A Valuable Product of Microbial Cell Factories: Microbial Lipase

In silico mining and identification of a novel lipase from Paenibacillus larvae: Rational protein design for improving catalytic performance

Lipases play a vital role in various biological processes, from lipid metabolism to industrial applications. However, the ever-evolving challenges and diverse substrates necessitate the continual exploration of novel high-performance lipases. In this study, we employed an in silico mining approach to search for lipases with potential high sn-1,3 selectivity and catalytic activity. The identified novel lipase, PLL, from Paenibacillus larvae subsp. larvae B-3650 exhibited a specific activity of 111.2 ± 5.5 U/mg towards the substrate p-nitrophenyl palmitate (pNPP) and 6.9 ± 0.8 U/mg towards the substrate olive oil when expressed in Escherichia coli (E. coli). Computational design of cysteine mutations was employed to enhance the catalytic performance of PLL. Superior stability was achieved with the mutant K7C/A386C/H159C/K108C (2M3/2M4), showing an increase in melting temperature (Tm) by 1.9°C, a 2.05-fold prolonged half-life at 45°C, and no decrease in enzyme activity. Another mutant, K7C/A386C/A174C/A243C (2M1/2M3), showed a 4.9-fold enhancement in specific activity without compromising stability. Molecular dynamics simulations were conducted to explore the mechanisms of these two mutants. Mutant 2M3/2M4 forms putative disulfide bonds in the loop region, connecting the N- and C-termini of PLL, thus enhancing overall structural rigidity without impacting catalytic activity. The cysteines introduced in mutant 2M1/2M3 not only form new intramolecular hydrogen bonds but also alter the polarity and volume of the substrate-binding pocket, facilitating the entry of large substrate pNPP. These results highlight an efficient in silico exploration approach for novel lipases, offering a rapid and efficient method for enhancing catalytic performance through rational protein design.

Lipidic drug delivery systems are responsive to the human microbiome

In vitro and in vivo tests for therapeutic agents are typically conducted in sterile environments, but many target areas for drug delivery are home to thousands of microbial species. Here, we examine the behaviour of lipidic nanomaterials after exposure to representative strains of four bacterial species found in the gastrointestinal tract and skin. Small angle X-ray scattering measurements show that the nanostructure of monoolein cubic and inverse hexagonal phases are transformed, respectively, into inverse hexagonal and inverse micellar cubic phases upon exposure to a strain of live Staphylococcus aureus often present on skin and mucosa. Further investigation demonstrates that enzymatic hydrolysis and cell membrane lipid transfer are both likely responsible for this effect. The structural responses to S. aureus are rapid and significantly reduce the rate of drug release from monoolein-based nanomaterials. These findings are the first to demonstrate how a key species in the live human microbiome can trigger changes in the structure and drug release properties of lipidic nanomaterials. The effect appears to be strain specific, varies from patient to patient and body region to body region, and is anticipated to affect the bioapplication of monoglyceride-based formulations.

Ultrasensitive Nanofiber Biosensor: Rapid In Situ Chromatic Detection of Bacteria for Healthcare Innovation

Rapid detection of bacterial presence in skin wounds is crucial to prevent the transition from acute to chronic wounds and the onset of systemic infections. Current methods for detecting infections, particularly at low concentrations (<1.0 × 105 CFU/cm2), often require complex technologies and direct sampling, which can be invasive and time-consuming. Addressing this gap, we introduce a colorimetric nanofibrous biosensor enabling real-time in situ monitoring of bacterial concentrations in wounds. This biosensor employs a colorimetric hemicyanine dye (HCy) probe, which changes color in response to bacterial lipase, a common secretion in infected wounds. To enhance the biosensor's sensitivity, we incorporated two key materials science strategies: aligning the nanofibers to promote efficient bacterial attachment and localization and integrating Tween 80, a surfactant, within the nanofiber matrix. This combination of physical and chemical cues results in a notable increase in lipase activity. The cross-aligned core-shell nanofibers, embedded with Tween 80 and HCy, demonstrate an immediate and distinct color change when exposed to as low as 3.0 × 104 CFU/cm2 of common pathogens such as Pseudomonas aeruginosa and MRSA. Significantly, the presence of Tween 80 amplifies the colorimetric response, making visual detection more straightforward and four times more pronounced. Our nanobiosensor design facilitates the detection of low-concentration bacterial infections in situ without the need to remove wound dressings. This advancement marks a significant step forward in real-time wound monitoring, offering a practical tool for the early detection of clinical bacterial infections.

