A broader view: microbial enzymes and their relevance in industries, medicine, and beyond

Hybrid chemoenzymatic heterogeneous catalyst prepared in one step from zeolite nanocrystals and enzyme-polyelectrolyte complexes

The combination of inorganic heterogeneous catalysts and enzymes, in so-called hybrid chemoenzymatic heterogeneous catalysts (HCEHCs), is an attractive strategy to effectively run chemoenzymatic reactions. Yet, the preparation of such bifunctional materials remains challenging because both the inorganic and the biological moieties must be integrated in the same solid, while preserving their intrinsic activity. Combining an enzyme and a zeolite, for example, is complicated because the pores of the zeolite are too small to accommodate the enzyme and a covalent anchorage on the surface is often ineffective. Herein, we developed a new pathway to prepare a nanostructured hybrid catalyst built from glucose oxidase and TS-1 zeolite. Such hybrid material can catalyse the in situ biocatalytic formation of H₂O₂, which is subsequently used by the zeolite to trigger the epoxidation of allylic alcohol. Starting from an enzymatic solution and a suspension of zeolite nanocrystals, the hybrid catalyst is obtained in one step, using a continuous spray drying method. While enzymes are expectedly unable to resist the conditions used in spray drying (temperature, shear stress, etc.), we leverage on the preparation of "enzyme-polyelectrolyte complexes" (EPCs) to increase the enzyme stability. Interestingly, the use of EPCs also prevents enzyme leaching and appears to stabilize the enzyme against pH changes. We show that the one-pot preparation by spray drying gives access to hybrid chemoenzymatic heterogeneous catalysts with unprecedented performance in the targeted chemoenzymatic reaction. The bifunctional catalyst performs much better than the two catalysts operating as separate entities. We anticipate that this strategy could be used as an adaptable method to prepare other types of multifunctional materials starting from a library of functional nanobuilding blocks and biomolecules.

Microbial Enzymes Used in Bioremediation

Emerging pollutants in nature are linked to various acute and chronic detriments in biotic components and subsequently deteriorate the ecosystem with serious hazards. Conventional methods for removing pollutants are not efficient; instead, they end up with the formation of secondary pollutants. Significant destructive impacts of pollutants are perinatal disorders, mortality, respiratory disorders, allergy, cancer, cardiovascular and mental disorders, and other harmful effects. The pollutant substrate can recognize different microbial enzymes at optimum conditions (temperature/pH/contact time/concentration) to efficiently transform them into other rather unharmful products. The most representative enzymes involved in bioremediation include cytochrome P450s, laccases, hydrolases, dehalogenases, dehydrogenases, proteases, and lipases, which have shown promising potential degradation of polymers, aromatic hydrocarbons, halogenated compounds, dyes, detergents, agrochemical compounds, etc. Such bioremediation is favored by various mechanisms such as oxidation, reduction, elimination, and ring-opening. The significant degradation of pollutants can be upgraded utilizing genetically engineered microorganisms that produce many recombinant enzymes through eco-friendly new technology. So far, few microbial enzymes have been exploited, and vast microbial diversity is still unexplored. This review would also be useful for further research to enhance the efficiency of degradation of xenobiotic pollutants, including agrochemical, microplastic, polyhalogenated compounds, and other hydrocarbons.

Insights into the structure and conformation of potato resistant starch (type 2) using asymmetrical flow field-flow fractionation coupled with multiple detectors

Insight into the structure and conformation characteristics of starch that influence its enzyme susceptibility is import for its potential application. In this study, the capacity of asymmetrical flow field-flow fractionation (AF4) coupled online with multi-angle light scatting (MALS) and differential refractive index (dRI) detectors (AF4-MALS-dRI) for monitoring of change in structure and conformation of potato starch during enzymatic hydrolysis was evaluated. The dissolution behavior of potato resistant starch (type 2) (PRS) was investigated. The effect of incubation time and amyloglucosidase concentration on the structure and conformation of potato starch was studied. The apparent density and the ratio of R_g (radius of gyration) to R_h (hydrodynamic radius) obtained from AF4-MALS-dRI were proven to be important parameters as they offer an insight into conformation of PRS at molecular level. Results suggested that gelatinization process made potato amylose molecules have a loose and random coil conformation which could contribute to an acceleration of enzymatic hydrolysis of potato starch. Furthermore, an intermediate with an elongated branched conformation was found between amylose and amylopectin populations, which may play a role in digestion property of potato starch. The results demonstrated that AF4-MALS-dRI is a powerful tool for better understanding of conformation of PRS.

Marine Bacterial Esterases: Emerging Biocatalysts for Industrial Applications

The marine ecosystem has been known to be a significant source of novel enzymes. Esterase enzymes (EC 3.1.1.1) represent a diverse group of hydrolases that catalyze the cleavage and formation of ester bonds. Although esterases are widely distributed among marine organisms, only microbial esterases are of paramount industrial importance. This article discusses the importance of marine microbial esterases, their biochemical and kinetic properties, and their stability under extreme conditions. Since culture-dependent techniques provide limited insights into microbial diversity of the marine ecosystem, therefore, genomics and metagenomics approaches have widely been adopted in search of novel esterases. Additionally, the article also explains industrial applications of marine bacterial esterases particularly for the synthesis of optically pure substances, the preparation of enantiomerically pure drugs, the degradation of human-made plastics and organophosphorus compounds, degradation of the lipophilic components of the ink, and production of short-chain flavor esters.

