Modular Engineering to Enhance Keratinase Production for Biotransformation of Discarded Feathers

Protein engineering, expression optimization, and application of alkaline protease from Alkalihalobacillus clausii FYX

Alkaline protease has been commercially used in the areas of detergents, food and agriculture, and improving the performance and production of alkaline protease serves as an important role in promoting its market expansion. Here, an alkaline protease AE0 from Alkalihalobacillus clausii FYX was firstly characterized in Bacillus licheniformis DW2△aprE, the optimal temperature and pH of AE0 were 60 °C and 10.5, the Km and Kcat values for casein were 17.25 mg/mL and 60.51 s-1, respectively, as well as the specific activity was 21,365.93 U/mg. Subsequently, six mutants (G113I, H118D, T141Y, S151A, N167S and Q185S) were obtained through semi-rational design, and G113I exhibited the most optimal performance with a specific activity of 28,150.64 U/mg. Furthermore, the double mutant AE0DM1 and triple mutant AE0MM2 were attained, and their specific activities reached 31,026.32 U/mg and 31,868.56 U/mg, respectively. Concurrently, through the evaluation of thermal stability and measurement of reaction kinetic parameters, G113I was advantageous for enhancing the thermal stability of AE0, while H118D and N167S were more beneficial for enhancing the catalytic efficiency. In addition, the enzyme activity of AE0MM2 produced by strain DW2△aprE/RC0-AE0MM2 was increased by 178.5 % through promoter engineering, reached 36,685.33 U/mL, which also showed the wonderful performance on enzymatic hydrolysis of soybean meal to enhance its utilization rate. Taken together, this work provided an alkaline protease with improved thermal stability and catalytic efficiency, as well as an efficient expression system of alkaline protease for industrial application.

Cell membrane engineering of Bacillus licheniformis for the enhancement of heterologous protein production

Heterologous expression is crucial to produce various recombinants proteins, yet consistently achieving high yields poses a significant challenge. The main objective of our research was to engineer the cell membrane components of Bacillus licheniformis for improving heterologous proteins production. This engineering strategy was achieved by overexpressing genes bkdR, plsY, plsC, and deleting pssA and clsA, which significantly increased the production of nattokinase, α-amylase and keratinase. Furthermore, a combined engineered strain was constructed by integrating all these approaches into a single strain (DW2-RYCAS) which led to an increase in the negative charge and permeability of the cell membrane by 41.11 % and 57.62 %, respectively, and reduced cell membrane integrity by 81.45 % compared to the control strain DW2. Ultimately, the production of nattokinase, α-amylase, and keratinase in DW2-RYCAS were 406.02 ± 8.17 FU/mL, 526.80 ± 14.77 U/mL, and 18.27 ± 0.70 KU/mL, respectively, which increased by 493.59 %, 273.40 %, and 213.91 % compared to the control strain DW2. These results represent the highest production of nattokinase, α-amylase, and keratinase in shake flasks reported to date. Our research illustrated the promising application of cell membrane engineering in B. licheniformis, creating an excellent platform for the biosynthesis of heterologous proteins.

Efficient production of spermidine from Bacillus amyloliquefaciens by enhancing synthesis pathway, blocking degradation pathway and increasing precursor supply

Spermidine has broad application potential in food, medicine and other fields. In this study, a novel Bacillus amyloliquefaciens cell factory was constructed for production of spermidine from renewablebiomass resources. Firstly, the speB gene was found to be optimal for synthesis of spermidine, and the function of SpeB was explained by amino acid sequence analysis and molecular docking. By replacing the native promoter of the speEB operon with the P43, the synthesis of spermidine was significantly enhanced in B. amyloliquefaciens HSPM1-P43speEB. After knockout of the genes yobN and bltD associated with spermidine degradation, the spermidine titer of the strain HSPM2 was further improved to 115.96 mg/L, increased by 108 % compared to HSPM1-P43speEB. Subsequently, the titer of spermidine was further increased to 277.47 mg/L through enhancing the supply of the precursor methionine by overexpression of speD. Finally, the renewable biomass resources, xylose and feather meal were optimized to produce spermidine, and the maximum titer is up to 588.10 mg/L after optimization. In conclusion, an efficient spermidine producing B. amyloliquefaciens was constructed through combinatorial metabolic engineering strategies, and the sustainable production of spermidine was achieved using the biomass resources of xylose and feather meal.