Bioaccessibility of docosahexaenoic acid in naturally and artificially enriched milk

This study aimed to compare the bioaccessibility of docosahexaenoic acid (DHA) in naturally and artificially enriched milk and investigate the potential mechanisms involved. The results indicated that the DHA in naturally enriched milk (NEM) had a higher bioaccessibility (76.9 %) and a lower digestive loss rate (18.1 %) compared to artificially enriched milk (ArEM). Moreover, NEM contained a higher proportion of DHA-containing glycerophospholipids and sn-2 DHA, with fewer long-chain fatty acids and more saturated fatty acids adjacent to DHA in the same lipid molecule. During simulated intestinal digestion, NEM had a higher free fatty acid release and lipid digestion rate than ArEM. These findings suggested that the bioaccessibility of endogenous DHA in milk was superior to that of externally added DHA due to its more easily digestible and absorbable chemical binding form and lower digestive loss rate. The easy digestibility of milk lipids in NEM also contributed to its high DHA bioaccessibility.

Upstream and Downstream Bioprocessing in Enzyme Technology

The development of biotransformation must integrate upstream and downstream processes. Upstream bioprocessing will influence downstream bioprocessing. It is essential to consider this because downstream processes can constitute the highest cost in bioprocessing. This review comprehensively overviews the most critical aspects of upstream and downstream bioprocessing in enzymatic biocatalysis. The main upstream processes discussed are enzyme production, enzyme immobilization methodologies, solvent selection, and statistical optimization methodologies. The main downstream processes reviewed in this work are biocatalyst recovery and product separation and purification. The correct selection and combination of upstream and downstream methodologies will allow the development of a sustainable and highly productive system.

The Conformational Transitions and Dynamics of Burkholderia cepacia Lipase Regulated by Water-Oil Interfaces

Structural dynamics and conformational transitions are crucial for the activities of enzymes. As one of the most widely used industrial biocatalysts, lipase could be activated by the water-oil interfaces. The interface activations were believed to be dominated by the close-to-open transitions of the lid subdomains. However, the detailed mechanism and the roles of structure transitions are still under debate. In this study, the dynamic structures and conformational transitions of Burkholderia cepacia lipase (LipA) were investigated by combining all-atom molecular dynamics simulations, enhanced sampling simulation, and spectrophotometric assay experiments. The conformational transitions between the lid-open and lid-closed states of LipA in aqueous solution are directly observed by the computational simulation methods. The interactions between the hydrophobic residues on the two lid-subdomains are the driven forces for the LipA closing. Meanwhile, the hydrophobic environment provided by the oil interfaces would separate the interactions between the lid-subdomains and promote the structure opening of LipA. Moreover, our studies demonstrate the opening of the lids structure is insufficient to initiate the interfacial activation, providing explanations for the inability of interfacial activation of many lipases with lid structures.

Characterization of a New Thermostable and Organic Solution-Tolerant Lipase from Pseudomonas fluorescens and Its Application in the Enrichment of Polyunsaturated Fatty Acids