Formulation of an exoskeleton degrading bacterial consortium from seafood processing effluent for the biocontrol of crustacean parasite Alitropus typus

Parasitic infestations on cultured fish due to the crustacean isopod Alitropus typus has been on the rise in recent years, causing large scale mortality, leading to significant economic loss to the farmer. Crustaceans are encased by an exoskeleton composed of chitin, protein and lipid microfibril frameworks, in which calcium carbonate is deposited. A strategy focused on the degradation of the exoskeletal framework utilizing nonpathogenic microorganisms that produce a wide variety of hydrolytic enzymes may be an environment-friendly and safe alternative to control these pests. The present study was aimed to formulate a microbial consortium having chitinase, protease, lipase and urease producing bacteria from seafood processing effluents that can potentially degrade the exoskeleton of A. typus. Based on the qualitative and quantitative assessment of the extracellular enzymes produced by the isolates, a novel consortium was prepared with three strains that were not antagonistic to each other and were nonpathogenic. The chitinase producing - Stenotrophomonas maltophilia and Bacillus altitudinis that produced protease and lipase as well; and non-chitinase producing Klebsiella pneumoniae were taken in the ratio of 1:1:2 respectively (10⁹ CFU/mL). The result showed 100 % mortality of the isopods within five days when applied at a concentration of 2% (v/v) of 10⁷ CFU/mL without any adverse effect on the fish host Oreochromis niloticus. Analysis of the ultrastructural alterations of the parasites by Environmental Scanning Electron microscopy (ESEM) showed noticeable exoskeletal damages. The microbial members of the consortium displayed remarkable chemotactic properties towards A. typus. The results suggest that the microbial consortium acts as a potential parasiticide that can be used for the control of A. typus infestation in aquaculture ponds., thus benefitting the aquaculture industry especially the small-scale farmers.

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.

Recombinant expression, purification, and characterization of an α-amylase from Massilia timonae

This work reports the amy1 gene cloning from Massilia timonae CTI-57, and its successful expression in Escherichia coli Rosetta™ (DE3) from the pTRCHis2B plasmid. The recombinant AMY1 protein had 47 kDa, and its modeled structure showed a monomer composed of three domains. An N-terminal domain with the characteristic (β/α)₈-barrel structure of α-amylases, which contained the catalytic amino acid residues. The second domain was small, and the C-terminal domain was similar to those found in the barley α-amylase. A phylogenetic analysis demonstrated a high sequence identity of the studied protein with bacterial and plant α-amylases from the GH13_6 subfamily. This is the first characterized bacterial α-amylase from this glucoside hydrolase subfamily. Besides starch, the enzyme was also active against maltodextrin, amylopectin, and blocked p-nitrophenyl α-d-maltoheptaoside, but could not use β-cyclodextrin or 4-nitrophenyl α-d-glucopyranoside. The K _M for highly pure grade soluble starch from potato and V _max values were 0.79 mg/mL and 0.04 mg/min, respectively. The calcium ion showed to be essential for the purified enzyme's activity, while EDTA, molybdenum, cobalt, and mercury were strong inhibitors. The enzyme was almost fully active in SDS presence. The enzyme's optimal pH and temperature were 6.0 and 60 °C, respectively, and its denaturation T _m was 79 °C. A TLC analysis revealed that glucose and maltose are products of the enzyme's action on starch. In conclusion, this work described the M. timonae GH13_6 subfamily α-amylase, which showed to be thermostable and anionic detergent-resistant.

Plasma-mediated enhancement of enzyme secretion in Aspergillus oryzae

Technical bottlenecks in protein production and secretion often limit the efficient and robust industrial use of microbial enzymes. The potential of non-thermal atmospheric pressure plasma to overcome these technical barriers was examined. Spores of the fermenting fungus Aspergillus oryzae (A. oryzae) were submerged in potato dextrose broth (PDB) (5 × 106 per ml) and treated with micro dielectric barrier discharge plasma at an input voltage of 1.2 kV and current of 50 to 63 mA using nitrogen as the feed gas. The specific activity of α-amylase in the broth was increased by 7.4 to 9.3% after 24 and 48 h of plasma treatment. Long-lived species, such as NO2 - and NO3 - , generated in PDB after plasma treatment may have contributed to the elevated secretion of α-amylase. Observations after 24 h of plasma treatment also included increased accumulation of vesicles at the hyphal tip, hyphal membrane depolarization and higher intracellular Ca2+ levels. These results suggest that long-lived nitrogen species generated in PDB after plasma treatment can enhance the secretion of α-amylase from fungal hyphae by depolarizing the cell membrane and activating Ca2+ influx into hyphal cells, eventually leading to the accumulation of secretory vesicles near the hyphal tips.

A critical review on marine serine protease and its inhibitors: A new wave of drugs?

Marine organisms are rich sources of enzymes and their inhibitors having enormous therapeutic potential. Among different proteolytic enzymes, serine proteases, which can be obtained from various marine organisms show a potential to biomedical application as thrombolytic agents. Although this type of proteases plays a crucial role in almost all biological processes, their uncontrolled activity often leads to several diseases. Accordingly, the actions of these types of proteases are regulated by serine protease inhibitors (SPIs). Marine SPIs control complement activation and various other physiological functions, such as inflammation, immune function, fibrinolysis, blood clotting, and cancer metastasis. This review highlights the potential use of serine proteases and their inhibitors as the new wave of promising drugs.

