Lipase production from a novel thermo-tolerant and extreme acidophile Bacillus pumilus using palm oil as the substrate and treatment of palm oil-containing wastewater

Highly efficient expression of Rasamsonia emersonii lipase in Pichia pastoris: characterization and gastrointestinal simulated digestion in vitro

BACKGROUND

Acidic lipases with high catalytic activities under acidic conditions have important application values in the food, feed and pharmaceutical industries. However, the availability of acidic lipases is still the main obstacle to their industrial applications. Although a novel acidic lipase Rasamsonia emersonii (LIPR) was heterologously expressed in Escherichia coli, the expression level was unsatisfactory.

RESULTS

To achieve the high-efficiency expression and secretion of LIPR in Pichia pastoris GS115, the combinatorial optimization strategy was adopted including gene codon preference, signal peptide, molecular chaperone co-expression and disruption of vacuolar sorting receptor VPS10. The activity of the combinatorial optimization engineered strain in a shake flask reached 1480 U mL-1, which was 8.13 times greater than the P. pastoris GS115 parental strain. After high-density fermentation in a 5-L bioreactor, the highest enzyme activity reached as high as 11 820 U mL-1. LIPR showed the highest activity at 40 °C and pH 4.0 in the presence of Ca2+ ion. LIPR exhibited strong tolerance to methanol, indicating its potential application in biodiesel biosynthesis. Moreover, the gastrointestinal digestion simulation results demonstrated that LIPR was tolerant to pepsin and trypsin, but its activity was inhibited by sodium taurodeoxycholate.

CONCLUSION

This study provided an effective approach for the high expression of acidic lipase LIPR. LIPR was more appropriate for lipid digestion in the stomach than in intestine according to the gastrointestinal digestion simulation results. © 2024 Society of Chemical Industry.

Production, purification, properties and current perspectives for modification and application of microbial lipases

With the industrialization and development of modern science, the application of enzymes as green and environmentally friendly biocatalysts in industry has been increased widely. Among them, lipase (EC. 3.1.1.3) is a very prominent biocatalyst, which has the ability to catalyze the hydrolysis and synthesis of ester compounds. Many lipases have been isolated from various sources, such as animals, plants and microorganisms, among which microbial lipase is the enzyme with the most diverse enzymatic properties and great industrial application potential. It therefore has promising applications in many industries, such as food and beverages, waste treatment, biofuels, leather, textiles, detergent formulations, ester synthesis, pharmaceuticals and medicine. Although many microbial lipases have been isolated and characterized, only some of them have been commercially exploited. In order to cope with the growing industrial demands and overcome these shortcomings to replace traditional chemical catalysts, the preparation of new lipases with thermal/acid-base stability, regioselectivity, organic solvent tolerance, high activity and yield, and reusability through excavation and modification has become a hot research topic.

An Appraisal on Prominent Industrial and Biotechnological Applications of Bacterial Lipases

Microbial lipases expedite the hydrolysis and synthesis of long-chain acyl esters. They are highly significant commercial biocatalysts to biotechnologists and organic chemists. The market size of lipase is anticipated to reach $590 million by 2023. This is all owing to their versatility in properties, including stability in organic solvents, interfacial activation in micro-aqueous environments, high substrate specificity, and activity in even non-aqueous milieu. Lipases are omnipresent and synthesized by various living organisms, including animals, plants, and microorganisms. Microbial lipases are the preferred choice for industrial applications as they entail low production costs, higher yield independent of seasonal changes, easier purification practices, and are capable of being genetically modified. Microbial lipases are employed in several common industries, namely various food manufactories (dairy, bakery, flavor, and aroma enhancement, etc.), leather tanneries, paper and pulp, textiles, detergents, cosmetics, pharmaceuticals, biodiesel synthesis, bioremediation and waste treatment, and many more. In recent decades, circumspection toward eco-friendly and sustainable energy has led scientists to develop industrial mechanisms with lesser waste/effluent generation, minimal overall energy usage, and biocatalysts that can be synthesized using renewable, low-cost, and unconventional raw materials. However, there are still issues regarding the commercial use of lipases which make industrialists wary and sometimes even switch back to chemical catalysis. Industrially relevant lipase properties must be further optimized, analyzed, and explored to ensure their continuous successful utilization. This review comprehensively describes the general background, structural characteristics, classifications, thermostability, and various roles of bacterial lipases in important industries.