The search for and characterization of new lipases with excellent properties has always been urgent and is of great importance to meet industrial needs. In this study, a new lipase, lipB, from Pseudomonas fluorescens SBW25, belonging to the lipase subfamily I.3, was cloned and expressed in Bacillus subtilis WB800N. Enzymatic properties studies of recombinant LipB found that it exhibited the highest activity towards p-nitrophenyl caprylate at 40 °C and pH 8.0, retaining 73% of its original activity after incubation at 70 °C for 6 h. In addition, Ca²⁺, Mg²⁺, and Ba²⁺ strongly enhanced the activity of LipB, while Cu²⁺, Zn²⁺, Mn²⁺, and CTAB showed an inhibiting effect. The LipB also displayed noticeable tolerance to organic solvents, especially acetonitrile, isopropanol, acetone, and DMSO. Moreover, LipB was applied to the enrichment of polyunsaturated fatty acids from fish oil. After hydrolyzing for 24 h, it could increase the contents of polyunsaturated fatty acids from 43.16% to 72.18%, consisting of 5.75% eicosapentaenoic acid, 19.57% docosapentaenoic acid, and 46.86% docosahexaenoic acid, respectively. The properties of LipB render it great potential in industrial applications, especially in health food production.

Scale-up Lipase Production and Development of Methanol Tolerant Whole-Cell Biocatalyst from Magnusiomyces spicifer SPB2 in Stirred-Tank Bioreactor and Its Application for Biodiesel Production

This study aimed to economically develop the yeast whole-cell biocatalyst from the lipase-secreting Magnusiomyces spicifer SPB2 to serve green biodiesel production. The scaled-up productions of lipases were optimized using a 5-L stirred-tank bioreactor. The maximum extracellular lipase and cell-bound lipase (CBL) yields of 1189.65 U/L and 5603.74 U/L were achieved at 24 h and 60 h, respectively, in the modified IMY medium (pH 5.0) containing 2% of soybean oil as a carbon source and 0.2% Gum Arabic as an emulsifying agent. The optimized cultivation was initiated with an inoculum size of 1 × 107 cells/mL and conducted under an aeration rate of 0.75 vvm with an agitation speed of 400 rpm. The obtained whole-cell biocatalyst of M. spicifer SPB2 was applied to catalyze the transesterification reaction using palm oil and methanol as substrates. The greatest yield of 97.93% fatty acid methyl ester (FAME) was reached at 72 h using a palm oil/methanol ratio of 1:7, indicating high methanol stability of the biocatalyst. Moreover, substrate homogenization accelerated the reaction to achieve FAME production of 97.01% at 48 h and remained stable afterwards. Without homogenization, the highest FAME of 98.20% was obtained at 60 h. The whole-cell biocatalyst prepared from lipase-secreting M. spicifer SPB2 at an up-scaled level greatly enhanced efficiency and feasibility for commercial biodiesel production through a green conversion process.

The first detection of two Aeromonas strains in mice of the genus Apodemus

Aeromonas spp. are gram-negative facultatively anaerobic bacilli recovered mainly from aquatic environments. Aeromonas spp. were reported to be associated with infections primarily in aquatic and to a lesser extent in terrestrial animals as well as in humans. Up-to-date little is known about aeromonads associated with wild animals, especially with rodents. This study reported the first isolation and characterization of two Aeromonas spp. from internal organs of apparently healthy wild rodents Apodemus uralensis and Apodemus flavicollis captured in the wild environment in the European part of Russia. Isolates were identified as A. hydrophila M-30 and A. encheleia M-2 using the multilocus sequence analysis (MLSA) approach. The isolation of the A. encheleia from rodents is the first described case. Both strains demonstrated beta-hemolytic activity towards human erythrocytes. Antimicrobial susceptibility testing showed that both Aeromonas strains were resistant and intermediate to carbapenems and piperacillin-tazobactam, which was caused by the expression of the genus-specific CphA carbapenemases. A. hydrophila M-30 also demonstrated trimethoprim resistant phenotype. This is usually caused by the carriage of the dfrA or dfrB genes in aeromonads which are frequently associated with integron class I. The latter however was absent in both isolates. Our results expand our understanding of possible aeromonad reservoirs and demonstrate the likelihood of the formation of natural foci of Aeromonas infection and a new link in the chain of the spread of antimicrobial resistance as well.