Reducing the cell lysis to enhance yield of acid-stable alpha amylase by deletion of multiple peptidoglycan hydrolase-related genes in Bacillus amyloliquefaciens

Bacillus amyloliquefaciens is a major industrial host for extracellular protein production, with great potential in the enzyme industry. However, the strain has accelerated the autolysis drawback in the process of secreting extracellular enzymes, which can significantly lower the density of cells and decrease the product yield. To identify target genes, we employed comparative transcriptome sequencing and KEGG analysis to indicate the increased expression of peptidoglycan hydrolase-regulated genes from the exponential phase to the apoptotic phase of growth; this was further confirmed by quantitative RT-PCR. By deleting lytD, lytE, and sigD genes, cell lysis was reduced and the production of acid-stable Bacillus licheniformis alpha-amylase was enhanced. After 36 h of culture, multiple deletion mutant BA ΔSDE had significantly more viable cells compared to the control strain BA Δupp, and flow cytometry analysis indicated that 48.43% and 64.03% of the cells were lysed in cultures of BA ΔSDE and BA Δupp, respectively. In a 2-L fed-batch fermenter, viable cell number of the triple deletion mutant BA ΔSDE increased by 2.79 Log/cfu/mL, and the activity of acid-stable alpha-amylase increased by 48.4%, compared to BA Δupp. Systematic multiple peptidoglycan hydrolases deletion relieved the autolysis and increased the production of industrial enzymes, and provided a useful strategy for guiding efforts to manipulate the genomes of other B. amyloliquefaciens used for chassis host.

Optimization of bio-chemical degumming of Ramie fiber for improved strength & luster

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A bacterial consortium tailor-made for appropriate degumming of partially chemically treated Ramie fiber developed.

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Stronger (6.3 folds) ramie fiber following biochemical processing than chemical degumming.

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Biochemically processed fiber more soft and lustrous, forming much finer fabric than seen earlier.

Textile industries are currently not showing much interest in Ramie fibers due to the difficulties associated with their post-harvest downstream processing. The degumming chemicals are often detrimental to the environment upon discharged. Chemical degumming alone results in fibril-released coarse and brittle fibers. This problem has been addressed by combining partial chemical treatment with microbial degumming of the fibers for 72 h at 37 °C using a novel microbial formulation with Bacillus thuringiensis MCC2138 and Bacillus subtilis ABDR01. The extracellular microbial enzyme-based degumming without the release of fibrils produced a durable, soft, and lustrous fiber with higher tensile strength while utilizing fewer chemicals, thereby leading to lower discharge toxicity. The improved texture and strength compared to complete chemical treatment are attributed to even degumming of the fiber ensuring proper spinnability. Through this approach, Ramie is expected to gain visibility in the global textile market, thereby leading to Ramie cultivators' economic benefits.

Exploitation of Ultrasound Technique for Enhancement of Microbial Metabolites Production

Microbial metabolites have significant impacts on our lives from providing valuable compounds for nutrition to agriculture and healthcare. Ever-growing demand for these natural compounds has led to the need for smart and efficient production techniques. Ultrasound is a multi-applicable technology widely exploited in a range of industries such as chemical, medical, biotechnological, pharmaceutical, and food processes. Depending on the type of ultrasound employed, it can be used to either monitor or drive fermentation processes. Ultrasonication can improve bioproduct productivity via intensifying the performance of living organisms. Controlled ultrasonication can influence the metabolites' biosynthesis efficiency and growth rates by improvement of cell permeability as well as mass transfer and nutrient uptake rates through cell membranes. This review contains a summarized description about suitable microbial metabolites and the applications of ultrasound technique for enhancement of the production of these metabolites as well as the associated downstream processing.

Production and characterization of psychrophilic α-amylase from a psychrophilic bacterium, Shewanella sp. ISTPL2

A psychrophilic and halophilic bacterial isolate, Shewanella sp. ISTPL2, procured from the pristine Pangong Lake, Ladakh, Jammu and Kashmir, India, was used for the production and characterization of the psychrophilic and alkalophilic α-amylase enzyme. The α-amylase is a critical enzyme that catalyses the hydrolysis of α-1,4-glycosidic bonds of starch molecules and is predominately utilized in biotechnological applications. The highest enzyme activity of partially purified extracellular α-amylase was 10,064.20 U/mL after 12 h of incubation in a shake flask at pH 6.9 and 10 °C. Moreover, the maximum intracellular α-amylase enzyme activity (259.62 U/mL) was also observed at 6 h of incubation. The extracellular α-amylase was refined to the homogeneity with the specific enzyme activity of 36,690.47 U/mg protein corresponding to 6.87-fold purification. The optimized pH and temperature for the α-amylase were found to be pH 8 and 4 °C, respectively, suggesting its stability at alkaline conditions and low or higher temperatures. The amylase activity was highly activated by Cu2+, Fe2+ and Ca2+, while inhibited by Cd2+, Co2+ and Na2+. As per our knowledge, the current study reports the highest activity of a psychrophilic α-amylase enzyme providing prominent biotechnological potential.

Application of deep neural techniques in predictive modelling for the estimation of Escherichia coli growth rate

AIMS

To develop a predictive model for Escherichia coli using deep neural networks.