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

BACKGROUND

Thermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called "uncultivable" microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs.

RESULTS

In this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance.

CONCLUSION

Our results indicate that the modified ichip approach can be successfully applied in a hot spring environment.

The response surface methodology for optimization of Halomonas sp. C2SS100 lipase immobilization onto CaCO3 for treatment of tuna wash processing wastewater

An immobilized enzyme could exhibit selectively modified physicochemical properties, and it might offer a better environment for the enzyme activity. In this study, the immobilization yield of crude Halomonas sp. lipase was optimized to improve its stability. Thanks to its high adsorption capacity, CaCO₃ has been chosen as support for the immobilization process. Furthermore, response surface methodology (RSM) was used to determine optimal conditions for the immobilization of the bacterial lipase. Five tested factors (enzyme solution, support amount, time, temperature, and acetone volume) were optimized applying a central composite design of RSM. The maximum yield of lipase immobilization was improved to 96%. Furthermore, a biochemical characterization proved a significant improvement of the immobilized lipase stability. The immobilized enzyme is more stable at extreme pH values and high temperatures than the free one. We also tested the reusability of the immobilized lipase by evaluating the recovery of the support using simple filtration. Thanks to its high stability, the immobilized lipase was invested in an effective treatment of tuna wash processing wastewater. The oil biodegradation efficiency was established at 81.5% and was confirmed by Fourier transformation infrared spectrometry. Likewise, the biological oxygen demand values were reduced which makes a possible reduction of the wastewater pollution degree.

Extremophilic lipases for industrial applications: A general review

With industrialization and development in modern science enzymes and their applications increased widely. There is always a hunt for new proficient enzymes with novel properties to meet specific needs of various industrial sectors. Along with the high efficiency, the green and eco-friendly side of enzymes attracts human attention, as they form a true answer to counter the hazardous and toxic conventional industrial catalyst. Lipases have always earned industrial attention due to the broad range of hydrolytic and synthetic reactions they catalyse. When these catalytic properties get accompanied by features like temperature stability, pH stability, and solvent stability lipases becomes an appropriate tool for use in many industrial processes. Extremophilic lipases offer the same, thermostable: hot and cold active thermophilic and psychrophilic lipases, acid and alkali resistant and active acidophilic and alkaliphilic lipases, and salt tolerant halophilic lipases form excellent biocatalyst for detergent formulations, biofuel synthesis, ester synthesis, food processing, pharmaceuticals, leather, and paper industry. An interesting application of these lipases is in the bioremediation of lipid waste in harsh environments. The review gives a brief account on various extremophilic lipases with emphasis on thermophilic, psychrophilic, halophilic, alkaliphilic, and acidophilic lipases, their sources, biochemical properties, and potential applications in recent decades.

Expression of novel acidic lipase from Micrococcus luteus in Pichia pastoris and its application in transesterification

Background

Lipases are promising biocatalysts for industrial applications and attract attention to be explored. A novel acidic lipase has been isolated from the lipolytic bacteria Micrococcus luteus EMP48-D (LipEMP48-D) screened from tempeh. The lipase gene had previously been overexpressed in Escherichia coli BL21, but the expression level obtained was relatively low. Here, to improve the expression level, the lipase gene was cloned to Pichia pastoris. We eliminated the native signal sequence of M. luteus and replaced it with α-mating factor (α-MF) signal sequence. We also optimized and synthesized the lipase gene based on codon preference in P. pastoris.

