Large-scale production of enzymes for biotechnology uses

Fermenter scale production of recombinant beta-mannanase by E. coli BL21 cells under microaerobic environment

Aim of the study was to optimize and produce beta-mannanase at fermenter scale by using cheaper minimal media. Increased production of beta-mannanase from Microbacterium camelliasinensis CIAB417 was achieved by heterologous expression in E. coli BL21 (DE3). The scale-up production of beta-mannanase was optimized from shake flask to 5-L fermenter. The cost-effective minimal media (M9+e) without any vitamins was found to be most effective and optimized for culturing the cells. The same media displayed no significant fluctuation in the pH while culturing the cells for the production of beta-mannanase both at shake flask and fermenter level. Additionally, E. coli cells were able to produce similar amount of dry cell weight and recombinant beta-mannanase both in the presence of micro and macro-oxygen environment. The optimized media was demonstrated to show no significant drop in pH throughout the recombinant protein production process. In one litre medium, 2.0314 g dry weight of E. coli cells yielded 1.8 g of purified recombinant beta-mannanase. The purified enzyme was lyophilized and demonstrated to hydrolyse locust bean gum to release mannooligosaccharides.

Biocatalyst immobilization on magnetic nano-architectures for potential applications in condensation reactions

In this review article, a perspective on the immobilization of various hydrolytic enzymes onto magnetic nanoparticles for synthetic organic chemistry applications is presented. After a first part giving short overview on nanomagnetism and highlighting advantages and disadvantages of immobilizing enzymes on magnetic nanoparticles (MNPs), the most important hydrolytic enzymes and their applications were summarized. A section reviewing the immobilization techniques with a particular focus on supporting enzymes on MNPs introduces the reader to the final chapter describing synthetic organic chemistry applications of small molecules (flavour esters) and polymers (polyesters and polyamides). Finally, the conclusion and perspective section gives the author's personal view on further research discussing the new idea of a synergistic rational design of the magnetic and biocatalytic component to produce novel magnetic nano-architectures.

Coproduction of alkaline protease and xylanase from genetically modified Indonesian local Bacillus halodurans CM1 using corncob as an inducing substrate

The production of corn generates a substantial amount of agro-industrial waste, with corncob accounting for a significant portion of this waste. In this study, we focused on utilizing corncob as a carbon source and inducer to simultaneously produce two valuable industrial enzymes, protease, and xylanase, using a recombinant strain of B. halodurans CM1. Interestingly, xylan-rich corncob not only enhanced the xylanase activity but also induced protease activity of the modified B. halodurans CM1 strain. The effect of corncob concentration on the coproduction of protease and xylanase was investigated. Corncob with 6 % concentration induced protease activity of 1020.7 U/mL and xylanase activity of 502.8 U/mL in a 7 L bioreactor under the condition of 1 vvm aeration, 250 rpm agitation, 37 °C temperature, initial pH 9.0, and 40 h incubation period. The protease produced was an alkalothermophilic enzyme whose highest activity was at pH 12 and 50 °C, and it belonged to a serine protease family. This alkalothermophilic protease's activity to some degree was reduced by Co2+, Mg2+, Fe2+, Zn2+, and K+, but enhanced by Ca2+ and Ni2+ (at 5 mM). The protease was stable even under the presence of a 15 % concentration of acetone, DMSO, ethanol, and isopropyl alcohol. The protease activity at 30 °C was not considerably changed by the presence of detergent, indicating excellent potential as a washing detergent additive. According to these findings, corncob has the potential to be a substrate for the coproduction of protease and xylanase, which have a wide range of industrial uses.

Boosting Enzyme Activity in Enzyme Metal-Organic Framework Composites

Enzymes, as highly efficient biocatalysts, excel in catalyzing diverse reactions with exceptional activity and selective properties under mild conditions. Nonetheless, their broad applications are hindered by their inherent fragility, including low thermal stability, limited pH tolerance, and sensitivity to organic solvents and denaturants. Encapsulating enzymes within metal-organic frameworks (MOFs) can protect them from denaturation in these harsh environments. However, this often leads to a compromised enzyme activity. In recent years, extensive research efforts have been dedicated to enhancing enzymatic activity within MOFs, leading to the development of new enzyme-MOF composites that not only preserve their catalytic potential but also outperform their free counterparts. This Review provides a comprehensive review on recent developments in enzyme-MOF composites with a specific emphasis on their enhanced enzymatic activity compared to free enzymes.

Abridgement of Microbial Esterases and Their Eminent Industrial Endeavors

Esterases are hydrolases that contribute to the hydrolysis of ester bonds into both water-soluble acyl esters and emulsified glycerol-esters containing short-chain acyl groups. They have garnered significant attention from biotechnologists and organic chemists due to their immense commercial value. Esterases, with their diverse and significant properties, have become highly sought after for various industrial applications. Synthesized ubiquitously by a wide range of living organisms, including animals, plants, and microorganisms, these enzymes have found microbial esterases to be the preferred choice in industrial settings. The cost-effective production of microbial esterases ensures higher yields, unaffected by seasonal variations. Their applications span diverse sectors, such as food manufacturing, leather tanneries, paper and pulp production, textiles, detergents, cosmetics, pharmaceuticals, biodiesel synthesis, bioremediation, and waste treatment. As the global trend shifts toward eco-friendly and sustainable practices, industrial processes are evolving with reduced waste generation, lower energy consumption, and the utilization of biocatalysts derived from renewable and unconventional raw materials. This review explores the background, structural characteristics, thermostability, and multifaceted roles of bacterial esterases in crucial industries, aiming to optimize and analyze their properties for continued successful utilization in diverse industrial processes. Additionally, recent advancements in esterase research are overviewed, showcasing novel techniques, innovations, and promising areas for further exploration.