METHODS AND RESULTS

Batch experiments are conducted at different temperatures closer to optimum value (36·5°C, 37°C, 37·5°C, 38°C and 38·5°C) to obtain the growth curves of E .coli K-12. Two primary models namely modified Gompertz and new logistic are chosen. Three secondary models namely Gaussian, nonlinear autoregressive eXogenous (NARX) model and long short-term memory (LSTM) are developed. The novelty in this paper is the development of secondary models using artificial neural network (ANN) and deep network. The performance measures chosen to compare the developed primary and secondary models are correlation coefficient (R² ), root-mean-square error (RMSE) and accuracy factor (A_f ). Results show that modified Gompertz model has better R² (0·99) and RMSE (0·019) when compared to new logistic model. Also, the deep network model outperforms other secondary models. Based on the primary and novel secondary model, a predictive model (tertiary model) is developed with improved accuracy and is validated.

CONCLUSIONS

The proposed predictive model exhibit good validation results in terms of RMSE and R² values and can be applied for determining the growth rate of E. coli at a particular temperature value.

SIGNIFICANCE AND IMPACT OF THE STUDY

The proposed model can be used in food processing industries during enzyme production such as Chymosin, to predict the growth rate of E. coli as a function of temperature. Also, the developed LSTM and NARX models can be used to predict maximum specific growth rate of other microbial strains with proper training.

Production, purification and application of Cutinase in enzymatic scouring of cotton fabric isolated from Acinetobacter baumannii AU10

Conventional cotton scouring in the textile industry using alkali results in huge environmental impact which can be overcome by using enzymes. Pectinase along with cutinase gives enhanced bioscouring results. Cutin was extracted from tomato peels and was used as substrate in the microbial media. The strain isolated from tomato peel was identified as Acinetobacter baumannii AU10 by 16S rDNA sequencing. The cutinase production was optimized by Placket-Burman and Response Surface Methodology (RSM) and the maximum production of 82.75 U/mL obtained at sucrose 6.68% (w/v), gelatin 2.74 g/L at a temperature of 35.93 °C. Cutinase was purified by ammonium sulfate precipitation, hydrophobic interaction chromatography and ion exchange chromatography with a recovery of 25.6% and specific activity of 38030 U/mg. The confirmation test for the purity of cutinase was analyzed by RP-HPLC. The molecular mass of cutinase was determined as 28.9 kDa by SDS-PAGE technique. Scanning electron microscopic analysis showed a rough and open primary wall surface on the cutinase bioscoured fabric which confirmed its activity on cutin present in the cotton fabric. Additionally, the cutinase-bioscoured samples showed better absorbency than the untreated samples. Therefore, enzymatic scouring increases wetting capacity of scoured cotton and also helps to reduce environmental pollution.

Technical integrative approaches to cheese whey valorization towards sustainable environment

Whey, a byproduct of cheese production, is often treated as an industrial dairy waste. A large volume of this product is disposed of annually due to inadequate bioconversion approaches. With its high pollutant load, disposal without pretreatment has raised a lot of environmental concerns alerting the need to seek optimal methods for adequately extracting and utilizing its organic content. In recent years, several techniques for whey valorization have emerged which may serve as interventionary measures against its environmental effects after disposal. In this review, we discuss five major approaches, by which whey can be converted into eco-friendly products, to significantly cut whey wastage. The approaches to whey valorization are therefore examined under the following perspectives: whey as a raw material for the production of bioethanol and prebiotic oligosaccharides via β-galactosidase and microbe catalyzed reactions, for the production of refined lactose as an excipient for pharmaceutical purposes, and the clinical significance of whey hydrolysates and their antifungal activity in food processing.

Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools

Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.

Escherichia coli strain engineering for enhanced production of serratiopeptidase for therapeutic applications

Serratiopeptidase is an extracellular zinc-containing metalloprotease that is produced by Serratia marcescens having molecular weight of about 53kD. It has shown therapeutic (anti-inflammatory, anti-fibrinolytic and analgesic) as well as industrial applications (detergents, food processing, leather, paper and brewing etc.). The evolution of Serratia marcescens as an opportunistic pathogen associated with various infections has led researchers to think and develop an alternate strategy for its industrial production. The study presents successful cloning, expression and purification of active serratiopeptidase, using Escherichia coli BL21 [DE3] and pET SUMO vector followed by optimization of synthetic media and culture conditions for enhanced serratiopeptidase production. Initial optimization of physical parameters was done followed by a screening of different carbon and nitrogen sources. The significant media components for serratiopeptidase production as shown by factorial screening experiment were subjected to Response Surface Methodology (RSM) based optimization. The optimized media yielded 86 mg L^-1 of biologically active refolded serratiopeptidase from 20 g L^-1 wet weight of induced pellet as predicted by the equation. The success of the application of a statistical model for designing an optimized media for enhanced serratiopeptidase production also suggests a new insight for the scale-up of serratiopeptidase towards industrial applications.

Activity and specificity studies of the new thermostable esterase EstDZ2

In this paper, we study the activity and specificity of EstDZ2, a new thermostable carboxyl esterase of unknown function, which was isolated from a metagenome library from a Russian hot spring. The biocatalytic reaction employing EstDZ2 proved to be an efficient method for the hydrolysis of aryl p-, o- or m-substituted esters of butyric acid and esters of secondary alcohols. Docking studies revealed structural features of the enzyme that led to activity differences among the different substrates.

