An Appraisal on Prominent Industrial and Biotechnological Applications of Bacterial Lipases

Martini 3 coarse-grained model of enzymes: Framework with validation by all-atom simulations and x-ray diffraction measurements

Recent experiments have shown that complexation with a stabilizing compound can preserve enzyme activity in harsh environments. Such complexation is believed to be driven by noncovalent interactions at the enzyme surface, including hydrophobicity and electrostatics. Molecular modeling of these interactions is costly at the all-atom scale due to the long time scales and large particle counts needed to characterize binding. Protein structure at the scale of amino acid residues is parsimoniously represented by a coarse-grained model in which one particle represents several atoms, significantly reducing the cost of simulation. Coarse-grained models may then be used to generate reduced surface descriptions to underlie detailed theories of surface adhesion. In this study, we present two coarse-grained enzyme models-lipase and dehalogenase-that have been prepared using the Martini 3 top-down modeling framework. We simulate each enzyme in aqueous solution and calculate the statistics of protein surface features and shape descriptors. The values from the coarse-grained data are compared with the same calculations performed on all-atom reference systems, revealing key similarities of surface chemistry at the two scales. Structural measures are calculated from the all-atom reference systems and compared with estimates from small-angle x-ray scattering experiments, with good agreement between the two. The described procedures of modeling and analysis comprise a framework for the development of coarse-grained models of protein surfaces with validation to experiment.

UV mutagenesis for lipase overproduction from Bacillus cereus ATA179, nutritional optimization, characterization and its usability in the detergent industry

In this study, the wild-type Bacillus cereus ATA179 was mutagenized by random UV mutagenesis to increase lipase production. The mutant with maximum lipolytic activity was named Bacillus cereus EV4. The mutant strain (10.6 U/mL at 24 h) produced 60% more enzyme than the wild strain (6.6 U/mL at 48 h). Nutritional factors on lipase production were investigated. Sucrose was the best carbon source, (NH4)2HPO4 was the best nitrogen source and CuSO4 was the best metal ion source. Mutant EV4 showed a 32% increase in lipase production in the modified medium. The optimum temperature and pH were found to be 60 °C and 7.0, respectively. CuSO4, CaCl2, LiSO4, KCl, BaCl2, and Tween 20 had an activating effect on the enzyme. Vmax and Km values were found to be 17.36 U/mL and 0.036 mM, respectively. The molecular weight was determined as 28.2 kDa. The activity of lipase was found to be stable up to 60 days at 20 °C, 75 days at 4 °C, and 90 days at -20 °C. The potential of lipase in the detergent industry was investigated. The enzyme was not affected by detergent additives but was effective in removing stains in fabrics contaminated with oily substances.

Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A

The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations.

A Novel Lipase from Streptomyces exfoliatus DSMZ 41693 for Biotechnological Applications

Genome mining of Streptomyces exfoliatus DSMZ 41693 has allowed us to identify four different lipase-encoding sequences, and one of them (SeLipC) has been successfully cloned and extracellularly expressed using Rhodococcus sp. T104 as a host. SeLipC was purified by one-step hydrophobic interaction chromatography. The enzyme is a monomeric protein of 27.6 kDa, which belongs to subfamily I.7 of lipolytic enzymes according to its phylogenetic analysis and biochemical characterization. The purified enzyme shows the highest activity at 60 °C and an optimum pH of 8.5, whereas thermal stability is significantly improved when protein concentration is increased, as confirmed by thermal deactivation kinetics, circular dichroism, and differential scanning calorimetry. Enzyme hydrolytic activity using p-nitrophenyl palmitate (pNPP) as substrate can be modulated by different water-miscible organic cosolvents, detergents, and metal ions. Likewise, kinetic parameters for pNPP are: KM = 49.6 µM, kcat = 57 s-1, and kcat/KM = 1.15 × 106 s-1·M-1. SeLipC is also able to hydrolyze olive oil and degrade several polyester-type polymers such as poly(butylene succinate) (PBS), poly(butylene succinate)-co-(butylene adipate) (PBSA), and poly(ε-caprolactone) (PCL). Moreover, SeLipC can catalyze the synthesis of different sugar fatty acid esters by transesterification using vinyl laurate as an acyl donor, demonstrating its interest in different biotechnological applications.

Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics

Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.

