Extracellular peptidases from Deinococcus radiodurans

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

Homoscleromorpha-derived Bacillus spp. as potential sources of biotechnologically-relevant hydrolases and biosurfactants

Despite hydrolytic exoenzymes and biosurfactants having been gradually reported from the poriferan microbiome, little is known about these bioproducts in microorganisms inhabiting Homoscleromorpha sponges. Here, we investigated the production of hydrolases and biosurfactants in bacteria isolated from three shallow-water homoscleromorph species, Oscarella sp., Plakina cyanorosea, and Plakina cabofriense. A total of 99 of 107 sponge-associated bacterial isolates exhibited activity for at least one of the analyzed hydrolases. Following fermentation in Luria-Bertani (LB) and Tryptic Soy Broth (TSB), two isolates, 80BH11 and 80B1:1010b, showed higher lipase and peptidase activities. Both of them belonged to the Bacillus genus and were isolated from Oscarella. Central composite design leveraged up the peptidase activity in 280% by Bacillus sp. 80BH11 in the TSB medium for 48 h at 30 °C. The optimized model also revealed that pH 6.5 and 45 °C were the best conditions for peptidase reaction. In addition, Bacillus sp. 80BH11 was able to release highly emulsifying and remarkably stable surfactants in the LB medium. Surfactin was finally elucidated as the biosurfactant generated by this sponge-derived Bacillus. In conclusion, we hope to have set the scenery for further prospecting of industrial enzymes and biosurfactants in Homoscleromorpha microbiomes.

Isolation of Bacillus sp. A5.3 Strain with Keratinolytic Activity

Simple Summary

In this study, we described keratinolytic properties of a strain of Bacillus (sp. A5.3) isolated from sites of feather waste accumulation. The proteolytic enzymes secreted by Bacillus sp. A5.3 are serine proteases, are alkaline enzymes, have a wide substrate specificity, and have high thermal stability. Bacillus sp. A5.3 effectively hydrolyzes feathers and can be used in feather-processing technologies and as a source of alkaline and thermostable proteases and keratinases.

Abstract

Environmental safety and economic factors necessitate a search for new ways of processing poultry farm feathers, which are 90% β-keratin and can be used as a cheap source of amino acids and peptones. In this study, feather-decomposing bacteria were isolated from a site of accumulation of rotten feathers and identified as Bacillus. Among them, the Bacillus sp. A5.3 isolate showed the best keratinolytic properties. Scanning electron microscopy indicated that Bacillus sp. A5.3 cells closely adhere to the feather surface while degrading the feather. It was found that Bacillus sp. A5.3 secretes thermostable alkaline proteolytic and keratinolytic enzymes. Zymographic analysis of the enzymatic extract toward bovine serum albumin, casein, gelatin, and β-keratin revealed the presence of proteases and keratinases with molecular weights 20–250 kDa. The proteolytic and keratinolytic enzymes predominantly belong to the serine protease family. Proteome analysis of the secreted proteins by nano-HPLC coupled with Q-TOF mass spectrometry identified 154 proteins, 13 of which are proteases and peptidases. Thus, strain Bacillus sp. A5.3 holds great promise for use in feather-processing technologies and as a source of proteases and keratinases.

Molecular Identification of Keratinase DgokerA from Deinococcus gobiensis for Feather Degradation

Keratin is a tough fibrous structural protein that is difficult to digest with pepsin and trypsin because of the presence of a large number of disulfide bonds. Keratin is widely found in agricultural waste. In recent years, especially, the development of the poultry industry has resulted in a large accumulation of feather keratin resources, which seriously pollute the environment. Keratinase can specifically attack disulfide bridges in keratin, converting them from complex to simplified forms. The keratinase thermal stability has drawn attention to various biotechnological industries. It is significant to identify keratinases and improve their thermostability from microorganism in extreme environments. In this study, the keratinases DgoKerA was identified in Deinococcus gobiensis I-0 from the Gobi desert. The amino acid sequence analysis revealed that DgoKerA was 58.68% identical to the keratinase MtaKerA from M. thermophila WR-220 and 40.94% identical to the classical BliKerA sequence from B. licheniformis PWD-1. In vitro enzyme activity analysis showed that DgoKerA exhibited an optimum temperature of 60 °C, an optimum pH of 7 and a specific enzyme activity of 51147 U/mg. DgoKerA can degrade intact feathers at 60 °C and has good potential for industrial applications. The molecular modification of DgoKerA was also carried out using site-directed mutagenesis, in which the mutant A350S enzyme activity was increased by nearly 30%, and the results provide a theoretical basis for the development and optimization of keratinase applications.