Cutting edge tools in the field of soil microbiology

The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.

Support Materials of Organic and Inorganic Origin as Platforms for Horseradish Peroxidase Immobilization: Comparison Study for High Stability and Activity Recovery

In the presented study, a variety of hybrid and single nanomaterials of various origins were tested as novel platforms for horseradish peroxidase immobilization. A thorough characterization was performed to establish the suitability of the support materials for immobilization, as well as the activity and stability retention of the biocatalysts, which were analyzed and discussed. The physicochemical characterization of the obtained systems proved successful enzyme deposition on all the presented materials. The immobilization of horseradish peroxidase on all the tested supports occurred with an efficiency above 70%. However, for multi-walled carbon nanotubes and hybrids made of chitosan, magnetic nanoparticles, and selenium ions, it reached up to 90%. For these materials, the immobilization yield exceeded 80%, resulting in high amounts of immobilized enzymes. The produced system showed the same optimal pH and temperature conditions as free enzymes; however, over a wider range of conditions, the immobilized enzymes showed activity of over 50%. Finally, a reusability study and storage stability tests showed that horseradish peroxidase immobilized on a hybrid made of chitosan, magnetic nanoparticles, and selenium ions retained around 80% of its initial activity after 10 repeated catalytic cycles and after 20 days of storage. Of all the tested materials, the most favorable for immobilization was the above-mentioned chitosan-based hybrid material. The selenium additive present in the discussed material gives it supplementary properties that increase the immobilization yield of the enzyme and improve enzyme stability. The obtained results confirm the applicability of these nanomaterials as useful platforms for enzyme immobilization in the contemplation of the structural stability of an enzyme and the high catalytic activity of fabricated biocatalysts.

Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration

Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.

Adsorption of lipases on porous silica-based materials for esterification in a solvent-free system

This study deals with lipase immobilization on micro- and mesoporous silica-based materials. The effects of the type of support (silica MCM-41, zeolite HZSM-5 (SAR 25), zeolite HZSM-5 (SAR 280), and the silica-aluminas Siral 10, Siral 20, and Siral 40) were investigated on the immobilization of lipase B from Candida antarctica (CALB) and lipase from Rhizomucor miehei (RML). The supports that allowed the highest immobilization efficiencies for the CALB were Siral 40 (91.4%), HZSM-5 (SAR 280) (90.6%), and MCM-41 (89.4%). Siral 20 allowed the highest immobilization efficiency for RML (97.6%), followed by HZSM-5 (SAR 25) (77.1%) and HZSM-5 (SAR 280) (62.7%). The effect of protein concentration on lipase immobilization was investigated, and the results adjusted well on the Langmuir isotherm model (R2 > 0.9). The maximum protein adsorption capacity of the support determined by the Langmuir model was equal to 10.64 and 20.97 mgprotein gsupport-1 for CALB and RML, respectively. The effects of pH (pH 7.0 and pH 11.0) and phosphate buffer solution concentration (5 and 100 mmol L-1) were also investigated on lipase immobilization. The immobilization efficiency for both lipases was similar for the different pH values. The use of 100 mmol L-1 phosphate buffer decreased the lipase immobilization efficiency. The biocatalysts (CALB-Siral 40 and RML-Siral 20) were tested in the ethyl oleate synthesis. The conversion of 61.7% was obtained at 60 °C in the reaction catalyzed by CALB-Siral 40. Both heterogeneous biocatalysts showed increased thermal stability compared with their free form. Finally, the reuse of the biocatalysts was studied. CALB-Siral 40 and RML-Siral 20 maintained about 30% of the initial conversion after 3 batches of ethyl oleate synthesis. Silica-aluminas (Siral 20 and 40) proved to be a support that allowed a high efficiency of immobilization of lipases and activity for esterification reaction.

Identification of potential mutational hotspots in serratiopeptidase to address its poor pH tolerance issue

Serratiopeptidase is the multifunctionality metalloendopeptidase extensively employed in biopharmaceutical and industrial biotechnology. Despite its poor pH tolerance, serratiopeptidase must withstand the highly acidic environment of the gastrointestinal tract to be used as a potent anti-inflammatory and analgesic medication. In earlier studies, post-translational deamination related mutations showed alteration in the net charge of protein's surface. Therefore, the current study aimed to enhance the acid resistance of serratiopeptidase via implementing computational interventions to screen out the most stable mutational hotspot. The methodology used in this study is as follows: (a) Higher accessibility to surface (b) 4 Å away from active site region to avoid interference with its proteolytic activity, and (c) By converting non-conserved amide residues to acidic residues. A docking study has been conducted to establish the substrate specificity and binding affinity to native and mutant proteins. The docking outcomes were then validated using molecular dynamic simulations to clarify each mutant's molecular stability and conformation while preserving their activity. The results showed that N412D is the best-screened mutant with negative electrostatic potential that can alter the overall charge on the protein's surface with increased H+ ions. Alteration in overall charge leads to protein surface more acidic that causes a common ion effect in stomach pH and act as a buffer which could stabilize the serratiopeptidase amid extreme pH.Communicated by Ramaswamy H. Sarma.