A thermostable organic solvent-tolerant lipase from Brevibacillus sp.: production and integrated downstream processing using an alcohol-salt-based aqueous two-phase system

Lipases are used for the synthesis of different compounds in the chemical, pharmaceutical, and food industries. Most of the reactions are carried out in non-aqueous media and often at elevated temperature, requiring the use of organic solvent-tolerant thermostable lipases. However, most known lipases are not stable in the presence of organic solvents and at elevated temperature. In this study, an organic solvent-tolerant thermostable lipase was obtained from Brevibacillus sp. SHI-160, a moderate thermophile isolated from a hot spring in the East African Rift Valley. The enzyme was optimally active at 65°C and retained over 90% of its activity after 1 h of incubation at 70°C. High lipase activity was measured in the pH range of 6.5 to 9.0 with an optimum pH of 8.5. The enzyme was stable in the presence of both polar and non-polar organic solvents. The stability of the enzyme in the presence of polar organic solvents allowed the development of an efficient downstream processing using an alcohol-salt-based aqueous two-phase system (ATPS). Thus, in the presence of 2% salt, over 98% of the enzyme partitioned to the alcohol phase. The ATPS-recovered enzyme was directly immobilized on a solid support through adsorption and successfully used to catalyze a transesterification reaction between paranitrophenyl palmitate and short-chain alcohols in non-aqueous media. This shows the potential of lipase SHI-160 to catalyze reactions in non-aqueous media for the synthesis of valuable compounds. The integrated approach developed for enzyme production and cheap and efficient downstream processing using ATPS could allow a significant reduction in enzyme production costs. The results also show the potential of extreme environments in the East African Rift Valley as sources of valuable microbial genetic resources for the isolation of novel lipases and other industrially important enzymes.

Characterization of Detergent-Compatible Lipases from Candida albicans and Acremonium sclerotigenum under Solid-State Fermentation

The purpose of this study was to compare and explore the potential of two distinct lipases at industrial levels after their production using wheat bran substrate in solid-state fermentation. Lipases from Candida albicans (C. albicans) and Acremonium sclerotigenum (A. sclerotigenum) were characterized to assess their compatibility and suitability for use in laundry detergents. The effects of pH, temperature, metal ions, inhibitors, organic solvents, and various commercially available detergents on these lipases were studied in order to compare their activity and stability profiles and check their stain removal ability. Both lipases remained stable across the wide pH (7-10) and temperature (30-50 °C) ranges. C. albicans lipase exhibited optimum activity (51.66 U/mL) at pH 7.0 and 37 °C, while A. sclerotigenum lipase showed optimum activity (52.12 U/mL) at pH 8.0 and 40 °C. The addition of Ca2+ and Mg2+ ions enhanced their activities, while sodium dodecyl sulfate (SDS) and ethylenediamine tetraacetic acid (EDTA) reduced their activities. Lipase from both strains showed tolerance to various organic solvents and considerable stability and compatibility with commercially available laundry detergents (>50%); however, A. sclerotigenum lipase performed slightly better. Characterization of these crude lipases showed nearly 60% relative activity after incubation for 2 h in various detergents, thus suggesting their potential to be employed in the formulation of laundry detergents with easy and efficient enzyme production. The production of thermostable and alkaline lipases from both strains makes them an attractive option for economic gain by lowering the amount of detergent to be used, thus reducing the chemical burden on the environment.

Aspergillus sclerotiorum lipolytic activity and its application in bioremediation of high-fat dairy wastewater environments

Oils and grease (O&G) have low affinity for water and represent a class of pollutants present in the dairy industry. Enzyme-mediated bioremediation using biocatalysts, such as lipases, has shown promising potential in biotechnology, as they are versatile catalysts with high enantioselectivity and regioselectivity and easy availability, being considered a clean technology (white biotechnology). Specially in the treatment of effluents from dairy industries, these enzymes are of particular importance as they specifically hydrolyze O&G. In this context, the objective of this work is to prospect filamentous fungi with the ability to synthesize lipases for application in a high-fat dairy wastewater environment. We identified and characterized the fungal species Aspergillus sclerotiorum as a good lipase producer. Specifically, we observed highest lipolytic activity (20.72 U g^-1) after 96 h of fermentation using sunflower seed as substrate. The fungal solid fermented was used in the bioremediation in dairy effluent to reduce O&G. The experiment was done in kinetic from 24 to 168 h and reduced over 90% of the O&G present in the sample after 168 h. Collectively, our work demonstrated the efficiency and applicability of fungal fermented solids in bioremediation and how this process can contribute to a more sustainable wastewater pretreatment, reducing the generation of effluents produced by dairy industries.

The Recent Advances in the Utility of Microbial Lipases: A Review

Lipases are versatile biocatalysts and are used in different bioconversion reactions. Microbial lipases are currently attracting a great amount of attention due to the rapid advancement of enzyme technology and its practical application in a variety of industrial processes. The current review provides updated information on the different sources of microbial lipases, such as fungi, bacteria, and yeast, their classical and modern purification techniques, including precipitation and chromatographic separation, the immunopurification technique, the reversed micellar system, aqueous two-phase system (ATPS), aqueous two-phase flotation (ATPF), and the use of microbial lipases in different industries, e.g., the food, textile, leather, cosmetics, paper, and detergent industries. Furthermore, the article provides a critical analysis of lipase-producing microbes, distinguished from the previously published reviews, and illustrates the use of lipases in biosensors, biodiesel production, and tea processing, and their role in bioremediation and racemization.