Production of commercially important enzymes from Bacillus licheniformis KIBGE-IB3 using date fruit wastes as substrate

BACKGROUND

Pakistan is one of the top five date fruit-producing countries and produced more than 30% wastes in picking, packing, storage, and commercialization stages. The date fruit wastes are usually considered inedible for humans and only used for livestock feed. In current research, Bacillus licheniformis KIBGE-IB3 was screened for pectinase, xylanase, cellulase, and amylase production using date fruit wastes as substrate through solid state fermentation.

RESULTS

The B. licheniformis KIBGE-IB3 produced higher concentration of pectinase using date fruit wastes as substrate as compared to amylase, cellulase, and xylanase. B. licheniformis KIBGE-IB3 produced maximum pectinase using 5.0 g/dl date fruit wastes and 0.5 g/dl yeast extract. B. licheniformis KIBGE-IB3 required pH 7.0, 37 °C incubation temperature, and 72 h incubation period for maximum production of pectinase.

CONCLUSION

It has been concluded that date fruit waste is a good source of biomass and can be utilized for the commercial production of pectinase.

Microbial lipases and their industrial applications: a comprehensive review

Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in 2018 and it is projected to reach USD 590.2 Million by 2023, growing at a CAGR of 6.8% from 2018. Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides. The microbial origins of lipase enzymes are logically dynamic and proficient also have an extensive range of industrial uses with the manufacturing of altered molecules. The unique lipase (triacylglycerol acyl hydrolase) enzymes catalyzed the hydrolysis, esterification and alcoholysis reactions. Immobilization has made the use of microbial lipases accomplish its best performance and hence suitable for several reactions and need to enhance aroma to the immobilization processes. Immobilized enzymes depend on the immobilization technique and the carrier type. The choice of the carrier concerns usually the biocompatibility, chemical and thermal stability, and insolubility under reaction conditions, capability of easy rejuvenation and reusability, as well as cost proficiency. Bacillus spp., Achromobacter spp., Alcaligenes spp., Arthrobacter spp., Pseudomonos spp., of bacteria and Penicillium spp., Fusarium spp., Aspergillus spp., of fungi are screened large scale for lipase production. Lipases as multipurpose biological catalyst has given a favorable vision in meeting the needs for several industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. This review represents a discussion on microbial sources of lipases, immobilization methods increased productivity at market profitability and reduce logistical liability on the environment and user.

Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck

Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.

Biochemical Prospects of Various Microbial Pectinase and Pectin: An Approachable Concept in Pharmaceutical Bioprocessing

Both pectin and pectinase are vitally imperative biomolecules in the biotechnological sector. These molecules are a feasible non-toxic contrivance of nature with extensive applicative perception. Understanding pectic substances and their structure, unique depolymerization, and biochemical properties such as a catalytic mechanism and the strong interrelationship among these molecules could immensely enhance their applicability in industries. For instance, gaining knowledge with respect to the versatile molecular heterogeneity of the compounds could be considered as the center of concern to resolve the industrial issues from multiple aspects. In the present review, an effort has been made to orchestrate the fundamental information related to structure, depolymerization characteristics, and classification of pectin as well as the types and biochemical properties of pectinase. Furthermore, various production methods related to the optimization of the product and its significant contribution to the pharmaceutical industry (either pectinase or derived pectic substances) are described in this article.

In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94

Serratia marcescens, rod-shaped Gram-negative bacteria is classified as an opportunistic pathogen in the family Enterobacteriaceae. It causes a wide variety of infections in humans, including urinary, respiratory, ocular lens and ear infections, osteomyelitis, endocarditis, meningitis and septicemia. Unfortunately, over the past decade, antibiotic resistance has become a serious health care issue; the effective means to control and dissemination of S. marcescens resistance is the need of hour. The whole genome sequencing of S. marcescens FGI94 strain contains 4434 functional proteins, among which 690 (15.56%) proteins were classified under hypothetical. In the present study, we applied the power of various bioinformatics tools on the basis of protein family comparison, motifs, functional properties of amino acids and genome context to assign the possible functions for the HPs. The pseudo sequences (protein sequence that contain ≤100 amino acid residues) are eliminated from the study. Although we have successfully predicted the function for 483 proteins, we were able to infer the high level of confidence only for 108 proteins. The predicted HPs were classified into various classes such as enzymes, transporters, binding proteins, cell division, cell regulatory and other proteins. The outcome of the study could be helpful to understand the molecular mechanism in bacterial pathogenesis and also provide an insight into the identification of potential targets for drug and vaccine development.

Response surface methodology based optimization and scale-up production of amylase from a novel bacterial strain, Bacillus aryabhattai KIIT BE-1

A novel strain KIIT BE-1 isolated from a specialized environment, screened through starch iodine test from a set of eighty-five biodigestate isolates, produced amylase maximally when cultured for 48 h at 37 °C. The molecular and biochemical characterization confirmed it as a strain of Bacillus aryabhattai. It exhibited optimal amylase activity (3.20 U/ml) at 36 h post incubation with a media combination of starch and yeast extract for C-N source respectively. Statistical optimisation by response surface modeling showed R² values of 0.9645 for biomass and 0.9831 for amylase activity, suggesting the significance of the model. The optimised medium (10.25 % starch, 5.0 % peptone, 5.18 % yeast extract, pH 7.3) enhanced the enzyme activity to 4.16 U/ml (1.39-fold) from 3.20 U/ml of un-optimised medium. Further, the biomass yield and the enzymatic activity in optimized medium and process conditions increased by 1.14 and 1.21 folds subjected to a 5 l scaled-up operation in a lab-scale bioreactor.