Renewable, sustainable, and natural lignocellulosic carriers for lipase immobilization: A review

It is well-known that enzymes are molecules particularly susceptible to pH and temperature variations. Immobilization techniques may overcome this weakness besides improving the reusability of the biocatalysts. Given the strong push toward a circular economy, the use of natural lignocellulosic wastes as supports for enzyme immobilization has been increasingly attractive in recent years. This fact is mainly due to their high availability, low costs, and the possibility of reducing the environmental impact that can occur when they are improperly stored. In addition, they have physical and chemical characteristics suitable for enzyme immobilization (large surface area, high rigidity, porosity, reactive functional groups, etc.). This review aims to guide readers and provide them with the tools necessary to select the most suitable methodology for lipase immobilization on lignocellulosic wastes. The importance and the characteristics of an increasingly interesting enzyme, such as lipase, and the advantages and disadvantages of the different immobilization methods will be discussed. The various kinds of lignocellulosic wastes and the processing required to make them suitable as carriers will be also reported.

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.

Biochemical characterization of an alkaline and detergent-stable Lipase from Fusarium annulatum Bugnicourt strain CBS associated with olive tree dieback

This work describes a novel extracellular lipolytic carboxylester hydrolase named FAL, with lipase and phospholipase A1 (PLA1) activity, from a newly isolated filamentous fungus Ascomycota CBS strain, identified as Fusarium annulatum Bunigcourt. FAL was purified to about 62-fold using ammonium sulphate precipitation, Superdex® 200 Increase gel filtration and Q-Sepharose Fast Flow columns, with a total yield of 21%. The specific activity of FAL was found to be 3500 U/mg at pH 9 and 40°C and 5000 U/mg at pH 11 and 45°C, on emulsions of triocanoin and egg yolk phosphatidylcholine, respectively. SDS-PAGE and zymography analysis estimated the molecular weight of FAL to be 33 kDa. FAL was shown to be a PLA1 with a regioselectivity to the sn-1 position of surface-coated phospholipids esterified with α-eleostearic acid. FAL is a serine enzyme since its activity on triglycerides and phospholipids was completely inhibited by the lipase inhibitor Orlistat (40 μM). Interestingly, compared to Fusarium graminearum lipase (GZEL) and the Thermomyces lanuginosus lipase (Lipolase®), this novel fungal (phospho)lipase showed extreme tolerance to the presence of non-polar organic solvents, non-ionic and anionic surfactants, and oxidants, in addition to significant compatibility and stability with some available laundry detergents. The analysis of washing performance showed that it has the capability to efficiently eliminate oil-stains. Overall, FAL could be an ideal choice for application in detergents.

Application of Milk Permeate as an Inducer for the Production of Microbial Recombinant Lipolytic Enzymes

Recombinantly produced enzymes are applied in many fields, ranging from medicine to food and nutrition, production of detergents, textile, leather, paper, pulp, and plastics. Thus, the cost-effectiveness of recombinant enzyme synthesis is an important issue in biotechnological industry. Isopropyl-β-D-thiogalactoside (IPTG), an analog of lactose, is currently the most widely used chemical agent for the induction of recombinant enzyme synthesis. However, the use of IPTG can lead to production of toxic elements and can introduce physiological stress to cells. Thus, this study aims to find a simpler, cheaper, and safer way to produce recombinant enzymes. In this study, production of several previously designed recombinant lipolytic enzymes (GDEst-95 esterase, GD-95RM lipase, fused GDEst-lip lipolytic enzyme, and putative cutinase Cut+SP from Streptomyces scabiei 87.22) is induced in E. coli BL21 (DE3) using 4 mM milk permeate, a type of waste of the milk manufacturing process possessing >82% lactose. The SDS-PAGE analysis clearly indicates synthesis of all target enzymes during a 2–12 h post-induction timeframe. Further investigation of GDEst-95, GD-95RM, GDEst-lip, and Cut+SP biocatalysts was carried out spectrophotometrically and using zymography method, confirming production of fully active enzymes.