Results

LipEMP48-D lipase was expressed as an extracellular protein. Codon optimization has been conducted for 20 codons, with the codon adaption index reaching 0.995. The highest extracellular lipase activity obtained reached 145.4 ± 4.8 U/mg under AOX1 promoter in P. pastoris KM71 strain, which was 9.7-fold higher than the previous activity in E. coli. LipEMP48-D showed the highest specific activity at pH 5.0 and stable within the pH range 3.0–5.0 at 40 °C. LipEMP48-D also has the capability of hydrolyzing various long-chain triglycerides, particularly olive oil (100%) followed by sunflower oil (88.5%). LipEMP48-D exhibited high tolerance for various polar organic solvents with low log P, such as isopropanol (115.7%) and butanol (114.6%). The metal ions (Na⁺, K⁺, Ca²⁺, Mg²⁺, Mn⁺) decreased enzyme activity up to 43.1%, while Fe²⁺ increased relative activity of enzymes up to 200%. The conversion of free fatty acid (FFA) into fatty acid methyl ester (FAME) was low around 2.95%.

Conclusions

This study was the first to report overexpression of Micrococcus lipase in yeast. The extracellular expression of this acidic lipase could be potential for biocatalyst in industrial fields, especially organic synthesis, food industry, and production of biodiesel.

Current perspectives for microbial lipases from extremophiles and metagenomics

Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of α/β hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.

Purification, biochemical and molecular study of lipase producing from a newly thermoalkaliphilic Aeribacillus pallidus for oily wastewater treatment

Treatment of oily wastewater is constantly a challenge; biological wastewater treatment is an effective, cheap and eco-friendly technology. A newly thermostable, haloalkaline, solvent tolerant and non-induced lipase from Aeribacillus pallidus designated as GPL was purified and characterized of biochemical and molecular study for apply in wastewater treatment. The GPL showed a maximum activity at 65°C and pH 10 after 22 h of incubation, with preference to TC4 substrates. Pure enzyme was picked up after one chromatographic step. It displayed an important resistance at high temperature, pH, NaCl, at the presence of detergents and organic solvents. In fact, GPL exhibited a prominent stability in wide range of organic solvents at 50% (v/v) concentration for 2 h of incubation. The efficiency of the GPL in oil wastewater hydrolysis was established at 50°C for 1 h, the oil removal efficiency was established at 96, 11% and the oil biodegradation was confirmed through fourier transform infrared (FT-IR) spectroscopy. The gene that codes for this lipase was cloned and sequenced and its open reading frame encoded 236 amino acid residues. The deduced amino acids sequence of the GPL shows an important level of identity with Geobacillus lipases.

A combined treatment using ethylmethane sulfonate and ultraviolet light to compare amylase production by three Bacillus sp. isolates

In this study, three Bacillus sp.-producing amylase enzymes were isolated from soil samples and identified using 16S rDNA sequence analysis. Amylase production and total protein productions were spectrophotometrically measured. The following media were tested to increase enzyme production: LB medium and molasses. Three Bacillus sp. were identified as follows: Bacillus subtilis subtilis, Bacillus thuringiensis, and Bacillus cereus. Amylase production levels were in the range of 10 U/mL, whereas total protein production levels were at 15 mg/mL. Higher amylase activity was found in the Bacillus subtilis isolate. Ethylmethane sulfonate (EMS) and ultraviolet (UV) mutagenesis in combination were applied to compare amylase production. Amylase activity was increased to around 58% in the treatment with 0.03 mL of EMS and UV when compared to the control group. A pilot scale bioreactor with a total working volume of 10 liters was used to produce amylase by B. subtilis subtilis. In conclusion, B. subtilis subtilis can be used to produce amylase enzyme for various industrial purposes, and, for the first time, the amylase activities of B. subtilis can be enhanced with EMS and UV treatment.