Valorization of orange peels exploiting fungal solid-state and lacto-fermentation

BACKGROUND

Orange peels can serve as a cost-effective raw material for the production of lactic acid. Indeed, given their high concentration of carbohydrates and low content of lignin, they represent an important source of fermentable sugars, recoverable after a hydrolytic step.

RESULTS

In the present article, the fermented solid, obtained after 5 days of Aspergillus awamori growth, was used as the only source of enzymes, mainly composed of xylanase (40.6 IU g^-1 of dried washed orange peels) and exo-polygalacturonase (16.3 IU g^-1 of dried washed orange peels) activities. After the hydrolysis, the highest concentration of reducing sugars (24.4 g L^-1 ) was achieved with 20% fermented and 80% non-fermented orange peels. The hydrolysate was fermented with three lactic acid bacteria strains (Lacticaseibacillus casei 2246 and 2240 and Lacticaseibacillus rhamnosus 1019) which demonstrated good growth ability. The yeast extract supplementation increased the lactic acid production rate and yield. Overall, L. casei 2246 produced the highest concentration of lactic acid in mono-culture.

CONCLUSION

To the best of our knowledge this is the first study exploiting orange peels as low-cost raw material for the production of lactic acid avoiding the employment of commercial enzymes. The enzymes necessary for the hydrolyses were directly produced during A. awamori fermentation and the reducing sugars obtained were fermented for lactic acid production. Despite this preliminary work carried out to study the feasibility of this approach, the concentrations of reducing sugars and lactic acid produced were encouraging, leaving open the possibility of other studies for the optimization of the strategy proposed here. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Microwave-assisted enzymatic synthesis of geraniol esters in solvent-free systems: optimization of the reaction parameters, purification and characterization of the products, and biocatalyst reuse

Various geraniol esters act as insect pheromones and display pharmacological activities, especially as neuroprotective agents. Therefore, the search for synthetic strategies alternative to traditional chemical synthesis could help designing ecofriendly routes for the preparation of such bioactive compounds. Hence, this work aims at the microwave-assisted enzymatic synthesis of geranyl esters in solvent-free systems. The process variables were optimized for the synthesis of geranyl acetoacetate, achieving 85% conversion after 60 min using a 1:5 substrates molar ratio (ester to geraniol), 80 °C and 8.4% of Lipozyme 435 lipase without removal of the co-produced methanol. On the other hand, a 95% conversion was reached after 30 min using 1:6 substrates molar ratio, 70 °C and 7% lipase in the presence of 5Å molecular sieves for the methanol capture. In addition, the lipase showed good reusability, maintaining the same activity for five reaction cycles. Finally, under the above optimized conditions, other geraniol esters were successfully synthetized such as the geranyl butyrate (98%), geranyl hexanoate (99%), geranyl octanoate (98%), and geranyl (R)-3-hydroxybutyrate (56%). These results demonstrate the microwave-assisted lipase-catalyzed transesterification in a solvent-free system as an excellent and sustainable catalytic methodology to produce geraniol esters.

Bioengineered Enzymes and Precision Fermentation in the Food Industry

Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.

Statistical bioprocess optimization for enhanced production of a thermo alkalophilic polygalacturonase (PGase) from Pseudomonas sp. 13156349 using solid substrate fermentation (SSF)

In this study, a polygalacturonase (PGase) producing bacterial strain was isolated and identified as Pseudomonas sp. 13159349 from fruit market soils, and TLC analysis confirmed its pectinolytic activity. Additionally, SSF, Plackett-Burman design (PB), and response surface methodology (RSM) were used to optimize the production of this thermostable and alkalophilic PGase. Wheat bran demonstrated the highest activity (60.13 ± 3.39 U/gm) among the various agricultural wastes used as solid substrates. To further enhance the enzyme production, statistical optimization of media components was investigated using the PB design. Among the 11 variables tested, pH (p < 0.0001), inoculum size (p < 0.0001), incubation time (p < 0.0001), and temperature (p < 0.0041) were found to have a positive effect on the production. The interaction and concentration of the selected factors were examined by RSM, which demonstrated the optimal conditions for maximum production (315.65 U/gm) of the enzyme using wheat bran as the solid substrate were pH 10.5, 61-66 h of incubation, and 6-7.5% inoculum size. The model was highly significant, with a p-value of <0.0001, an F-value of 95.33, and a low CV of 2.31. The RSM model was validated by a laboratory-scale experiment showing 30600 ± 400.32 U/100 gm PGase activity. Thus, SSF and the statistical design of media components resulted in a significant 5.2-fold increase in PGase output solely by using agro waste and optimizing the physical parameters, making this a highly cost-effective bioprocess.