Genomic and in silico protein structural analyses provide insights into marine polysaccharide-degrading enzymes in the sponge-derived Pseudoalteromonas sp. PA2MD11

Active heterotrophic metabolism is a critical metabolic role performed by sponge-associated microorganisms, but little is known about their capacity to metabolize marine polysaccharides (MPs). Here, we investigated the genome of the sponge-derived Pseudoalteromonas sp. strain PA2MD11 focusing on its macroalgal carbohydrate-degrading potential. Carbohydrate-active enzymes (CAZymes) for the depolymerization of agar and alginate were found in PA2MD11's genome, including glycoside hydrolases (GHs) and polysaccharide lyases (PLs) belonging to families GH16, GH50 and GH117, and PL6 and PL17, respectively. A gene potentially encoding a sulfatase was also identified, which may play a role in the strain's ability to consume carrageenans. The complete metabolism of agar and alginate by PA2MD11 could also be predicted and was consistent with the results obtained in physiological assays. The polysaccharide utilization locus (PUL) potentially involved in the metabolism of agarose contained mobile genetic elements from other marine Gammaproteobacteria and its unusual larger size might be due to gene duplication events. Homology modelling and structural protein analyses of the agarases, alginate lyases and sulfatase depicted clear conservation of catalytic machinery and protein folding together with suitable industrially-relevant features. Pseudoalteromonas sp. PA2MD11 is therefore a source of potential MP-degrading biocatalysts for biorefinery applications and in the preparation of pharmacologically-active oligosaccharides.

Biodegradation of Keratin-Rich Husbandry Waste as a Path to Sustainable Agriculture

Every year, the size of the human population grows; with it, the need for agricultural products increases. This leads to an increment in the volume of waste, including hard-to-degrade keratin-rich ones, such as feathers. Currently, most of the agro-industrial complex protein by-products are utilized by incineration, landfilling, and chemical hydrolysis. Such methods do not meet modern trends in the development of a sustainable economy, negatively affecting the environment and humans, and preventing the reusing of waste. An alternative is biodegradation, which consists of the application of living organisms and their enzymes to recycle by-products. This approach is not only sustainable, but also makes it possible to obtain products of waste hydrolysis that are in demand for the manufacture of fertilizers and feed additives. This brings the development of agriculture closer to a circular economy and makes the recycling process more profitable. This review article emphasizes the significance of keratinolytic microorganisms and keratinases for the improvement of green methods for processing hard-to-degrade protein waste of the agro-industrial complex, which is necessary for sustainable economic development.

A Novel Thermostable Keratinase from Deinococcus geothermalis with Potential Application in Feather Degradation

Keratinase can specifically attack disulfide bridges in keratin to convert them from complex to simplified forms. Keratinase thermal stability has drawn attention to various biotechnological industries. In this study, a keratinase DgeKer was identified from a slightly thermophilic species, D. geothermalis. The in silico analysis showed that DgeKer is composed of signal peptide, N-terminal propeptide, mature domain, and C-terminal extension. DgeKer and its C-terminal extension-truncated enzyme (DgeKer-C) were cloned and expressed in E. coli. The purified DgeKer and DgeKer-C showed maximum activity at 70 °C and pH 9–The thermal stability assay (60 °C) showed that the half-life value of DgeKer and DgeKer-C were 103.45 min and 169.10 min, respectively. DgeKer and DgeKer-C were stable at the range of pH from 9 to 11 and showed good tolerance to some metal ions, surfactants and organic solvent. Furthermore, DgeKer could degrade feathers at 70 °C for 60 min. However, the medium became turbid with obvious softening of barbules after being treated with DgeKer-C, which might be due to C-terminal extension. In summary, a thermostable keratinase DgeKer with high efficiency degradation of feathers may have great potential in industry.

