglycerol into its component free fatty acids and glycerol backbone. Lipase exists widely in nature, most prominently in plants, animals and microorganisms, among which microorganisms are the most important source of lipase. Microbial lipases have been adapted for numerous industrial applications due to their substrate specificity, heterogeneous patterns of expression and versatility (i.e., capacity to catalyze reactions at the extremes of pH and temperature as well as in the presence of metal ions and organic solvents). Now they have been introduced into applications involving the production and processing of food, pharmaceutics, paper making, detergents, biodiesel fuels, and so on. In this mini-review, we will focus on the most up-to-date research on microbial lipases and their commercial and industrial applications. We will also discuss and predict future applications of these important technologies.

Wastewater from the Edible Oil Industry as a Potential Source of Lipase- and Surfactant-Producing Actinobacteria

Wastewaters generated from various stages of edible oil production in a canola processing facility were collected with the aim of determining the presence of lipase-producing actinobacteria of potential industrial significance. The high chemical oxygen demand (COD) readings (up to 86,700 mg L⁻¹ in some samples) indicated that the wastewater exhibited the nutritional potential to support bacterial growth. A novel approach was developed for the isolation of metagenomic DNA from the oil-rich wastewater samples. Microbiota analysis of the buffer tank and refinery condensate tank wastewater samples showed a dominance of Cutibacterium acnes subsp. defendens, followed by a limited number of other actinobacterial genera, indicating the presence of a highly specialized actinobacterial population. Cultured isolates with typical actinobacterial morphology were analyzed for their ability to produce lipases and biosurfactants. Two strains, designated as BT3 and BT4, exhibited the highest lipase production levels when grown in the presence of tributyrin and olive oil (1.39 U mg⁻¹ crude protein and 0.8 U mg⁻¹ crude protein, respectively) and were subsequently definitively identified by genome sequencing to be related to Streptomyces albidoflavus. Cultivation of the strains in media containing different types of oils did not markedly increase the level of enzyme production, with the exception of strain BT4 (1.0 U mg⁻¹ crude protein in the presence of peanut oil). Genome sequencing of the two strains, BT3 and BT4, revealed the presence of a range of lipase and esterase genes that may be involved in the production of the enzymes detected in this study. The presence of gene clusters involved in the production of biosurfactants were also detected, notably moreso in strain BT3 than BT4.

An integrated overview of bacterial carboxylesterase: Structure, function and biocatalytic applications

Carboxylesterases (CEs) are members of prominent esterase, and as their name imply, they catalyze the cleavage of ester linkages. By far, a considerable number of novel CEs have been identified to investigate their exquisite physiological and biochemical properties. They are abundant enzymes in nature, widely distributed in relatively broad temperature range and in various sources; both macroorganisms and microorganisms. Given the importance of these enzymes in broad industries, interest in the study of their mechanisms and structural-based engineering are greatly increasing. This review presents the current state of knowledge and understanding about the structure and functions of this ester-metabolizing enzyme, primarily from bacterial sources. In addition, the potential biotechnological applications of bacterial CEs are also encompassed. This review will be useful in understanding the molecular basis and structural protein of bacterial CEs that are significant for the advancement of enzymology field in industries.

A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity

Halotolerant lipolytic enzymes have gained growing interest, due to potential applications under harsh conditions, such as hypersalinity and presence of organic solvents. In this study, a lipolytic gene, est56, encoding 287 amino acids was identified by functional screening of a compost metagenome. Subsequently, the gene was heterologously expressed, and the recombinant protein (Est56) was purified and characterized. Est56 is a mesophilic (T_opt 50 °C) and moderate alkaliphilic (pH_opt 8) enzyme, showing high thermostability at 30 and 40 °C. Strikingly, Est56 is halotolerant as it exhibited high activity and stability in the presence of up to 4 M NaCl or KCl. Est56 also displayed enhanced stability against high temperatures (50 and 60 °C) and urea (2, 4, and 6 M) in the presence of NaCl. In addition, the recently reported halotolerant lipolytic enzymes were summarized. Phylogenetic analysis grouped these enzymes into 13 lipolytic protein families. The majority (45%) including Est56 belonged to family IV. To explore the haloadaptation of halotolerant enzymes, the amino acid composition between halotolerant and halophilic enzymes was statistically compared. The most distinctive feature of halophilic from non-halophilic enzymes are the higher content of acidic residues (Asp and Glu), and a lower content of lysine, aliphatic hydrophobic (Leu, Met and Ile) and polar (Asn) residues. The amino acid composition and 3-D structure analysis suggested that the high content of acidic residues (Asp and Glu, 12.2%) and low content of lysine residues (0.7%), as well as the excess of surface-exposed acidic residues might be responsible for the haloadaptation of Est56.

Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment

Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.

Identification, characterization, and immobilization of a novel YbfF esterase from Halomonas elongata

The YbfF esterase family, which has a bifurcated binding pocket for diverse ligands, could serve as excellent biocatalysts in industrial and biotechnological applications. Here, the identification, characterization, and immobilization of a novel YbfF esterase (YbfF_{Halomonas elongata}) from Halomonas elongata DSM 2581 is reported. Biochemical characterization of YbfF was carried out using activity staining, chromatographic analysis, kinetic analysis, activity assay, acetic acid release, and pH-indicator-based hydrolysis. YbfF_H.elongata displayed broad substrate specificity, including that for p-nitrophenyl esters, glucose pentaacetate, tert-butyl acetate, and β-lactam-containing compounds, with high efficiency. Based on a homology model of YbfF_H.elongata, Trp²³⁷ in the substrate-binding pocket, a critical residue for catalytic activity and substrate specificity was identified and characterized. Furthermore, crosslinked enzyme aggregates and nanoflower formation were explored to enhance the chemical stability and recyclability of YbfF_H.elongata. The present study is the first report of a YbfF esterase from extremophiles, and explains its protein stability, catalytic activity, substrate specificities and diversities, kinetics, functional residues, amyloid formation, and immobilization.

Characterization of a novel halotolerant esterase from Chromohalobacter canadensis isolated from salt well mine

A esterase gene was characterized from a halophilic bacterium Chromohalobacter canadensis which was originally isolated from a salt well mine. Sequence analysis showed that the esterase, named as EstSHJ2, contained active site serine encompassed by a conserved pentapeptide motif (GSSMG). The EstSHJ2 was classified into a new lipase/esterase family by phylogenetic association analysis. Molecular weight of EstSHJ2 was 26 kDa and the preferred substrate was p-NP butyrate. The EstSHJ2 exhibited a maximum activity at 2.5 M NaCl concentration. Intriguingly, the optimum temperature, pH and stability of EstSHJ2 were related to NaCl concentration. At 2.5 M NaCl concentration, the optimum temperature and pH of EstSHJ2 were 65 ℃ and pH 9.0, and enzyme remained 81% active after 80 ℃ treatment for 2 h. Additionally, the EstSHJ2 showed strong tolerance to metal ions and organic solvents. Among these, 10 mM K⁺, Ca²⁺ , Mg²⁺ and 30% hexane, benzene, toluene has significantly improved activity of EstSHJ2. The EstSHJ2 was the first reported esterase from Chromohalobacter canadensis, and may carry considerable potential for industrial applications under extreme conditions.

Characterization of a novel carboxylesterase belonging to family VIII hydrolyzing β-lactam antibiotics from a compost metagenomic library

A novel esterase, EstCS3, was isolated from a metagenomic library constructed from a compost. The EstCS3, which consists of 409 amino acids with an anticipated molecular mass of 44 kDa, showed high amino acid sequence identities to predicted esterases, serine hydrolases and β-lactamases from uncultured and cultured bacteria. Phylogenetic analysis suggested that EstCS3 belongs to family VIII of lipolytic enzymes. EstCS3 had catalytic Ser78 residue in the consensus tetrapeptide motif SXXK, which is characteristic of family VIII esterases. Two conserved YXX and W(H or K)XG motifs in an oxyanion hole of family VIII esterases were also present in EstCS3. EstCS3 demonstrated the highest activity toward p-nitrophenyl butyrate (C4) and was stable up to 70 °C with optimal activity at 55 °C. EstCS3 had optimal activity at pH 8 and maintained its stability within pH range of 7-10. EstCS3 had over 70% activity in the presence of 20% (v/v) methanol and DMSO and hydrolyzed sterically hindered tertiary alcohol esters of t-butyl acetate and linalyl acetate. EstCS3 hydrolyzed ampicillin, cephalothin and cefepime. The properties of EstCS3, including moderate thermostability, stability against organic solvents and activity toward esters of tertiary alcohols, indicated that it has the potential to be used in industrial applications.