Modification of isolation methods and physico-biochemical properties of preparations of fungal oxidoreductases

The results of the modification of methods for producing enzymatic preparations (EP) of peroxidases and catalases of extra- and intracellular finding from fungal cultures are presented. Strains of Flammulina velutipes F-vv, Lentinula edodes 523 and Pleurotus ostreatus P-01 were used as producers of oxidoreductases. The producers were cultured in glucose-peptone medium, modified for each strain. Protein fractionation was carried out by leaching with ammonium sulfate at a saturation of 40–70% for peroxidases and 80% for catalases. The obtained solutions of protein fractions were additionally subjected to purification by dialysis, gel filtration on Molselect G-50 and G-75 granules, and also freeze drying. The yield of enzymatic preparations per unit mass of mycelium and the volume of culture fluid were calculated. The individual characteristics of EP – enzymatic activity, the mass percentage of protein and associated amino acids, the ratio of the latter in groups depending on the nature of the radicals (amphotericity) of protein molecules are established. It was proved that the amino acid content in the proteins of fungal EP catalases and peroxidases indicates their acidic nature and this is confirmed by the pH values of aqueous solutions. Examination and toxicity testing of enzymatic preparations were carried out in certified laboratories, which confirmed their characteristics and compliance with safety requirements. The therapeutic properties of amino acids that are part of proteins or are in a free state in enzyme preparations are analyzed. In this way, the methods have been developed for producing enzymatic preparations of peroxidases and catalases of extra- and intracellular location, which allow new antioxidant enzymes with individual properties to be obtained, and, as a result, bring prospects for use in various industries and scientific research.

A comprehensive review on freshness of fish and assessment: Analytical methods and recent innovations

Fish, a highly nutritious, containing a good amount of protein and fatty acids, has TMA and TVB-N present as major factors responsible for quality deterioration during storage and maintaining of fish freshness. Freshness is one of the most important parameters in the fish market. There are many methods of estimating fish freshness, out of which some are very costly while others are not user-friendly. However, with more technological innovations, there have been efforts to make a more reliable method of calculating and analyzing freshness. Parameters chosen for assessing the freshness are sensory, physical, chemical and microbiological including the recent trends such as SDS-PAGE, fast protein liquid chromatography, hyper Spectral Imaging Technique, etc. focused on reducing time, destruction and labor. Traditional and recent methods of evaluation of freshness along with their comparison based on several parameters are needed to link them and making it convenient for upcoming researchers to have a detailed study for having a universal indicator for assessing the freshness of fish. Information in the present article has all the methods of assessing the fish freshness been discussed in detail. There has also been focus on bringing the readers knowledge about the comprehensive information related to recent developments. The recommended limit for different indicators signifies the time period for which the particular fish can be stored and it depends upon several factors like species, surrounding environment and enzymatic and non-enzymatic actions. Based on these demands, this paper is uniquely worked upon to review the different literature which brought all the discussions from the past including the recent innovations in assessing the freshness of different fishes with the help of various indicators as well as a complete study of spoilage and toxicity mechanism leading to deterioration in quality, making it easy for the reader and researchers to have quick glance over the trends and innovations.

Aislamiento e identificación de microorganismos potencialmente amilolíticos y celulolíticos de suelos de humedales de Bogotá

Las amilasas y celulasas de origen microbiano se han utilizado desde hace más de tres décadas en la industria; el aislamiento de cepas microbianas nativas productoras de enzimas es el punto de partida para aprovechar la biodiversidad microbiana para la obtención de enzimas con propiedades para la obtención de nuevos productos en la optimización de procesos industriales. El objetivo de este trabajo, fue aislar, a partir de suelo de cinco humedales en Bogotá, cepas microbianas con capacidad para producir enzimas amilolíticas y celulolíticas. Se realizó la medición de halos de hidrólisis en agar almidón y agar carboximetilcelulosa. Se determinaron las unidades enzimáticas (U/ml/min) por medio de azúcares reductores por la técnica de DNS. Se seleccionaron cuatro cepas de Bacillus subtillis amiloliquefaciens productoras de amilasas con actividades entre 752±33 y 480 ± 35 U/ml/min a 60ºC y cinco cepas celulolíticas identificadas como Bacillus subtillis amiloliquefaciens, Stenotrophomonas nitritireducens y Yersinia massiliensis, capaces de producir celulasas con actividades enzimáticas entre 19.11 ± 2.3 y 13.82 ± 2.5 UA/ml/min a 50ºC. Con estos resultados se demostró que a partir de suelos de humedales, se pueden recuperar microrganismos con capacidad de producción enzimática, como punto de partida para una posterior aplicación en procesos industriales.

Interaction Analysis of Commercial Graphene Oxide Nanoparticles with Unicellular Systems and Biomolecules

The ability of commercial monolayer graphene oxide (GO) and graphene oxide nanocolloids (GOC) to interact with different unicellular systems and biomolecules was studied by analyzing the response of human alveolar carcinoma epithelial cells, the yeast Saccharomyces cerevisiae and the bacteria Vibrio fischeri to the presence of different nanoparticle concentrations, and by studying the binding affinity of different microbial enzymes, like the α-l-rhamnosidase enzyme RhaB1 from the bacteria Lactobacillus plantarum and the AbG β-d-glucosidase from Agrobacterium sp. (strain ATCC 21400). An analysis of cytotoxicity on human epithelial cell line A549, S. cerevisiae (colony forming units, ROS induction, genotoxicity) and V. fischeri (luminescence inhibition) cells determined the potential of both nanoparticle types to damage the selected unicellular systems. Also, the protein binding affinity of the graphene derivatives at different oxidation levels was analyzed. The reported results highlight the variability that can exist in terms of toxicological potential and binding affinity depending on the target organism or protein and the selected nanomaterial.