Harnessing the potential of microbial keratinases for bioconversion of keratin waste

The increasing global consumption of poultry meat has led to the generation of a vast quantity of feather keratin waste daily, posing significant environmental challenges due to improper disposal methods. A growing focus is on utilizing keratinous polymeric waste, amounting to millions of tons annually. Keratins are biochemically rigid, fibrous, recalcitrant, physiologically insoluble, and resistant to most common proteolytic enzymes. Microbial biodegradation of feather keratin provides a viable solution for augmenting feather waste's nutritional value while mitigating environmental contamination. This approach offers an alternative to traditional physical and chemical treatments. This review focuses on the recent findings and work trends in the field of keratin degradation by microorganisms (bacteria, actinomycetes, and fungi) via keratinolytic and proteolytic enzymes, as well as the limitations and challenges encountered due to the low thermal stability of keratinase, and degradation in the complex environmental conditions. Therefore, recent biotechnological interventions such as designing novel keratinase with high keratinolytic activity, thermostability, and binding affinity have been elaborated here. Enhancing protein structural rigidity through critical engineering approaches, such as rational design, has shown promise in improving the thermal stability of proteins. Concurrently, metagenomic annotation offers insights into the genetic foundations of keratin breakdown, primarily predicting metabolic potential and identifying probable keratinases. This may extend the understanding of microbial keratinolytic mechanisms in a complex community, recognizing the significance of synergistic interactions, which could be further utilized in optimizing industrial keratin degradation processes.

Plant Growth Promotion and Plant Disease Suppression Induced by Bacillus amyloliquefaciens Strain GD4a

Botrytis cinerea, the causative agent of gray mold disease (GMD), invades plants to obtain nutrients and disseminates through airborne conidia in nature. Bacillus amyloliquefaciens strain GD4a, a beneficial bacterium isolated from switchgrass, shows great potential in managing GMD in plants. However, the precise mechanism by which GD4a confers benefits to plants remains elusive. In this study, an A. thaliana-B. cinerea-B. amyloliquefaciens multiple-scale interaction model was used to explore how beneficial bacteria play essential roles in plant growth promotion, plant pathogen suppression, and plant immunity boosting. Arabidopsis Col-0 wild-type plants served as the testing ground to assess GD4a's efficacy. Additionally, bacterial enzyme activity and targeted metabolite tests were conducted to validate GD4a's potential for enhancing plant growth and suppressing plant pathogens and diseases. GD4a was subjected to co-incubation with various bacterial, fungal, and oomycete pathogens to evaluate its antagonistic effectiveness in vitro. In vivo pathogen inoculation assays were also carried out to investigate GD4a's role in regulating host plant immunity. Bacterial extracellular exudate (BEE) was extracted, purified, and subjected to untargeted metabolomics analysis. Benzocaine (BEN) from the untargeted metabolomics analysis was selected for further study of its function and related mechanisms in enhancing plant immunity through plant mutant analysis and qRT-PCR analysis. Finally, a comprehensive model was formulated to summarize the potential benefits of applying GD4a in agricultural systems. Our study demonstrates the efficacy of GD4a, isolated from switchgrass, in enhancing plant growth, suppressing plant pathogens and diseases, and bolstering host plant immunity. Importantly, GD4a produces a functional bacterial extracellular exudate (BEE) that significantly disrupts the pathogenicity of B. cinerea by inhibiting fungal conidium germination and hypha formation. Additionally, our study identifies benzocaine (BEN) as a novel small molecule that triggers basal defense, ISR, and SAR responses in Arabidopsis plants. Bacillus amyloliquefaciens strain GD4a can effectively promote plant growth, suppress plant disease, and boost plant immunity through functional BEE production and diverse gene expression.