Novel thermostable lipase produced by a thermo-halophilic bacterium that catalyses hydrolytic and transesterification reactions

Lipase belongs to the class of hydrolytic enzymes that are widely used in the biotechnology industries. The goal of this research was to purify and characterize lipase produced from a thermo-halophilic bacterium, namely Pria Laot Sabang 80 (PLS 80). Purification was performed using ammonium sulphate fractionation, followed by gel filtration chromatography using Sepharose Cl-6B. After purification, the enzyme had a specific activity of 326.6 U/mg with a purity of 6.02 higher than the crude extract; with a molecular weight of around 50 kDa. The optimum activity was observed at 70 °C and pH 9. The activity increased in the presence of 10 mM Mn²⁺, K⁺ and Ca²⁺ ions, while Hg²⁺ only slightly increased the enzyme activity. In contrast, the activity decreased in 10 mM Mg²⁺, Zn²⁺, Co²⁺, EDTA, and PMSF. The enzyme showed good hydrolytic activity on long fatty acids substrates (p-nitrophenyl palmitate) with a value of 35.5 U/mL. It was also able to catalyze a transesterification reaction. GC-MS result showed that the biodiesel consisted of methyl octanoate (5.3%), methyl caprate (12.4%), methyl laurate (34.1%), methyl myristate (10.7%), methyl palmitate (3.9%), and methyl stearate (1.2%) when using coconut oil as the substrate. The results suggested that the lipase from PLS 80 had unique attributes that could be useful in various industrial applications.

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.

Characterization of a Novel Moderately Thermophilic Solvent-Tolerant Esterase Isolated From a Compost Metagenome Library

A novel esterase, EstCS1, was isolated from a compost metagenomics library. The EstCS1 protein, which consists of 309 amino acid residues with an anticipated molecular mass of 34 kDa, showed high amino acid sequence identities to predicted esterases and alpha/beta hydrolases (59%) from some cultured bacteria and to predicted lipases/esterases from uncultured bacteria. The phylogenetic analysis suggested that the EstCS1 belongs to the hormone-sensitive lipase family of lipolytic enzyme classification and contains a catalytic triad including Ser155–Asp255–His285. The Ser155 residue of the catalytic triad in the EstCS1 was located in the consensus active-site motif, GXSXG. Besides, a conserved HGGG motif placed in an oxyanion hole of the hormone-sensitive lipase family was discovered, too. The EstCS1 demonstrated the highest activity toward p-nitrophenyl propionate (C3) and caproate (C6) and was normally stable up to 60°C with optimal activity at 50°C. In addition, an optimal activity was observed at pH 8, and the EstCS1 possessed its stability within the pH range between 5 and 10. Interestingly, EstCS1 had an outstanding stability in up to 30% (v/v) organic solvents and activity over 50% in the presence of 50% (v/v) acetone, ethanol, dimethyl sulfoxide (DMSO), and N,N-dimethylformamide. The EstCS1 hydrolyzed sterically hindered tertiary alcohol esters of t-butyl acetate and linalyl acetate. Considering the properties, such as the moderate thermostability, stability against organic solvents, and activity toward esters of tertiary alcohols, the EstCS1 will be worthwhile to be used for organic synthesis and related industrial applications.

A proposed update for the classification and description of bacterial lipolytic enzymes

Bacterial lipolytic enzymes represent an important class of proteins: they provide their host species with access to additional resources and have multiple applications within the biotechnology sector. Since the formalisation of lipolytic enzymes into families and subfamilies, advances in molecular biology have led to the discovery of lipolytic enzymes unable to be classified via the existing system. Utilising sequence-based comparison methods, we have integrated these novel families within the classification system so that it now consists of 35 families and 11 true lipase subfamilies. Representative sequences for each family and subfamily have been defined as well as methodology for accurate comparison of novel sequences against the reference proteins, facilitating the future assignment of novel proteins. Both the code and protein sequences required for integration of additional families are available at: https://github.com/thh32/Lipase_reclassification.

