Metagenomic alkaline protease from mangrove sediment

Enzymes for production of whey protein hydrolysates and other value-added products

Whey is a byproduct of dairy industries, the aqueous portion which separates from cheese during the coagulation of milk. It represents approximately 85-95% of milk's volume and retains much of its nutrients, including functional proteins and peptides, lipids, lactose, minerals, and vitamins. Due to its composition, mainly proteins and lactose, it can be considered a raw material for value-added products. Whey-derived products are often used to supplement food, as they have shown several physiological effects on the body. Whey protein hydrolysates are reported to have different activities, including antihypertensive, antioxidant, antithrombotic, opioid, antimicrobial, cytomodulatory, and immuno-modulatory. On the other hand, galactooligosaccharides obtained from lactose can be used as prebiotic for beneficial microorganisms for the human gastrointestinal tract. All these compounds can be obtained through physicochemical, microbial, or enzymatic treatments. Particularly, enzymatic processes have the advantage of being highly selective, more stable than chemical transformations, and less polluting, making that the global enzyme market grow at accelerated rates. The sources and different products associated with the most used enzymes are particularly highlighted in this review. Moreover, we discuss metagenomics as a tool to identify novel proteolytic enzymes, from both cultivable and uncultivable microorganisms, which are expected to have new interesting activities. Finally enzymes for the transformation of whey sugar are reviewed. In this sense, carbozymes with ß-galactosidase activity are capable of lactose hydrolysis, to obtain free monomers, and transgalactosylation for prebiotics production. KEY POINTS: • Whey can be used to obtain value-added products efficiently through enzymatic treatments • Proteases transform whey proteins into biopeptides with physiological activities • Lactose can be transformed into prebiotic compounds using ß-galactosidases.

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments

BACKGROUND

Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.

RESULTS

Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.

CONCLUSIONS

The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.

Screening of marine sediment-derived microorganisms and their bioactive metabolites: a review

Marine sediments are one of the largest habitats on Earth, and their unique ecology, such as high salinity, high pressure, and hypoxia, may activate certain silent genes in marine microbes, resulting in microbes, enzymes, active products, and specific metabolic pathways that can adapt to these specific ecological environments. Marine sediment-derived microorganisms and their bioactive metabolites are of great significance and have potential commercial development prospects for food, pharmaceutical, chemical industries, agriculture, environmental protection and human nutrition and health. In recent years, although there have been numerous scientific reports surrounding marine sediment-derived microorganisms and their bioactive metabolites, a comprehensive review of their research progress is lacking. This paper presents the development and renewal of traditional culture-dependent and omics analysis techniques and their application to the screening of marine sediment-derived microorganisms producing bioactive substances. It also highlights recent research advances in the last five years surrounding the types, functional properties and potential applications of bioactive metabolites produced by marine sediment-derived microorganisms. These bioactive metabolites mainly include antibiotics, enzymes, enzyme inhibitors, sugars, proteins, peptides, and some other small molecule metabolites. In addition, the review ends with concluding remarks on the challenges and future directions for marine sediment-derived microorganisms and their bioactive metabolites. The review report not only helps to deepen the understanding of marine sediment-derived microorganisms and their bioactive metabolites, but also provides some useful information for the exploitation and utilization of marine microbial resources and the mining of new compounds with potential functional properties.

Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds

The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.

Unconventional microbial proteases as promising tools for the production of bioactive protein hydrolysates

Enzymatic hydrolysis is the most prominent strategy to release bioactive peptides from different food proteins and protein-rich by-products. Unconventional microbial proteases (UMPs) have gaining increased attention for such purposes, particularly from the 2010s. In this review, we present and discuss aspects related to UMPs production, and their use to obtain bioactive protein hydrolysates. Antioxidant and anti-hypertensive potentials, commonly evaluated through in vitro testing, are mainly reported. The in vivo bioactivities of protein hydrolysates and peptides produced through UMPs action are highlighted. In addition to bioactivities, enzymatic hydrolysis acts by modulating the functional properties of proteins for potential food uses. The compiled literature indicates that UMPs are promising biocatalysts to generate bioactive protein hydrolysates, adding up to commercially available enzymes. From the recent interest on this topic, continuous and in-depth research is needed to advance toward the applicability and commercial utility of both UMPs and obtained hydrolysates.