Recent Advances in Lipases and Their Applications in the Food and Nutraceutical Industry

Lipases are efficient enzymes with promising applications in the nutraceutical and food industry, as they can offer high yields, pure products under achievable reaction conditions, and are an environmentally friendly option. This review addresses the production of high-value-added compounds such as fatty acid esters, with the potential to be used as flavoring agents or antioxidant and antimicrobial agents, as well as structured lipids that offer specific functional properties that do not exist in nature, with important applications in different food products, and pharmaceuticals. In addition, the most recent successful cases of reactions with lipases to produce modified compounds for food and nutraceuticals are reported.

Intracellular-to-extracellular localization switch of acidic lipase in Enterobacter cloacae: evaluation of production kinetics and enantioselective esterification potential for pharmaceutical applications

Downstream processing is a significant part of a production process and accounts for 50-90% of the production cost of biotechnological products. Post-fermentation localization of a microbial metabolite contributes significantly to the recovery cost of the product. Enterobacter cloacae produced naturally, acidic lipase with a 0.023:1 extracellular localization ratio. This research aimed to re-direct the localization of lipase to the extracellular milieu to reduce recovery costs using multi-objective response surface optimization (MO-RSM). The approach resulted in a 1:0.32 extracellular: intracellular lipase ratio, with product formation kinetics of Luedeking-Piret function showing a significant switch from a completely growth-associated intracellular production to a predominantly non-growth-associated extracellular localization. The enzyme was purified by an aqueous two-phase system which extracted 95.22% lipase with 72.36 purity. Characterization of the enzyme showed a molecular weight of 55.7 kDa, kcat of 68.59 s^-1, and a K_m of 0.63 mmol. Lipase activity occurred optimally at pH 2.5-3.5 and 50 °C, and was stable in most organic solvents tested. The acidic lipase demonstrated pH-dependent enantioselective esterification in resolving (R, S)-ibuprofen (E = 14, pH 4.5) and (R, S)-Naproxen (E = 13, pH 2.5), with an enantioselective preference for (S)-enantiomer in both drugs thus underpinning its potential for pharmaceutical applications.

Functions and applications of glycolipid-hydrolyzing microbial glycosidases

Glycolipids are important components of cell membranes in several organisms. The major glycolipids in mammals are glycosphingolipids (GSLs), which are composed of ceramides. In mammals, GSLs are degraded stepwise from the non-reducing end of the oligosaccharides via exo-type glycosidases. However, endoglycoceramidase (EGCase), an endo-type glycosidase found in actinomycetes, is a unique enzyme that directly acts on the glycosidic linkage between oligosaccharides and ceramides to generate intact oligosaccharides and ceramides. Three molecular species of EGCase, namely EGCase I, EGCase II, and endogalactosylceramidase, have been identified based on their substrate specificity. EGCrP1 and EGCrP2, which are homologs of EGCase in pathogenic fungi, were identified as the first fungal glucosylceramide- and sterylglucoside-hydrolyzing glycosidases, respectively. These enzymes are promising targets for antifungal drugs against pathogenic fungi. This review describes the functions and properties of these microbial glycolipid-degrading enzymes, the molecular basis of their differential substrate specificity, and their applications.

Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.

Improvement of methanol tolerance and catalytic activity of Rhizomucor miehei lipase for one-step synthesis of biodiesel by semi-rational design

Exploiting highly active and methanol-resistant lipase is of great significance for biodiesel production. A semi-rational directed evolution method combined with N-glycosylation is reported, and all mutants exhibiting higher catalytic activity and methanol tolerance than the wild type (WT). Mutant N267 retained 64% activity after incubation in 50% methanol for 8 h, which was 48% greater than that of WT. The catalytic activity of mutants N267 and N167 was 30- and 71- fold higher than that of WT. Molecular dynamics simulations of N267 showed that the formation of new strong hydrogen bonds between glycan and the protein stabilized the structure of lipase and improved its methanol tolerance. N267 achieved biodiesel yields of 99.33% (colza oil) and 81.70% (waste soybean oil) for 24 h, which was much higher than WT (51.6% for rapeseed oil and 44.73% for wasted soybean oil). The engineered ProRML mutant has high potential for commercial biodiesel production.