Botryosphaeriaceae gene machinery: Correlation between diversity and virulence

The Botryosphaeriaceae family comprises numerous fungal pathogens capable of causing economically meaningful diseases in a wide range of crops. Many of its members can live as endophytes and turn into aggressive pathogens following the onset of environmental stress events. Their ability to cause disease may rely on the production of a broad set of effectors, such as cell wall-degrading enzymes, secondary metabolites, and peptidases. Here, we conducted comparative analyses of 41 genomes representing six Botryosphaeriaceae genera to provide insights into the genetic features linked to pathogenicity and virulence. We show that these Botryosphaeriaceae genomes possess a large diversity of carbohydrate-active enzymes (CAZymes; 128 families) and peptidases (45 families). Botryosphaeria, Neofusicoccum, and Lasiodiplodia presented the highest number of genes encoding CAZymes involved in the degradation of the plant cell wall components. The genus Botryosphaeria also exhibited the highest abundance of secreted CAZymes and peptidases. Generally, the secondary metabolites gene cluster profile was consistent in the Botryosphaeriaceae family, except for Diplodia and Neoscytalidium. At the strain level, Neofusicoccum parvum NpBt67 stood out among all the Botryosphaeriaceae genomes, presenting a higher number of secretome constituents. In contrast, the Diplodia strains showed the lowest richness of the pathogenicity- and virulence-related genes, which may correlate with their low virulence reported in previous studies. Overall, these results contribute to a better understanding of the mechanisms underlying pathogenicity and virulence in remarkable Botryosphaeriaceae species. Our results also support that Botryosphaeriaceae species could be used as an interesting biotechnological tool for lignocellulose fractionation and bioeconomy.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Enzyme-Linked Metal Organic Frameworks for Biocatalytic Degradation of Antibiotics

Metal organic frameworks (MOFs) are multi-dimensional network of crystalline material held together by bonding of metal atoms and organic ligands. Owing to unique structural, chemical, and physical properties, MOFs has been used for enzyme immobilization to be employed in different catalytic process, including catalytic degradation of antibiotics. Immobilization process other than providing large surface provides enzyme with enhanced stability, catalytic activity, reusability, and selectivity. There are various approaches of enzyme immobilization over MOFs including physical adsorption, chemical bonding, diffusion and in situ encapsulation. In situ encapsulation is one the best approach that provides extra stability from unfolding and denaturation in harsh industrial conditions. Presence of antibiotic in environment is highly damaging for human in particular and ecosystem in general. Different methods such as ozonation, oxidation, chlorination and catalysis are available for degradation or removal of antibiotics from environment, however these are associated with several issues. Contrary to these, enzyme immobilized MOFs are novel system to be used in catalytic degradation of antibiotics. Enzyme@MOFs are more stable, reusable and more efficient owing to additional support of MOFs to natural enzymes in well-established process of photocatalysis for degradation of antibiotics aimed at environmental remediation. Prime focus of this review is to present catalytic degradation of antibiotics by enzyme@MOFs while outlining their synthetics approaches, characterization, and mechanism of degradation. Furthermore, this review highlights the significance of enzyme@MOFs system for antibiotics degradation in particular and environmental remediation in general. Current challenges and future perspective of research in this field are also outlined along with concluding comments.

Graphical Abstract

Characterization of a novel cold-adapted intracellular serine protease from the extremophile Planococcus halocryophilus Or1

The enzymes of microorganisms that live in cold environments must be able to function at ambient temperatures. Cold-adapted enzymes generally have less ordered structures that convey a higher catalytic rate, but at the cost of lower thermodynamic stability. In this study, we characterized P355, a novel intracellular subtilisin protease (ISP) derived from the genome of Planococcus halocryophilus Or1, which is a bacterium metabolically active down to -25°C. P355's stability and activity at varying pH values, temperatures, and salt concentrations, as well as its temperature-dependent kinetics, were determined and compared to an uncharacterized thermophilic ISP (T0099) from Parageobacillus thermoglucosidasius, a previously characterized ISP (T0034) from Planococcus sp. AW02J18, and Subtilisin Carlsberg (SC). The results showed that P355 was the most heat-labile of these enzymes, closely followed by T0034. P355 and T0034 exhibited catalytic constants (k _cat ) that were much higher than those of T0099 and SC. Thus, both P355 and T0034 demonstrate the characteristics of the stability-activity trade-off that has been widely observed in cold-adapted proteases.

Evaluation of wool protein hydrolysate as peptone for production of microbial enzymes

Peptones are one of the most expensive components of microbial culture media. The present study was conducted to test the usability of low-cost sheep wool peptone (SWP) as an organic nitrogen source in the production of six industrially important enzymes (lipase, amylase, tannase, pectinase, cellulase and invertase). SWP was prepared by alkaline hydrolysis and acid neutralization. Bacillus licheniformis and Aspergillus niger were selected as test microorganisms for enzyme production. To evaluate the efficacy of SWP in enzyme production, it was compared with commercial tryptone peptone (TP) in the shaking flask cultures of the test microorganisms. The optimum concentration of both SWP and TP was determined to be 8 g/L for the production of B. licheniformis-derived enzymes, but 6 g/L for the production of A. niger-derived enzymes. It was determined that SWP was superior to TP in the production of four enzymes (lipase, amylase, tannase and pectinase) of both B. licheniformis and A. niger. This is the first study about the usage of sheep wool protein hydrolysate (SWP) as an organic nitrogen source or a peptone in fermentative production of microbial enzymes.

