Enzymatic Process Research Articles

The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies

AbstractNeurodegenerative disorders encompass a group of age‐related conditions characterized by the gradual decline in both the structure and functionality of the central nervous system (CNS). RNA modifications, arising from the epitranscriptome or RNA‐modifying protein mutations, have recently been observed to contribute significantly to neurodegenerative disorders. Specific modifications like N6‐methyladenine (m6A), N1‐methyladenine (m1A), 5‐methylcytosine (m5C), pseudouridine and adenosine‐to‐inosine (A‐to‐I) play key roles, with their regulators serving as crucial therapeutic targets. These epitranscriptomic changes intricately control gene expression, influencing cellular functions and contributing to disease pathology. Dysregulation of RNA metabolism, affecting mRNA processing and noncoding RNA biogenesis, is a central factor in these diseases. This review underscores the complex relationship between RNA modifications and neurodegenerative disorders, emphasizing the influence of RNA modification and the epitranscriptome, exploring the function of RNA modification enzymes in neurodegenerative processes, investigating the functional consequences of RNA modifications within neurodegenerative pathways, and evaluating the potential therapeutic advancements derived from assessing the epitranscriptome.

Exploring cheese production enzymes from various plants as an alternative to Calf rennet

Milk coagulation, traditionally relied on Calf rennet, is a crucial enzymatic process in cheese production. Ethical and practical constraints in using Calf rennet have led to the exploration of alternative sources. This study aimed to identify plant-based substitutes for calf rennet by investigating the coagulating potential of extracts from three plants: Calotropis procera, lemon, and Solanum incanum. Each plant tested with three extract levels (15, 20, and 25 ml), and replicated three times. Juices were extracted from lemon and Solanum incanum fruits through incision and squeezing. Meanwhile, Calotropis procera aqueous filtrates were separated from its polymeric gum using centrifugation. Then after, all extracts were further purified through muslin cloth and Whatman filter paper. Extracts were added to a beaker containing 500 ml of milk heated at 50 °C, and allowed to coagulate, resulting in the separation of cheese, curds and whey. Then after whey production, fresh and dry weights of cheese, and cheese yield percentage were measured and recorded. Statistical analysis using SAS Studio showed that there is highly significant differences with P < 0.0001 among plant extracts in their effects on the cheese-making potential. For all extract levels, the highest cheese-dry weight and percentage of cheese yield were observed in Calotropis procera and the lowest cheese formation starting times observed from lemon juice. These findings offer insights into optimizing cheese-making processes using natural sources and suggest that Calotropis procera, along with lemon juice and Solanum incanum, could serve as alternative sources of rennet.

Microbial Cellulase Production: Current Technologies and Future Prospects

Enzymes are biocatalysts, that facilitate chemical reactions by lowering their activation energy. Among these, cellulase emerges as a significant enzyme, consisting of a triad of components that work in synergy to degrade cellulosic biomass. Its significance is mostly pronounced in agricultural contexts, where there is an abundance of lignocellulosic biomass making it pivotal for utilization and conversion of biomass. Utilizing the biomass as a substrate for cellulase production offers dual advantages. Firstly, it simplifies the enzymatic synthesis process by the utilization of naturally occurring precursors. Secondly, it contributes to cost reduction by leveraging readily available resources thereby making it economically viable. Microbial cellulases, sourced from diverse microbes found globally, can aid in efficient enzymatic production. Advances in fermentation processes, coupled with the application of biotechnological tools, have significant impacts in production scalability and cost-effectiveness. Optimizing production strategies is crucial to meet the increasing demands of industrial applications while ensuring sustainability. Emphasizing the utilization of biomass substrates and harnessing the potential of emerging biotechnological advancements are key aspects of enzyme production. This review shall aim to provide an in-depth exploration of current cellulase production technologies and future prospects. By elucidating the underlying principles of cellulase catalysis and the intricacies of production methodologies.

Ethyl biodiesel production from crude soybean oil using enzymatic degumming-transesterification associated process

Brazil is one of the largest soybean producers in the world. Biodiesel production in Brazil (specially soybean oil biodiesel) has been growing every year and demanding more effective and sustainable technologies, which is the case of enzymatic processes. Enzymatic degumming could be an alternative to provide better quality products, before biodiesel production but also, in a one reaction step as a proposal to reduce time and costs. Therefore, this work was aimed at evaluating enzymatic degumming (previously optimized) of crude soybean oil using a phospholipase cocktail associated with transesterification using lipase from Aspergillus oryzae for ethyl biodiesel production. For this, transesterification was optimized for ethanol:oil (E:O) ratio, water and lipase % through a central composite rotatable design (CCRD). Optimal conditions were used to evaluate two degumming-transesterification associated processes: i) a one-pot reaction (OPR) where degumming and transesterification were performed at the same reactor; and ii) a two-pot reaction (TPR) where oil was first degummed, followed by transesterification. The optimal transesterification condition were achieved for E:O = 4.48:1, water = 3.41 % and lipase = 2.43 %, where 97 % fatty acid ethyl esters (FAEE) were obtained. Both OPR and TPR provided biodiesels with FAEE > 94 %: TPR was the best with 97.5 % and 99.98 % before and after biodiesel purification. Mineral elements (including phosphorus) and other impurities (anions) were low, and within quality standards. Glycerol produced also presented very low content of impurities which is quite advantageous. Although lipase achieves good conversion to FAEE (95.7 ± 0.29 %) using crude oil (Control), the final biodiesel carries many impurities (P=80.07 ± 0.1 mg/kg), thus requiring subsequent biodiesel purification steps. In addition, the high impurity content generates a biodiesel that does not comply with ANP legislative standards, P<10 mg/kg. The use of enzymatic degumming in the biodiesel production process generates a biodiesel with low impurities and higher final quality, in addition to being a process that generates less effluent. Enzymatic degumming was essential for obtaining high quality biodiesel and its association with transesterification showed to be a great option for decreasing time and costs for biodiesel production.