Indoxyl Acetate as a Substrate for Analysis of Lipase Activity

Lipases play a crucial role in metabolism of microbes, fungi, plants, and animals, and in analytical chemistry, they are often used in detection of fats and triglycerides. Determination of lipase activity is also important in toxicology, when lipase activity can be both increased and decreased by organophosphates and other pesticides and in medicine for diagnosis of heart diseases. The standard method for lipase activity determination is based on cleaving ester bonds in lipase buffer containing Tween. Our aim was to find a method with faster and more sensitive response. It is known that acetylcholinesterase belongs to the same group of hydrolases enzymes as lipases and it cleaves indoxyl acetate, so we assume indoxyl acetate could report a similar reaction with lipase. Our method is based on indoxyl acetate as a substrate for lipase, where indoxyl acetate is cleaved by lipase to indoxyl and acetate moiety and blue indigo is created. The method was optimized for different times and amount of enzyme and compared with the standard Tween assay. The calibration curve measured in reaction time 20 minutes with 10 μl of lipase exhibited the best analytical parameters, and it showed Michaelis-Menten response with the Michaelis-Menten constant equal to 8.72 mmol/l. The indoxyl acetate-based method showed faster and more sensitive response than the standard method for lipase activity determination, so it has great potential in biosensor construction and it could be used in industry, medicine, toxicology, and common practice where the activity of lipases is need to be measured.

Disulfide Engineered Lipase to Enhance the Catalytic Activity: A Structure-Based Approach on BTL2

Enhancement, control, and tuning of hydrolytic activity and specificity of lipases are major goals for the industry. Thermoalkaliphilic lipases from the I.5 family, with their native advantages such as high thermostability and tolerance to alkaline pHs, are a target for biotechnological applications. Although several strategies have been applied to increase lipases activity, the enhancement through protein engineering without compromising other capabilities is still elusive. Lipases from the I.5 family suffer a unique and delicate double lid restructuration to transition from a closed and inactive state to their open and enzymatically active conformation. In order to increase the activity of the wild type Geobacillus thermocatenulatus lipase 2 (BTL2) we rationally designed, based on its tridimensional structure, a mutant (ccBTL2) capable of forming a disulfide bond to lock the open state. ccBTL2 was generated replacing A191 and F206 to cysteine residues while both wild type C64 and C295 were mutated to serine. A covalently immobilized ccBTL2 showed a 3.5-fold increment in esterase activity with 0.1% Triton X-100 (2336 IU mg⁻¹) and up to 6.0-fold higher with 0.01% CTAB (778 IU mg⁻¹), both in the presence of oxidizing sulfhydryl agents, when compared to BTL2. The remarkable and industrially desired features of BTL2 such as optimal alkaliphilic pH and high thermal stability were not affected. The designed disulfide bond also conferred reversibility to the enhancement, as the increment on activity observed for ccBTL2 was controlled by redox pretreatments. MD simulations suggested that the most stable conformation for ccBTL2 (with the disulfide bond formed) was, as we predicted, similar to the open and active conformation of this lipase.

Structural and Functional Characterization of Three Novel Fungal Amylases with Enhanced Stability and pH Tolerance

Amylases are probably the best studied glycoside hydrolases and have a huge biotechnological value for industrial processes on starch. Multiple amylases from fungi and microbes are currently in use. Whereas bacterial amylases are well suited for many industrial processes due to their high stability, fungal amylases are recognized as safe and are preferred in the food industry, although they lack the pH tolerance and stability of their bacterial counterparts. Here, we describe three amylases, two of which have a broad pH spectrum extending to pH 8 and higher stability well suited for a broad set of industrial applications. These enzymes have the characteristic GH13 α-amylase fold with a central (β/α)₈-domain, an insertion domain with the canonical calcium binding site and a C-terminal β-sandwich domain. The active site was identified based on the binding of the inhibitor acarbose in form of a transglycosylation product, in the amylases from Thamnidium elegans and Cordyceps farinosa. The three amylases have shortened loops flanking the nonreducing end of the substrate binding cleft, creating a more open crevice. Moreover, a potential novel binding site in the C-terminal domain of the Cordyceps enzyme was identified, which might be part of a starch interaction site. In addition, Cordyceps farinosa amylase presented a successful example of using the microseed matrix screening technique to significantly speed-up crystallization.

Enzyme Immobilization on Polymer Membranes: A Quantum and Molecular Mechanics Study

Adsorption of the phosphotriesterase on a polysulfone membrane surface was investigated in this paper through a double-scale computational approach. Surface charges of the enzyme, as well as membrane, were calculated at sub and nanoscale while protein adsorption was simulated at larger scale. Adsorption energies were calculated as a function of the enzyme–surface distance, and for each distance, several protein rotations were tested to find the most stable orientations of the macromolecule. The results of this model were useful in obtaining information about the adhesion of the enzyme and to give indications on the orientations of its binding site. Adsorption energies agreed with the literature data. Furthermore, the binding site of the immobilized phosphotriesterase was less accessible with respect to native enzymes due to the steric hindrance of the polymer surface; thus, a reduction of its efficiency is expected. The proposed methodology made use of fundamental quantities, calculated without resorting to adjustable or empirical parameters, providing basic outputs useful for ascertaining enzymatic catalysis rate.