Gold Nanozymes: Smart Hybrids with Outstanding Applications

Nanozymes are nanostructured artificial enzymes that have attracted great attention among researchers because of their ability to mimic relevant biological reactions carried out by their natural counterparts, but with the capability to overcome natural enzymes’ drawbacks such as low thermostability or narrow substrate scope. The promising enzyme-like properties of these systems make nanozymes excellent candidates for innovative solutions in different scientific fields such as analytical chemistry, catalysis or medicine. Thus, nanozymes with different type of activities are of special interest owing to their versatility since they can reproduce several biological reactions according to the substrates and the environmental conditions. In this context, gold-based nanozymes are a representative example of multifunctional structures that can perform a great number of enzyme-like activities. In addition, the combination of gold-based materials with structures of organic and inorganic chemical nature yields even more powerful hybrid nanozymes, which enhance their activity by providing improved features. This review will carry out a deep insight into gold-based nanozymes, revisiting not only the different type of biological enzymatic reactions that can be achieved with these kinds of systems, but also structural features of some of the most relevant hybrid gold-based nanozymes described in the literature. This literature review will also provide a representative picture of the potential of these structures to solve future technological challenges.

Resolution of Racemic Aryloxy-Propan-2-yl Acetates via Lipase-Catalyzed Hydrolysis: Preparation of Enantiomerically Pure/Enantioenriched Mexiletine Intermediates and Analogs

The lipase kinetic resolution (KR) of aryloxy-propan-2-yl acetates, via hydrolysis, produced enantiomerically pure/enantioenriched mexiletine intermediates and analogs. Racemic acetates rac-1-(2,6-dimethylphenoxy)propan-2-yl acetate (rac-5a), rac-1-(2,4-dimethylphenoxy)propan-2-yl acetate (rac-5b), rac-1-(o-tolyloxy)propan-2-yl acetate (rac-5c) and rac-1-(naphthalen-1-yloxy)propan-2-yl acetate (rac-5d) were used as substrates. A preliminary screening (24 h, phosphate buffer pH 7.0 with 20% acetonitrile as co-solvent, 30 °C and enzyme:substrate ratio of 2:1, m:m) was carried out with twelve lipases using acetate 5a as substrate. Two enzymes stood out in the KR of 5a, the Amano AK lipase from Pseudomonas fluorescens and lipase from Thermomyces lanuginosus (TLL) immobilized on Immobead 150. Under these conditions, both the (R)-1-(2,6-dimethylphenoxy)propan-2-ol [(R)-4a] and the remaining (S)-1-(2,6-dimethylphenoxy)propan-2-yl acetate [(S)-5a] were obtained with enantiomeric excess (ee) > 99%, 50% conversion and enantiomeric ratio (E) > 200. The KR study was expanded to racemic acetates 5b-d, leading to the corresponding chiral remaining acetates with ≥95% ee, and the alcohols 4b-d with ≥98% ee, and conversion values close to 50%. The best conditions for KRs of rac-5b-d involved the use of lipase from P. fluorescens or TLL immobilized on Immobead 150, 24 or 48 h and 30 °C. These intermediates had their absolute configurations determined using 1H NMR spectroscopy (Mosher’s method), showing that the KRs of these acetates obeyed the Kazlauskas’ rule. Molecular docking studies corroborated the experimental results, indicating a preference for the hydrolysis of (R)-5a-d.

Giant Viruses as a Source of Novel Enzymes for Biotechnological Application

The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.

Agro-Industrial Food Waste as a Low-Cost Substrate for Sustainable Production of Industrial Enzymes: A Critical Review

The grave environmental, social, and economic concerns over the unprecedented exploitation of non-renewable energy resources have drawn the attention of policy makers and research organizations towards the sustainable use of agro-industrial food and crop wastes. Enzymes are versatile biocatalysts with immense potential to transform the food industry and lignocellulosic biorefineries. Microbial enzymes offer cleaner and greener solutions to produce fine chemicals and compounds. The production of industrially important enzymes from abundantly present agro-industrial food waste offers economic solutions for the commercial production of value-added chemicals. The recent developments in biocatalytic systems are designed to either increase the catalytic capability of the commercial enzymes or create new enzymes with distinctive properties. The limitations of low catalytic efficiency and enzyme denaturation in ambient conditions can be mitigated by employing diverse and inexpensive immobilization carriers, such as agro-food based materials, biopolymers, and nanomaterials. Moreover, revolutionary protein engineering tools help in designing and constructing tailored enzymes with improved substrate specificity, catalytic activity, stability, and reaction product inhibition. This review discusses the recent developments in the production of essential industrial enzymes from agro-industrial food trash and the application of low-cost immobilization and enzyme engineering approaches for sustainable development.

Factors affecting the competitiveness of bacterial fermentation

Sustainable production of chemicals and materials from renewable non-food biomass using biorefineries has become increasingly important in an effort toward the vision of 'net zero carbon' that has recently been pledged by countries around the world. Systems metabolic engineering has allowed the efficient development of microbial strains overproducing an increasing number of chemicals and materials, some of which have been translated to industrial-scale production. Fermentation is one of the key processes determining the overall economics of bioprocesses, but has recently been attracting less research attention. In this Review, we revisit and discuss factors affecting the competitiveness of bacterial fermentation in connection to strain development by systems metabolic engineering. Future perspectives for developing efficient fermentation processes are also discussed.