Microbial Proteases Applications

The use of chemicals around the globe in different industries has increased tremendously, affecting the health of people. The modern world intends to replace these noxious chemicals with environmental friendly products for the betterment of life on the planet. Establishing enzymatic processes in spite of chemical processes has been a prime objective of scientists. Various enzymes, specifically microbial proteases, are the most essentially used in different corporate sectors, such as textile, detergent, leather, feed, waste, and others. Proteases with respect to physiological and commercial roles hold a pivotal position. As they are performing synthetic and degradative functions, proteases are found ubiquitously, such as in plants, animals, and microbes. Among different producers of proteases, Bacillus sp. are mostly commercially exploited microbes for proteases. Proteases are successfully considered as an alternative to chemicals and an eco-friendly indicator for nature or the surroundings. The evolutionary relationship among acidic, neutral, and alkaline proteases has been analyzed based on their protein sequences, but there remains a lack of information that regulates the diversity in their specificity. Researchers are looking for microbial proteases as they can tolerate harsh conditions, ways to prevent autoproteolytic activity, stability in optimum pH, and substrate specificity. The current review focuses on the comparison among different proteases and the current problems faced during production and application at the industrial level. Deciphering these issues would enable us to promote microbial proteases economically and commercially around the world.

Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach

The aim of this study was to isolate a novel esterase from a hypersaline lake by sequence-based metagenomics. The metagenomic DNA was isolated from the enriched hypersaline lake sediment. Degenerate primers targeting the conserved regions of lipolytic enzymes of halophilic microorganisms were used for polymerase chain reaction (PCR) and a whole gene was identified by genome walking. The gene was composed of 783 bp, which corresponds to 260 amino acids with a molecular weight of 28.2 kDa. The deduced amino acid sequence best matched with the esterase from Halomonas gudaonensis with an identity of 91%. Recombinantly expressed enzyme exhibited maximum activity towards pNP-hexanoate with a k_cat value of 12.30 s^-1. The optimum pH and temperature of the enzyme were found as 9 and 30 °C, respectively. The effects of NaCl, solvents, metal ions, detergents and enzyme inhibitors were also studied. In conclusion, a novel enzyme, named as hypersaline lake "Acıgöl" esterase (hAGEst), was identified by sequence-based metagenomics. The high expression level, the ability to maintain activity at cold temperatures and tolerance to DMSO and metal ions are the most outstanding properties of the hAGEst.

Lipases: Sources, Production, Purification, and Applications

Background and Sources: Lipase enzyme is a naturally occurring enzyme found in the stomach and pancreatic juice. Its function is to digest fats and lipids, helping to maintain correct gallbladder function. Lipase is the one such widely used and versatile enzyme. These enzymes are obtained from animals, plants and as well as from several microorganisms and are sufficiently stable. These are considered as nature's catalysts, but commercially, only microbial lipases are being used significantly. Applications: They found enormous application in the industries of fat and oil processing, oleochemical industry, food industry, detergents, pulp and paper industry, detergents, environment management, tea processing, biosensors and cosmetics and perfumery. Various recent patents related to lipases have been revised in this review. Conclusion: Lipases are very peculiar as they have the ability to hydrolyse fats into fatty acids and glycerols at the water-lipid interface and can reverse the reaction in non-aqueous media. This natural ability makes it the most widely used enzyme in various industrial applications. This article deals with the immense versatility of lipase enzymes along with the recent advancements done in the various fields related to their purification and mass production in industries.

Characterization of a novel alkaline esterase from Altererythrobacter epoxidivorans CGMCC 1.7731T

A novel esterase gene (e25) was identified from Altererythrobacter epoxidivorans CGMCC 1.7731^T by genome sequence screening. The e25 gene is 948 nucleotides in length and encodes a 315 amino acid protein (E25) with a predicted molecular mass of 33,683 Da. A phylogenetic tree revealed that E25 belongs to the hormone-sensitive lipase (HSL) family of lipolytic enzymes. An activity assay of E25 showed that it exhibited the highest catalytic efficiency when using p-nitrophenyl caproate (C6) as a substrate. The optimum pH and temperature were determined to be approximately pH 9 and 45°C, and the K_m and V_max values were 0.12 mM and 1,772 µmol/min/mg, respectively. After an incubation at 40°C for 80 min, E25 retained 75% of its basal activity. The enzyme exhibited good tolerance to metal cations, such as Ba²⁺, Ca²⁺, and Cu²⁺ (10 mM), but its activity was strongly inhibited by Co²⁺, Ni²⁺, Mn²⁺, and Zn²⁺. The E25 enzyme was stimulated by glycerol and retained over 60% of its basal activity in the presence of 1% Tween-80 and Triton X-100. Overall, the activity of E25 under alkaline conditions and its organic solvent and detergent tolerance indicate that E25 could be useful as a novel industrial catalyst in biotechnological applications.