Draft genome sequence of Bacillus pumilus strain EZ-C07 isolated from digested agricultural wastes

Objectives

Bacillus species, belonging to the family Bacillaceae, are rod-shaped aerobic or facultative anaerobic Gram-positive bacteria that can be isolated from various environmental niches. Bacillus pumilus strains are resistant to unfavorable conditions such as UV, H₂O₂ and chemical disinfection. Furthermore, B. pumilus strains synthesize multifarious important enzymes and can be used in the production of some fermented foods, bioremediation of wastewater systems and biodegradation of environmental contaminants. Hence, investigation at the genomic level is required to understand their ecology, genetics and potential applications.

Data description

In this research, we provide the genomic insights into one Bacillus species (EZ-C07) isolated from digested agricultural waste materials. The draft genome of the strain EZ-C07 consists of 3,724,869 bp with 3890 coding sequences and 41.5% G + C content. Based on 16S rRNA gene sequence analysis followed by in silico DNA–DNA hybridization studies, the strain EZ-C07 was identified as Bacillus pumilus belonging to the family Bacillaceae within the phylum Firmicutes. The whole genome shotgun project of B. pumilus strain EZ-C07 can be accessed at DDBJ/ENA/GenBank under the Accession QLVI00000000.

Extracellular lipase from Pseudomonas aeruginosa JCM5962(T): Isolation, identification, and characterization

The study was done to isolate, identify, and characterize a good lipolytic strain from soil. Lipolytic strain isolation was done using tributyrin agar medium. The biochemical testing and 16S rRNA gene sequencing analysis was done for identification. The enzyme was purified using ammonium sulfate precipitation and column chromatography. Results have shown a novel high lipolytic strain of P. aeruginosa JCM5962(T), isolated from soil of sugarcane field. The 16S rRNA sequence analysis confirmed the strain as P. aeruginosa JCM5962(T); further, the sequence was submitted to Genbank (KX946966.1). The isolate produced an extracellular lipase which was purified as single band of 31 kDa. Maximum lipase activity was observed at 50 °C and pH 8.0. Activity was enhanced in the presence of cobalt and benzene solvent, whereas mercury, sodium dodecyl sulfate, and chloroform inhibited it. The enzyme's marked stability and activity at high temperature, alkaline pH and organic solvents suggest that this can be effectively used in a variety of applications in industries and as biotechnological tools.

Classification of lipolytic enzymes and their biotechnological applications in the pulping industry

In the pulp and paper industry, during the manufacturing process, the agglomeration of pitch particles (composed of triglycerides, fatty acids, and esters) leads to the formation of black pitch deposits in the pulp and on machinery, which impacts on the process and pulp quality. Traditional methods of pitch prevention and treatment are no longer feasible due to environmental impact and cost. Consequently, there is a need for more efficient and environmentally friendly approaches. The application of lipolytic enzymes, such as lipases and esterases, could be the sustainable solution to this problem. Therefore, an understanding of their structure, mechanism, and sources are essential. In this report, we review the microbial sources for the different groups of lipolytic enzymes, the differences between lipases and esterases, and their potential applications in the pulping industry.

Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy

Bacillus pumilus has been widely identified as a pathogen of plant and human, while the genetic information is rarely available for pathogenic B. pumilus strains. B. pumilus GR8 is a pathogen that causes ginger rhizome rot disease by invading ginger rhizome parenchymatous tissues, growing in the extracellular space, and producing plant cell wall-degrading enzymes to destroy ginger cells. In this study, the genome of GR8 was sequenced and characterized. This genome was the third completely sequenced genome of the B. pumilus species, and it exhibited high similarity to the genome of the B. pumilus strain B6033. The genome of GR8 was 3.67 Mb in length and encoded 3,713 putative ORFs. Among these predicted proteins, numerous plant cell wall-degrading enzymes and several proteins associated with invading and adapting to the environment in the extracellular space of the ginger rhizome parenchymatous tissue were found. The GR8 genome contained only one restriction-modification system and no CRISPR/Cas system. The lack of phage-resistant system suggested that phages might be potential agents for the control of GR8. The genomic analysis of GR8 provided the understanding to the pathogenesis and the phage-control strategy of pathogenic B. pumilus strains.

Thermophiles in the genomic era: Biodiversity, science, and applications

Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.