Sustainable valorizing high-protein feather waste utilization through solid-state fermentation by keratinase-enhanced Streptomyces sp. SCUT-3 using a novel promoter

Feather waste, a rich source of proteins, has traditionally been processed through high-temperature puffing and acid-base hydrolysis, contributing to generation of greenhouse gases and H2S. To address this issue, we employed circular economy techniques to recover the nutritional value of feather waste. Streptomyces sp. SCUT-3, an efficient proteolytic and chitinolytic bacterium, was isolated for feather degradation previously. This study aimed to valorize feather waste for feed purposes by enhancing its feather transformation ability through promoter optimization. Seven promoters were identified through omics analysis and compared to a common Streptomyces promoter ermE*p. The strongest promoter, p24880, effectively enhanced the expression of three candidate keratinases (Sep39, Sep40, and Sep53). The expression efficiency of double-, triple-p24880 and sandwich p24880-sep39-p24880 promoters were further verified. The co-overexpression strain SCUT-3-p24880-sep39-p24880-sep40 exhibited a 16.21-fold increase in keratinase activity compared to the wild-type. Using this strain, a solid-state fermentation process was established that increased the feather/water ratio (w/w) to 1:1.5, shortened the fermentation time to 2.5 days, and increased soluble peptide and free amino acid yields to 0.41 g/g and 0.14 g/g, respectively. The resulting has high protein content (90.49 %), with high in vitro digestibility (94.20 %). This method has the potential to revolutionize the feather waste processing industry.

Structure prediction, docking studies and molecular cloning of novel Pichia kudriavzevii YK46 metalloprotease (MetPr) for improvement of feather waste biodegradation

This study addresses the environmental risks associated with the accumulation of keratin waste from poultry, which is resistant to conventional protein degradation methods. To tackle this issue, microbial keratinases have emerged as promising tools for transforming resilient keratin materials into valuable products. We focus on the Metalloprotease (MetPr) gene isolated from novel Pichia kudriavzevii YK46, sequenced, and deposited in the NCBI GenBank database with the accession number OQ511281. The MetPr gene encodes a protein consisting of 557 amino acids and demonstrates a keratinase activity of 164.04 U/ml. The 3D structure of the protein was validated using Ramachandran's plot, revealing that 93% and 97.26% of the 557 residues were situated within the most favoured region for the MetPr proteins of template Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Computational analyses were employed to determine the binding affinities between the deduced protein and beta keratin. Molecular docking studies elucidated the optimal binding affinities between the metalloprotease (MetPr) and beta-keratin, yielding values of - 260.75 kcal/mol and - 257.02 kcal/mol for the template strains Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Subsequent molecular cloning and expression of the MetPr gene in E. coli DH5α led to a significantly higher keratinase activity of 281 ± 12.34 U/ml. These findings provide valuable insights into the potential of the MetPr gene and its encoded protein for keratin waste biotransformation, with implications for addressing environmental concerns related to keratinous waste accumulation.

Response surface methodology based optimization of keratinase from Bacillus velezensis strain ZBE1 and nanoparticle synthesis, biological and molecular characterization

The increasing demands of keratinases for biodegradation of recalcitrant keratinaceous waste like chicken feathers has lead to research on newer potential bacterial keratinases to produce high-value products with biological activities. The present study reports a novel keratinolytic bacterium Bacillus velezensis strain ZBE1 isolated from deep forest soil of Western Ghats of Karnataka, which possessed efficient feather keratin degradation capability and induced keratinase production. Production kinetics depicts maximum keratinase production (11.65 U/mL) on 4th day with protein concentration of 0.61 mg/mL. Effect of various physico-chemical factors such as, inoculum size, metal ions, carbon and nitrogen sources, pH and temperature influencing keratinase production were optimized and 3.74 folds enhancement was evidenced through response surface methodology. Silver (AgNP) and zinc oxide (ZnONP) nanoparticles with keratin hydrolysate produced from chicken feathers by the action of keratinase were synthesized and verified with UV-Visible spectroscopy that revealed biological activities like, antibacterial action against Bacillus cereus and Escherichia coli. AgNP and ZnONP also showed potential antioxidant activities through radical scavenging activities by ABTS and DPPH. AgNP and ZnONP revealed cytotoxic effect against MCF-7 breast cancer cell lines with IC50 of 5.47 µg/ml and 62.26 µg/ml respectively. Characterizations of nanoparticles were carried out by Fourier transform infrared spectroscopy, scanning electron microscopy with energy dispersive X-ray, X-ray diffraction, thermogravimetric analysis and atomic force microscopy analysis to elucidate the thermostability, structure and surface attributes. The study suggests the prospective applications of keratinase to trigger the production of bioactive value-added products and significant application in nanotechnology in biomedicine.