Molecular, biochemical and kinetic analysis of a novel, thermostable lipase (LipSm) from Stenotrophomonas maltophilia Psi-1, the first member of a new bacterial lipase family (XVIII)

Background

Microbial lipases catalyze a broad spectrum of reactions and are enzymes of considerable biotechnological interest. The focus of this study was the isolation of new lipase genes, intending to discover novel lipases whose products bear interesting biochemical and structural features and may have a potential to act as valuable biocatalysts in industrial applications.

Results

A novel lipase gene (lipSm), from a new environmental Stenotrophomonas maltophilia strain, Psi-1, originating from a sludge sample from Psittaleia (Greece), was cloned and sequenced. lipSm was further overexpressed in E. coli BL21(DE3) and the overproduced enzyme LipSm was purified and analyzed in respect to its biochemical and kinetic properties. In silico analysis of LipSm revealed that it is taxonomically related to several uncharacterized lipases from different genera, which constitute a unique clade, markedly different from all other previously described bacterial lipase families. All members of this clade displayed identical, conserved consensus sequence motifs, i.e. the catalytic triad (S, D, H), and an unusual, amongst bacterial lipases, Y-type oxyanion hole. 3D-modeling revealed the presence of a lid domain structure, which allows LipSm to act on small ester substrates without interfacial activation. In addition, the high percentage of alanine residues along with the occurrence of the AXXXA motif nine times in LipSm suggest that it is a thermostable lipase, a feature verified experimentally, since LipSm was still active after heating at 70 °C for 30 min.

Conclusions

The phylogenetic analysis of LipSm suggests the establishment of a new bacterial lipase family (XVIII) with LipSm being its first characterized member. Furthermore, LipSm is alkaliphilic, thermostable and lacks the requirement for interfacial activation, when small substrates are used. These properties make LipSm a potential advantageous biocatalyst in industry and biotechnology.

Two novel deep-sea sediment metagenome-derived esterases: residue 199 is the determinant of substrate specificity and preference

BACKGROUND

The deep-sea environment harbors a vast pool of novel enzymes. Owing to the limitations of cultivation, cultivation-independent has become an effective method for mining novel enzymes from the environment. Based on a deep-sea sediment metagenomics library, lipolytic-positive clones were obtained by activity-based screening methods.

RESULTS

Two novel esterases, DMWf18-543 and DMWf18-558, were obtained from a deep-sea metagenomic library through activity-based screening and high-throughput sequencing methods. These esterases shared 80.7% amino acid identity with each other and were determined to be new members of bacterial lipolytic enzyme family IV. The two enzymes showed the highest activities toward p-nitrophenyl (p-NP) butyrate at pH 7.0 and 35-40 °C and were found to be resistant to some metal ions (Ba²⁺, Mg²⁺, and Sr²⁺) and detergents (Triton X-100, Tween 20, and Tween 80). DMWf18-543 and DMWf18-558 exhibited distinct substrate specificities and preferences. DMWf18-543 showed a catalytic range for substrates of C2-C8, whereas DMWf18-558 presented a wider range of C2-C14. Additionally, DMWf18-543 preferred p-NP butyrate, whereas DMWf18-558 preferred both p-NP butyrate and p-NP hexanoate. To investigate the mechanism underlying the phenotypic differences between the esterases, their three-dimensional structures were compared by using homology modeling. The results suggested that residue Leu199 of DMWf18-543 shortens and blocks the substrate-binding pocket. This hypothesis was confirmed by the finding that the DMWf18-558-A199L mutant showed a similar substrate specificity profile to that of DMWf18-543.

CONCLUSIONS

This study characterized two novel homologous esterases obtained from a deep-sea sediment metagenomic library. The structural modeling and mutagenesis analysis provided insight into the determinants of their substrate specificity and preference. The characterization and mechanistic analyses of these two novel enzymes should provide a basis for further exploration of their potential biotechnological applications.