Improving on nature’s shortcomings: evolving a lipase for increased lipolytic activity, expression and thermostability

An enzyme must be soluble, stable, active and easy to produce to be useful in industrial applications. Not all enzymes possess these attributes. We set out to determine how many changes are required to convert an enzyme with poor properties into one that has useful properties. Lipase Lip3 from Drosophila melanogaster had been previously optimised for expression in Escherichia coli. The expression levels were good, but Lip3 was mainly insoluble with poor activity. Directed evolution was used to identify variants with enhanced activity along with improved solubility. Five variants and the wild-type (wt) enzyme were purified and characterised. The yield of the wt enzyme was just 2.2 mg/L of culture, while a variant, produced under the same conditions, gave 351 mg. The improvement of activity of the best variant was 200 times higher than that of the wt when the crude lysates were analysed using pNP-C8, but with purified protein, the improvement observed was 1.5 times higher. This means that most of the increase of activity is due to increase in solubility and stability. All the purified variants showed increased thermal stability compared with the wt enzyme that had a T1/2 of 37°C, while the mutant with P291L of 42.2°C and the mutant R7_47D with five mutations had a value of 52.9°C, corresponding to an improvement of 16°C. The improved variants had between five and nine changes compared with the wt enzyme. There were four changes that were found in all 30 final round variants for which sequences were obtained; three of these changes were found in the substrate-binding domain.

Mechanoenzymatic Breakdown of Chitinous Material to N-Acetylglucosamine: The Benefits of a Solventless Environment

Chitin is not only the most abundant nitrogen-containing biopolymer on the planet, but also a renewable feedstock that is often treated as a waste. Current chemical methods to break down chitin typically employ harsh conditions, large volumes of solvent, and generate a mixture of products. Although enzymatic methods have been reported, they require a harsh chemical pretreatment of the chitinous substrate and rely on dilute solution conditions that are remote from the natural environment of microbial chitinase enzymes, which typically consists of surfaces exposed to air and moisture. We report an innovative and efficient mechanoenzymatic method to hydrolyze chitin to the N-acetylglucosamine monomer by using chitinases under the recently developed reactive aging (RAging) methodology, based on repeating cycles of brief ball-milling followed by aging, in the absence of bulk solvent. Our results demonstrate that the activity of chitinases increases several times by switching from traditional solution-based conditions of enzymatic catalysis to solventless RAging, which operates on moist solid substrates. Importantly, RAging is also highly efficient for the production of N-acetylglucosamine directly from shrimp and crab shell biomass without any other processing except for a gentle wash with aqueous acetic acid.

Assessment of upstream bioprocessing

Depending on the purpose and use, bioprocesses are carried out in order to reduce, maintain or increase the molar O/C ratio of biomass as the initial substrate. Cascade use considers the holistic and efficient use of biomass. In the current debate of biomass use, however, one may admit that an efficient use of biomass can further be based on the maintenance of initially present molar O/C ratio and functionality. In this regard, what compound should be formed that possesses highest functionality and similar molar O/C ratio as the substrate? How much energy should be spent on bioprocesses for the conversion of biomass under aerobic or anaerobic conditions? This study discusses and contributes to the efficiency assessment of aerobic and anaerobic bioprocesses based on chemical functionality and molar O/C ratio and their scale-depended energy need for creating appropriate environmental conditions for biological agents.

Preparation and characterization of resistant starch type III from enzymatically hydrolyzed maize flour

Polysaccharides including resistant starch are categorized as dietary fiber and are used as an important prebiotic. Similar to soluble fibers, resistant starch also has a number of physiological effects that have been shown to be beneficial for health. Starch hydrolyzing enzymes, most importantly amylases, play essential roles in the production of resistant starch. This study aimed to develop α-amylase-treated maize flour with slow digestibility and unique physicochemical characteristics compared to native maize flour. In the current study, resistant starch type III from maize flour was prepared using α-amylase obtained from indigenously isolated Bacillus licheniformis. The α-amylase gene from B. licheniformis was amplified and cloned into the pET-24(a) vector, expressed in E. coli BL21 (DE3) cells and purified by metal ion affinity chromatography. The purified enzyme enhanced the yield of resistant starch 16-fold in maize flour. Scanning electron microscopy revealed that the granular structure of maize flour was disrupted into a dense network with irregular structure, and X-ray diffractograms confirmed the transformation from an amorphous to a crystalline structure upon α-amylase treatment. Thermogravimetric analysis revealed increased amylose content of α-amylase-treated maize flour. Moreover, α-amylase-treated maize flour resulted in a significant enhancement of the desired properties of maize flour, such as resistant starch content, amylose, milk absorption capacity, and iodine and fatty acid complexing ability, and a reduction in swelling power, water binding, oil absorption capacity, and in vitro digestibility compared to untreated maize flour. Resistant starch type III showed low digestibility and increased complexing ability with iodine and fatty acid and therefore could be a safe and beneficial alternative as a coating material for the delivery of active, sensitive ingredients to the colon.