Simultaneous hydrolysis of various protein-rich industrial wastes by a naturally evolved protease from tannery wastewater microbiota

Elimination of protein-rich waste materials is one of the vital environmental protection requirements. Using of non-naturally occurring chemicals for their remediation properties can potentially induce new pollutants. Therefore, enzymes encoded in the genomes of microorganisms evolved in the same environment can be considered suitable alternatives to chemicals. Identification of efficient proteases that can hydrolyze recalcitrant, protein-rich wastes produced by various industrial processes has been widely welcomed as an eco-friendly waste management strategy. In this direction, we attempted to screen a thermo-halo-alkali-stable metagenome-derived protease (PersiProtease1) from tannery wastewater. The PersiProtease1 exhibited high pH stability over a wide range and at 1 h in pH 11.0 maintained 87.59% activity. The enzyme possessed high thermal stability while retaining 76.64% activity after 1 h at 90 °C. Moreover, 65.34% of the initial activity of the enzyme remained in the presence of 6 M NaCl, showing tolerance against high salinity. The presence of various metal ions, inhibitors, and organic solvents did not remarkably inhibit the activity of the discovered protease. The PersiProtease1 was extracted from the tannery wastewater microbiota and efficiently applied for biodegradation of real sample tannery wastewater protein, chicken feathers, whey protein, dehairing sheepskins, and waste X-ray films. PersiProtease1 proved its enormous potential in simultaneous biodegradation of solid and liquid protein-rich industrial wastes based on the results.

Microbial proteases: ubiquitous enzymes with innumerable uses

Proteases are ubiquitous enzymes, having significant physiological roles in both synthesis and degradation. The use of microbial proteases in food fermentation is an age-old process, which is today being successfully employed in other industries with the advent of ‘omics’ era and innovations in genetic and protein engineering approaches. Proteases have found application in industries besides food, like leather, textiles, detergent, waste management, agriculture, animal husbandry, cosmetics, and pharmaceutics. With the rising demands and applications, researchers are exploring various approaches to discover, redesign, or artificially synthesize enzymes with better applicability in the industrial processes. These enzymes offer a sustainable and environmentally safer option, besides possessing economic and commercial value. Various bacterial and fungal proteases are already holding a commercially pivotal role in the industry. The current review summarizes the characteristics and types of proteases, microbial source, their current and prospective applications in various industries, and future challenges. Promoting these biocatalysts will prove significant in betterment of the modern world.

Two-step functional screen on multiple proteinaceous substrates reveals temperature-robust proteases with a broad-substrate range

Abstract

To support the bio-based industry in development of environment-friendly processes and products, an optimal toolbox of biocatalysts is key. Although functional screen of (meta)genomic libraries may potentially contribute to identifying new enzymes, the discovery of new enzymes meeting industry compliance demands is still challenging. This is particularly noticeable in the case of proteases, for which the reports of metagenome-derived proteases with industrial applicability are surprisingly limited. Indeed, proteolytic clones have been typically assessed by its sole activity on casein or skim milk and limited to mild screening conditions. Here, we demonstrate the use of six industry-relevant animal and plant by-products, namely bone, feather, blood meals, gelatin, gluten, and zein, as complementary substrates in functional screens and show the utility of temperature as a screening parameter to potentially discover new broad-substrate range and robust proteases for the biorefinery industry. By targeting 340,000 clones from two libraries of pooled isolates of mesophilic and thermophilic marine bacteria and two libraries of microbial communities inhabiting marine environments, we identified proteases in four of eleven selected clones that showed activity against all substrates herein tested after prolonged incubation at 55 °C. Following sequencing, in silico analysis and recombinant expression in Escherichia coli, one functional protease, 58% identical at sequence level to previously reported homologs, was found to readily hydrolyze highly insoluble zein at temperatures up to 50 °C and pH 9–11. It is derived from a bacterial group whose ability to degrade zein was unknown. This study reports a two-step screen resulting in identification of a new marine metagenome-derived protease with zein-hydrolytic properties at common biomass processing temperatures that could be useful for the modern biorefinery industry.