Cloning, expression and characterization of the esterase estUT1 from Ureibacillus thermosphaericus which belongs to a new lipase family XVIII

A new esterase gene from thermophilic bacteria Ureibacillus thermosphaericus was cloned into the pET32b vector and expressed in Escherichia coli BL21(DE3). Alignment of the estUT1 amino acid sequence revealed the presence of a novel canonical pentapeptide (GVSLG) and 41-47% identity to the closest family of the bacterial lipases XIII. Thus the esterase estUT1 from U. thermosphaericus was assigned as a member of the novel family XVIII. It also showed a strong activity toward short-chain esters (C2-C8), with the highest activity for C2. When p-nitrophenyl butyrate is used as a substrate, the temperature and pH optimum of the enzyme were 70-80 °C and 8.0, respectively. EstUT1 showed high thermostability and 68.9 ± 2.5% residual activity after incubation at 70 °C for 6 h. Homology modeling of the enzyme structure showed the presence of a putative catalytic triad Ser93, Asp192, and His222. The activity of estUT1 was inhibited by PMSF, suggesting that the serine residue is involved in the catalytic activity of the enzyme. The purified enzyme exhibited high stability in organic solvents. EstUT1 retained 85.8 ± 2.4% residual activity in 30% methanol at 50 °C for 6 h. Stability at high temperature and tolerance to organic solvents make estUT1 a promising enzyme for biotechnology application.

A Novel Halotolerant Thermoalkaliphilic Esterase from Marine Bacterium Erythrobacter seohaensis SW-135

A novel esterase gene, e69, was cloned from Erythrobacter seohaensis SW-135, which was isolated from a tidal flat sediment of the Yellow Sea in Korea. This gene is 825 bp in length and codes for a 29.54 kDa protein containing 274 amino acids. Phylogenetic analysis showed that E69 is a new member of the bacterial lipolytic enzyme family IV. This enzyme exhibited the highest level of activity toward p-nitrophenyl (NP) butyrate but little or no activity toward the other p-NP esters tested. The optimum temperature and pH of the catalytic activity of E69 were 60°C and pH 10.5, respectively. The enzyme exhibited stable activity over a wide range of alkaline pH values (7.5-9.5). In addition, E69 was found to be a halotolerant esterase as it exhibited the highest hydrolytic activity in the presence of 0.5 M NaCl and was still active in the presence of 3 M NaCl. Moreover, it possessed some degree of tolerance to Triton X-100 and several organic solvents. Through homology modeling and comparison with other esterases, it was suggested that the absence of the cap domain and its narrow substrate-binding pocket might be responsible for its narrow substrate specificity. Sequence and structural analysis results suggested that its high ratio of negatively to positively charged residues, large hydrophobic surface area, and negative electrostatic potential on the surface may be responsible for its alkaline adaptation. The results of this study provide insight into marine alkaliphilic esterases, and the unique properties of E69 make it a promising candidate as a biocatalyst for industrial applications.

Bacillus sp. JR3 esterase LipJ: A new mesophilic enzyme showing traces of a thermophilic past

A search for extremophile enzymes from ancient volcanic soils in El Hierro Island (Canary Islands, Spain) allowed isolation of a microbial sporulated strain collection from which several enzymatic activities were tested. Isolates were obtained after sample cultivation under several conditions of nutrient contents and temperature. Among the bacterial isolates, supernatants from the strain designated JR3 displayed high esterase activity at temperatures ranging from 30 to 100°C, suggesting the presence of at least a hyper-thermophilic extracellular lipase. Sequence alignment of known thermophilic lipases allowed design of degenerated consensus primers for amplification and cloning of the corresponding lipase, named LipJ. However, the cloned enzyme displayed maximum activity at 30°C and pH 7, showing a different profile from that observed in supernatants of the parental strain. Sequence analysis of the cloned protein showed a pentapeptide motif -GHSMG- distinct from that of thermophilic lipases, and much closer to that of esterases. Nevertheless, the 3D structural model of LipJ displayed the same folding as that of thermophilic lipases, suggesting a common evolutionary origin. A phylogenetic study confirmed this possibility, positioning LipJ as a new member of the thermophilic family of bacterial lipases I.5. However, LipJ clusters in a clade close but separated from that of Geobacillus sp. thermophilic lipases. Comprehensive analysis of the cloned enzyme suggests a common origin of LipJ and other bacterial thermophilic lipases, and highlights the most probable divergent evolutionary pathway followed by LipJ, which during the harsh past times would have probably been a thermophilic enzyme, having lost these properties when the environment changed to more benign conditions.