A critical review on biomass-based sustainable biorefineries using nanobiocatalysts: Opportunities, challenges, and future perspectives

Biocatalysts, including live microbial cells/enzymes, have been considered a predominant and advantageous tool for effectively transforming biomass into biofuels and valued biochemicals. However, high production costs, separation, and reusability limit its practical application. Immobilization of single and multi-enzymes by employing different nano-supports have gained massive attention because of its elevated exterior domain and high enzymatic performance. Application of nanobiocatalyst can overcome the drawbacks mainly, stability and reusability, thus reflecting the importance of biomass-based biorefinery to make it profitable and sustainable. This review provides an in-depth, comprehensive analysis of nanobiocatalysts systems concerning nano supports and biocatalytic performance characteristics. Furthermore, the effects of nanobiocatalyst on waste biomass to biofuel and valued bioproducts in the biorefinery approach and their critical assessment are discussed. Lastly, this review elaborates commercialization and market outlooks of the bioconversion process using nanobiocatalyst, followed by different strategies to overcome the limitations and future research directions on nanobiocatalytic-based industrial bioprocesses.

Exploitation of wasted bread as substrate for polyhydroxyalkanoates production through the use of Haloferax mediterranei and seawater

The use of the halophile microorganism Haloferax mediterranei, able to synthesize poly(hydroxybutyrate-hydroxyvalerate) (PHBV), is considered as a promising tool for the industrial production of bioplastic through bioprocessing. A consistent supplementation of the growth substrate in carbohydrates and minerals is overall necessary to allow its PHBV production. In this work, wasted bread was used as substrate for bioplastic production by microbial fermentation. Instead of the consistent and expensive minerals supplement required for Hfx. mediterranei DSM1411 growth, microfiltered seawater was added to the wasted bread-derived substrate. The suitable ratio of wasted bread homogenate and seawater, corresponding to 40:60, was selected. The addition of proteases and amylase to the bread homogenate promoted the microbial growth but it did not correspond to the increase of bioplastic production by the microorganism, that reach, under the experimental conditions, 1.53 g/L. An extraction procedure of the PHBV from cells, based on repeated washing with water, followed or not by a purification through ethanol precipitation, was applied instead of the conventional extraction with chloroform. Yield of PHBV obtained using the different extraction methods were 21.6 ± 3.6 (standard extraction/purification procedure with CHCl3:H2O mixture), 24.8 ± 3.0 (water-based extraction), and 19.8 ± 3.3 mg PHAs/g of wasted bread (water-based extraction followed by ethanol purification). Slightly higher hydroxyvalerate content (12.95 vs 10.78%, w/w) was found in PHBV obtained through the water-based extraction compared to the conventional one, moreover, the former was characterized by purity of 100% (w/w). Results demonstrated the suitability of wasted bread, supplemented with seawater, to be used as substrate for bioplastic production through fermentation. Results moreover demonstrated that a solvent-free extraction, exclusively based on osmotic shock, could be used to recover the bioplastic from cells.

A Convenient U-Shape Microreactor for Continuous Flow Biocatalysis with Enzyme-Coated Magnetic Nanoparticles-Lipase-Catalyzed Enantiomer Selective Acylation of 4-(Morpholin-4-yl)butan-2-ol

This study implements a convenient microreactor for biocatalysis with enzymes immobilized on magnetic nanoparticles (MNPs). The enzyme immobilized onto MNPs by adsorption or by covalent bonds was lipase B from Candida antarctica (CaLB). The MNPs for adsorption were obtained by covering the magnetite core with a silica shell and later with hexadecyltrimethoxysilane, while for covalent immobilization, the silica-covered MNPs were functionalized by a layer forming from mixtures of hexadecyl- and 3-(2-aminoethylamino)propyldimethoxymethylsilanes in 16:1 molar ratio, which was further activated with neopentyl glycol diglycidyl ether (NGDE). The resulting CaLB-MNPs were tested in a convenient continuous flow system, created by 3D printing to hold six adjustable permanent magnets beneath a polytetrafluoroethylene tube (PTFE) to anchor the MNP biocatalyst inside the tube reactor. The anchored CaLB-MNPs formed reaction chambers in the tube for passing the fluid through and above the MNP biocatalysts, thus increasing the mixing during the fluid flow and resulting in enhanced activity of CaLB on MNPs. The enantiomer selective acylation of 4-(morpholin-4-yl)butan-2-ol (±)-1, being the chiral alcohol constituent of the mucolytic drug Fedrilate, was carried out by CaLB-MNPs in the U-shape reactor. The CaLB-MNPs in the U-shape reactor were compared in batch reactions to the lyophilized CaLB and to the CaLB-MNPs using the same reaction composition, and the same amounts of CaLB showed similar or higher activity in flow mode and superior activity as compared to the lyophilized powder form. The U-shape permanent magnet design represents a general and easy-to-access implementation of MNP-based flow microreactors, being useful for many biotransformations and reducing costly and time-consuming downstream processes.