Key points

• A two-step multi-substrate strategy for discovery of robust proteases.

• Feasible approach for shortening enzyme optimization to industrial demands.

• A new temperature-tolerant protease efficiently hydrolyzes insoluble zein.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11235-9.

Cell-free Directed Evolution of a Protease in Microdroplets at Ultrahigh Throughput

Compartmentalization of single genes in water-in-oil emulsion droplets is a powerful approach to create millions of reactors for enzyme library selections. When these droplets are formed at ultrahigh throughput in microfluidic devices, their perfect monodispersity allows quantitative enzyme assays with a high precision readout. However, despite its potential for high quality cell-free screening experiments, previous demonstrations of enrichment have never been successfully followed up by actual enzyme library selections in monodisperse microfluidic droplets. Here we develop a three-step workflow separating three previously incompatible steps that thus far could not be carried out at once: first droplet-compartmentalized DNA is amplified by rolling circle amplification; only after completion of this step are reagents for in vitro protein expression and, finally, substrate added via picoinjection. The segmented workflow is robust enough to allow the first in vitro evolution in droplets, improving the protease Savinase that is toxic to E. coli for higher activity and identifying a 5-fold faster enzyme.

Immobilization of PR4A3 enzyme in pluronic F127 polymeric micelles against colorectal adenocarcinoma cells and increase of in vitro bioavailability

Traditional therapy for malignant neoplasms involving surgical procedures, radiotherapy and chemotherapy aims to kill neoplastic cells, but also affects normal cells. Therefore, exogenous proteases are the target of studies in cancer therapy, as they have been shown to be effective in suppressing tumors and reducing metastases. Pluronic F127 (F127) is a copolymer of amphiphilic blocks that has shown significant potential for drug administration, as it is capable of incorporating hydrophobic drugs and self-assembling in micrometers of nanometric size. This study investigated the effects of immobilization of the alkaline protease PR4A3 with pluronic F127 micelles on the enzyme-induced cytotoxicity. Protease immobilization was demonstrated through UV-visible and circular dichroism (CD) spectroscopies, as the enzyme interacts with the polymeric micelle of Pluronic F127 without changing its secondary structure. In addition, the immobilized form of the enzyme showed greater bioavailability after passing through the simulated gastrointestinal transit. Cell viability was assessed using the tetrazoic methylthiazole (MTT) assay. The results open perspectives for new research and development for PR4A3 in the treatment of colorectal carcinoma.

A novel thermostable serine protease from a metagenomic library derived from marine sediments in the East China Sea

Thermal activity and stability are important characteristics for proteases applied in the detergent, pharmaceutical, food, and other green industries. With the intent to discover thermostable novel proteases, we constructed a fosmid metagenomic library from marine sediments in the East China Sea and isolated a clone endowed with high proteolytic activity from this library. Sequence analysis of the positive subclones allowed the identification of a coding region of 1254 bp related to protease activity. The unrooted phylogenetic tree and alignment results revealed that the sequence might be derived from Anaerolineaceae bacterium and encodes a new member of the peptidase S8A subfamily with the typical catalytic triad Asp₁₁₉/His₁₅₀/Ser₃₂₅. The fusion protein, named pF1AL2, was expressed in Escherichia coli and showed a molecular weight of 35 kDa. pF1AL2 was active in the pH range of 5.0-11.0 with an optimal pH at 10.0 and had high stability under alkaline conditions, retaining more than 95% of its activity after 24 h at pH 11.0. The optimal temperature of pF1AL2 was 80 °C, and it retained nearly 80% of its activity after 6 h at 70 °C, showing great thermal activity and stability. In addition, the enzyme had great salt tolerance (the residual activity when kept in 3 M NaCl was 40%). Its thermal activity and stability, along with its halotolerance and pH-tolerance, indicate the high potential value of pF1AL2 in industrial applications. The exploitation of pF1AL2 could lay the foundation for the development and utilization of proteases with special features from marine resources by a metagenomic strategy. KEY POINTS: • A novel protease, pF1AL2, from marine sediments, was screened out by a metagenomic strategy. • The protease pF1AL2 analyzed in silico, cloned, and characterized. • pF1AL2 had an optimal temperature of 80 °C and retained nearly 80% of activity after 6 h at 70 °C. • pF1AL2 had great tolerance for high-temperature and acid, alkaline, and high salt environments.