Characterization of EstDR4, a Novel Cold-Adapted Insecticides-Metabolizing Esterase from Deinococcus radiodurans

Cold-adapted esterases are attracting increasing attention owing to their prospective use in biotechnology. In this study, a novel cold-adapted family Ⅳ esterase EstDR4 was identified and obtained from extremophile Deinococcus radiodurans (D. radiodurans). EstDR4 displayed significant substrate preference towards short and medium chain monoesters (C2–C12). It also showed regioselectivity, enantioselectivity and degradation effects on four insecticides. The optimum temperature and pH for EstDR4 activity were 30 °C and pH 8, respectively. Additionally, EstDR4 exhibited relatively high catalytic activity at 0 °C and high stability from 10–40 °C, with over 80% of its initial activity retained after 1 h of incubation. Moreover, EstDR4 activity was stimulated by Tween 80 and Triton X-100, and inhibited by metal ions such as Co2+, Cu2+ and Zn2+ and several organic solvents. Thus, this enzyme shows development potential for many industrial biotechnological applications, including the manufacture of thermolabile pharmaceutical products, cold-wash detergents and insecticide biodegradation.

Purification from Deinococcus radiodurans of a 66 kDa ABC transporter acting on peptides containing at least 3 amino acids

Deinococcus radiodurans is a Gram positive bacterium the capability of which to withstand high doses of ionizing radiations is well known. Physiologically speaking, D. radiodurans is a proteolytic prokaryote able to express and secrete quite a number of proteases, and to use amino acids as an energy source. When considering this, it is surprising that little information is available on the biochemical components responsible for the uptake of peptides in D. radiodurans. Here we report on the purification and characterization of an ABC peptide transporter, isolated from D. radiodurans cells grown in tryptone-glucose-yeast extract (TGY) medium. In particular, we show here that the action of this transporter (denoted DR1571, SwissProt data bank accession number Q9RU24 UF71_DEIRA) is exerted on peptides containing at least 3 amino acids. Further, using tetra-peptides as model systems, we were able to observe that the DR1571 protein does not bind to peptides containing phenylalanine or valine, but associates with high efficiency to tetra-glycine, and with moderate affinity to tetra-peptides containing arginine or aspartate.

A microplate assay for extracellular hydrolase detection

This article presents a new qualitative method to detect enzyme activity replacing the conventional Agar-Petri dishes. This new method is a simple rapid and low-cost technique that uses 24-well microplates. The detection of hydrolases producing microorganisms in bioprospecting studies by qualitative methods is time consuming, costly and requires a large quantity of strains or enzymatic extracts. Tests with different substrate concentrations (0 to 20 g/L) in agar solution for the enzymatic hydrolysis analysis were performed to determine the best substrate concentrations in 24-well microplates. Other quantitative and analytical methods, such as enzymatic assays and thin layer chromatography, were performed to validate this new method and to compare the relationship between enzymatic activity and substrate degradation. Statistically relevant results were observed for amylase, endoglucanase and polygalacturonase enzymes, even when there was a low substrate concentration in agar, where the halo diameter was high. The results also indicated that the concentrations for efficient enzyme index measurements were 4 g/L carboxymethylcellulose for endoglucanase detection and 8 g/L for amylase and polygalacturonase assays. The results were presented according to the traditional methods for detection of enzymatic activity. This new method can be used as a general test for the detection of important industrial hydrolases. It is a faster and less costly alternative for screening microbial enzyme producing microorganisms and is useful for studying the production of microbial enzymes under different growing conditions.