Aliivibrio fischeri L-Asparaginase production by engineered Bacillus subtilis: a potential new biopharmaceutical

L-Asparaginase (L-ASNase) is an enzyme applied in the treatment of lymphoid malignancies. However, an innovative L-ASNase with high yield and lower side effects than the commercially available preparations are still a market requirement. Here, a new-engineered Bacillus subtilis strain was evaluated for Aliivibrio fischeri L-ASNase II production, being the bioprocess development and the enzyme characterization studied. The pBS0E plasmid replicative in Bacillus sp and containing PxylA promoter inducible by xylose and its repressive molecule sequence (XylR) was used for the genetic modification. Initially, cultivations were carried out in orbital shaker, and then the process was scaled up to stirred tank bioreactor (STB). After the bioprocess, the cells were recovered and submitted to ultrasound sonication for cells disruption and intracellular enzyme recovery. The enzymatic extract was characterized to assess its biochemical, kinetic and thermal properties using L-Asparagine and L-Glutamine as substrates. The results indicated the potential enzyme production in STB achieving L-ASNase activity up to 1.539 U mL^-1. The enzymatic extract showed an optimum pH of 7.5, high L-Asparagine affinity (K_m = 1.2275 mmol L^-1) and low L-Glutaminase activity (0.568-0.738 U mL^-1). In addition, thermal inactivation was analyzed by two different Kinect models to elucidate inactivation mechanisms, low kinetic thermal inactivation constants for 25 ºC and 37 ºC (0.128 and 0.148 h^-1, respectively) indicate an elevated stability. The findings herein show that the produced recombinant L-ASNase has potential to be applied for pharmaceutical purposes.

Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization

Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.

Improved deinking and biobleaching efficiency of enzyme consortium from Thermomyces lanuginosus VAPS25 using genetic Algorithm-Artificial neural network based tools

The present study reports the combined enzymatic production efficiency of thermophilic fungus Thermomyces lanuginosus VAPS25 using a combinatory artificial intelligence-based tool, resulting in 2.7 IU/ml, 5.2 IU/ml, and 18.85 U/ml activity of endoglucanase, amylase, and lipase, respectively with good thermostability at 90 °C (pH 8-10). Interestingly, the metal ions viz. Cu²⁺ and Mg²⁺ increased the endoglucanase activity to 5 folds, i.e.,5.6 IU/ml compared to control. Further, the amylase and lipase activity was also enhanced by Fe²⁺ and Co²⁺ to 5.4 IU/ml and 19.57 U/ml, respectively. Additionally, the deinking efficiency was improved by 68.9%, 42.7%, and 52.8% by endoglucanase, amylase, and lipase, respectively, while the consortium increased the deinking efficiency to 72.7%. The bio-bleached paper strength parameters such as burst index, breaking length, tear index, and tensile index of sheets were significantly improved by 1.38%, 13.54%, 7.54%, and 20.88%, respectively. These enzymes at an industrial scale would help develop an economical paper recycling process.

Efficient hydrolysis of starch by α-amylase immobilized on cloisite 30B and modified forms of cloisite 30B by adsorption and covalent methods

In this paper, α-amylase from Bacillus subtilis was successfully immobilized on three supports. First, α-amylase was immobilized on cloisite 30B via the adsorption method. Then cloisite 30B was activated with tosyl chloride and epichlorohydrin. These activated supports were used for covalent immobilization of α-amylase, and their enzymatic activities were effectively tested in the starch hydrolysis. The results demonstrated that the specific activity of α-amylase immobilized on cloisite 30B was 2.39 ± 0.03, for α-amylase immobilized on activated cloisite 30B with epichlorohydrin was 1.96 ± 0.05 and for α-amylase immobilized on activated cloisite 30B with tosyl chloride was 2.17 ± 0.05 U mg^-1. The optimum pH for the activity of free α-amylase was 7, but for α-amylase immobilized on cloisite 30B was 8, and for α-amylase immobilized on activated supports was 7.5. The immobilized enzymes had better thermal resistance and storage stability than free α-amylase, and they also showed excellent reusability.

Learning Strategies in Protein Directed Evolution

Synthetic biology is a fast-evolving research field that combines biology and engineering principles to develop new biological systems for medical, pharmacological, and industrial applications. Synthetic biologists use iterative "design, build, test, and learn" cycles to efficiently engineer genetic systems that are reliable, reproducible, and predictable. Protein engineering by directed evolution can benefit from such a systematic engineering approach for various reasons. Learning can be carried out before starting, throughout or after finalizing a directed evolution project. Computational tools, bioinformatics, and scanning mutagenesis methods can be excellent starting points, while molecular dynamics simulations and other strategies can guide engineering efforts. Similarly, studying protein intermediates along evolutionary pathways offers fascinating insights into the molecular mechanisms shaped by evolution. The learning step of the cycle is not only crucial for proteins or enzymes that are not suitable for high-throughput screening or selection systems, but it is also valuable for any platform that can generate a large amount of data that can be aided by machine learning algorithms. The main challenge in protein engineering is to predict the effect of a single mutation on one functional parameter-to say nothing of several mutations on multiple parameters. This is largely due to nonadditive mutational interactions, known as epistatic effects-beneficial mutations present in a genetic background may not be beneficial in another genetic background. In this work, we provide an overview of experimental and computational strategies that can guide the user to learn protein function at different stages in a directed evolution project. We also discuss how epistatic effects can influence the success of directed evolution projects. Since machine learning is gaining momentum in protein engineering and the field is becoming more interdisciplinary thanks to collaboration between mathematicians, computational scientists, engineers, molecular biologists, and chemists, we provide a general workflow that familiarizes nonexperts with the basic concepts, dataset requirements, learning approaches, model capabilities and performance metrics of this intriguing area. Finally, we also provide some practical recommendations on how machine learning can harness epistatic effects for engineering proteins in an "outside-the-box" way.