Metagenomic applications in exploration and development of novel enzymes from nature: a review

BACKGROUND

Microbial community has an essential role in various fields, especially the industrial sector. Microbes produce metabolites in the form of enzymes, which are one of the essential compounds for industrial processes. Unfortunately, there are still numerous microbes that cannot be identified and cultivated because of the limitations of the culture-based method. The metagenomic approach is a solution for researchers to overcome these problems. Metagenomics is a strategy used to analyze the genomes of microbial communities in the environment directly. Metagenomics application used to explore novel enzymes is essential because it allows researchers to obtain data on microbial diversity, reaching of 99% and various types of genes encoding an enzyme that has not yet been identified. Basic methods in metagenomics have been developed and are commonly used in various studies. A basic understanding of metagenomics for researchers is needed, especially young researchers to support the success of the research.

SHORT CONCLUSION

Therefore, this review was done in order to provide a deep understanding of metagenomics. It also discussed the application and basic methods of metagenomics in the exploration of novel enzymes, especially in the latest research. Several types of enzymes, such as cellulases, proteases, and lipases, which have been explored using metagenomics, were reviewed in this article.

Development and application of a CRISPR/Cas9 system for Bacillus licheniformis genome editing

A highly efficient genome editing system for Bacillus licheniformis was developed based on single-plasmid CRISPR/Cas9. For highly efficient genome editing the shuttle vector pWH1520 was selected to construct the knockout plasmids. A construct harboring a pS promoter driving cas9 endonuclease expression, a strong pLY-2 promoter driving the transcription of a single guide RNA was demonstrated as being the most effective. To verify the feasibility of the method the uprT gene coding uracil phosphoribosyltransferase was selected as the reporter gene. The efficiency of introducing nucleotide point mutations and single gene deletion reached an editing efficiency of up to 99.2% and 97.3%, respectively. After a upp-deficient strain was engineered, the system and strain were applied to introduce genomic deletions of another two genes, amyL and chiA (encoding amylase and chitinase, respectively) with about 90% deletion efficiency. As two native extracellular proteins with relatively high secretion in the host, amylase and chitinase can hamper the secretion and expression of alkaline protease. It was demonstrated that the mutant with deletions of the two genes effectively improved the alkaline protease yield by 24.8%. The results illustrated that the establishment of a CRISPR/Cas9 system for Bacillus licheniformis is of significance, and confirmed the system's high efficiency. The system provides support for effective molecular modification and metabolic regulation of Bacillus licheniformis, and offers promise for applications in genetic modification of other industrially relevant Bacillus species.

Cloning, expression, and characterization of an alkaline protease, AprV, from Vibrio sp. DA1-1

A novel alkaline protease (named AprV) gene from Vibrio sp. DA1-1 was cloned and expressed in Escherichia coli BL21 (DE3) pLysS. The sequence analysis showed the highest homology of 68% with the characterized protease from Alkalimonas collagenimarina AC40^T. The recombinant AprV was purified with the molecular weight of 28 kDa. The optimum temperature and pH were determined to be 55 °C and 10.0, respectively. The enzyme activity was slightly enhanced by Ca²⁺, Mg²⁺, Zn²⁺, Ba²⁺, and, however, was highly inhibited by Sn²⁺ and EDTA. The AprV was stable in the presence of some surfactants and oxidizing agents, such as 1% Tween 20-80, 1% JFC-2, and 5% JFC-2. Casein was found to be the ideal substrate with specific activity of 1139 U/mg. Moreover, we found that AprV (10,000 U), together with commercial detergent, could completely remove the blood on the cotton. Furthermore, AprV also demonstrated dehairing activity on goat and bull skin. These results indicated that the alkaline protease AprV might be a potential candidate for applications in the detergent and leather industries.