Fungal Laccases: The Forefront of Enzymes for Sustainability

Enzymatic catalysis is one of the main pillars of sustainability for industrial production. Enzyme application allows minimization of the use of toxic solvents and to valorize the agro-industrial residues through reuse. In addition, they are safe and energy efficient. Nonetheless, their use in biotechnological processes is still hindered by the cost, stability, and low rate of recycling and reuse. Among the many industrial enzymes, fungal laccases (LCs) are perfect candidates to serve as a biotechnological tool as they are outstanding, versatile catalytic oxidants, only requiring molecular oxygen to function. LCs are able to degrade phenolic components of lignin, allowing them to efficiently reuse the lignocellulosic biomass for the production of enzymes, bioactive compounds, or clean energy, while minimizing the use of chemicals. Therefore, this review aims to give an overview of fungal LC, a promising green and sustainable enzyme, its mechanism of action, advantages, disadvantages, and solutions for its use as a tool to reduce the environmental and economic impact of industrial processes with a particular insight on the reuse of agro-wastes.

The Application of Biocatalysis in the Preparation and Resolution of Morita-Baylis-Hillman Adducts and Their Derivatives

The Morita-Baylis-Hillman (MBH) reaction affords highly functionalised allylic alcohols containing a new stereogenic centre. These MBH adducts are very versatile and have been transformed into a large range of products, some of which have medicinal potential. Several examples of asymmetric syntheses of MBH adducts have been reported, although a generally applicable method remains to be developed. Biocatalytic approaches for the synthesis and enzymatic kinetic resolution of MBH adducts have been reported, and are discussed in detail in this review. Enzymes able to catalyse the asymmetric MBH reaction have been identified, but selectivity and efficiency have generally been low. Lipases, esterases and nitrile-converting enzymes have all been successfully applied in the resolution of MBH adducts, with excellent selectivity being realised in most cases.

Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi

Fungi are key players in biotechnological applications. Although several studies focusing on fungal diversity and genetics have been performed, many details of fungal biology remain unknown, including how cellulolytic enzymes are modulated within these organisms to allow changes in main plant cell wall compounds, cellulose and hemicellulose, and subsequent biomass conversion. With the advent and consolidation of DNA/RNA sequencing technology, different types of information can be generated at the genomic, structural and functional levels, including the gene expression profiles and regulatory mechanisms of these organisms, during degradation-induced conditions. This increase in data generation made rapid computational development necessary to deal with the large amounts of data generated. In this context, the origination of bioinformatics, a hybrid science integrating biological data with various techniques for information storage, distribution and analysis, was a fundamental step toward the current state-of-the-art in the postgenomic era. The possibility of integrating biological big data has facilitated exciting discoveries, including identifying novel mechanisms and more efficient enzymes, increasing yields, reducing costs and expanding opportunities in the bioprocess field. In this review, we summarize the current status and trends of the integration of different types of biological data through bioinformatics approaches for biological data analysis and enzyme selection.

Purification, characterization, and antifungal activity of Bacillus cereus strain NK91 chitinase from rhizospheric soil samples of Himachal Pradesh, India

Newly isolated Bacillus cereus strain NK91 was characterized for extracellular chitinase production. Partially purified chitinase showed a molecular weight of 43.7 kDa in SDS-PAGE analysis. The optimum pH and temperature for the partially purified enzyme were 7.0 and 40°C, respectively. The addition of Mn²⁺ resulted in a 21% increase in enzyme activity as compared to the control. The V_max and K_m of the enzyme were determined as 76.9 μmol/min and 0.07 mg/mL, respectively. This enzyme exhibited stronger antifungal activity towards Fusarium oxysporum (66.7%), Rhizoctonia solani (64.6%), and Colletotrichum gloeosporioides (63%), and transmission electron microscopy and scanning transmission electron microscopy analysis showed considerable changes in cell wall structure with the treatment of purified chitinase as compared to control. Therefore, this enzyme reveals its biocontrol potential against potent phytopathogens in agriculture that can be helpful in swapping harmful as well as expensive fungicides.

Biocatalytic oxidation of fatty alcohols into aldehydes for the flavors and fragrances industry

From Egyptian mummies to the Chanel n°5 perfume, fatty aldehydes have long been used and keep impacting our senses in a wide range of foods, beverages and perfumes. Natural sources of fatty aldehydes are threatened by qualitative and quantitative variability while traditional chemical routes are insufficient to answer the society shift toward more sustainable and natural products. The production of fatty aldehydes using biotechnologies is therefore the most promising alternative for the flavors and fragrances industry. In this review, after drawing the portrait of the origin and characteristics of fragrant fatty aldehydes, we present the three main classes of enzymes that catalyze the reaction of fatty alcohols oxidation into aldehydes, namely alcohol dehydrogenases, flavin-dependent alcohol oxidases and copper radical alcohol oxidases. The constraints, challenges and opportunities to implement these oxidative enzymes in the flavors and fragrances industry are then discussed. By setting the scene on the biocatalytic production of fatty aldehydes, and providing a critical assessment of its potential, we expect this review to contribute to the development of biotechnology-based solutions in the flavors and fragrances industry.