Structural insights into human ELAC2 as a tRNA 3' processing enzyme.

Human elaC ribonuclease Z 2 (ELAC2) removes the 3' trailer of precursor transfer ribonucleic acid (pre-tRNA). Mutations in ELAC2 are highly associated with the development of prostate cancer and hypertrophic cardiomyopathy. However, the catalytic mechanism of ELAC2 remains unclear. We determined the cryogenic electron microscopy structures of human ELAC2 in various states, including the apo, pre-tRNA-bound and tRNA-bound states, which enabled us to identify the structural basis for its binding to pre-tRNA and cleavage of the 3' trailer. Notably, conformational rearrangement of the C-terminal helix was related to feeding of the 3' trailer into the cleavage site, possibly explaining why its mutations are associated with disease. We further used biochemical assays to analyse the structural effects of disease-related mutations of human ELAC2. Collectively, our data provide a comprehensive structural basis for how ELAC2 recruits pre-tRNA via its flexible arm domain and guides the 3' trailer of pre-tRNA into the active centre for cleavage by its C-terminal helix.

Classification of Cell Therapy Products by Cell Manipulation Degree and Functions Performed: Analysis of International Regulatory Approaches

INTRODUCTION. The degree of processing (manipulation) of cells included in a cell product and the functions performed after administration (homologous/non-homologous use) determine the classification of the cell product as a transplant or an advanced therapy medicinal product (ATMP) and, hence, the regulatory aspects of the product’s life cycle. Currently, the legislation of the Eurasian Economic Union (EAEU) and the Russian Federation does not sufficiently explain the terms ‘minimal manipulation’ and ‘homologous/non-homologous use’, which may lead to the use of cell products with unproven safety and efficacy in humans.AIM. This study aimed to compare Russian and international approaches to the interpretation of the terms ‘minimal manipulation’ and ‘homologous/non-homologous use’ for classifying cell products and determining their regulatory pathways, with stromal vascular fraction (SVF) products used as an example.DISCUSSION. This article reviews and summarises the regulatory approaches of the Russian Federation, the EAEU, the United States (US), and the European Union (EU) that are based on the classification of cell products according to the degree of cell manipulation and the functions performed after administration. The authors have analysed and compared the regulatory acts and approaches of the countries under consideration, with SVF products as a case study. The article highlights general aspects of interpreting the terms ‘minimal manipulation’ and ‘homologous/ non-homologous use’ and demonstrates the difference in regulatory approaches across several countries, which lies in the classification of enzymatic processing and selective collection of cells as substantial or minimal manipulation.CONCLUSIONS. The mechanism for regulating cell products depends on the degree of cell manipulation (substantial or minimal) and the intended use (homologous or non-homologous). A common principle adopted by regulatory agencies in the US, EU, EAEU, and Russia is to classify manipulation as minimal if the manipulated cells preserve their biological characteristics and physiological function. A defining characteristic of the homologous use of cells or tissues is their administration to perform their inherent functions in the body. In Russia, the regulatory acts for ATMPs and for transplants list the procedures classified as minimal manipulation. According to international standards, preparations based on minimally manipulated SVF cells are classified as ATMPs when used non-homologously. The lack of comprehensive and clear explanations of the terms ‘minimal manipulation’ and ‘homologous/non-homologous use’ in the legislation of the EAEU and the Russian Federation necessitates the development of relevant guidelines providing specific examples.

Advances in the biosynthesis of D-allulose.

D-allulose is a rare monosaccharide and a C-3 epimer of D-fructose. It has physiological functions, such as antihyperglycemic, obesity-preventing, neuroprotective, and reactive oxygen species (ROS) scavenging effects, making it an ideal sugar substitute. The synthesis methods for D-allulose include chemical synthesis and biosynthesis. Chemical synthesis requires strict reaction conditions and tends to produce byproducts. Biosynthesis is mainly an enzymatic process. Enzymatic catalysis for the conversion of starch or glycerol to D-allulose is performed mainly by enzymes such as isoamylase (IA), glucose isomerase (GI), D-allulose 3-epimerase (DPE), D-allulose-6-phosphate 3-epimerase (A6PE), D-allulose 6-phosphate phosphatase (A6PP), ribitol 2-dehydrogenase (RDH), glycerophosphate kinase (GK), glycerophosphate oxidase (GPO), and dihydroxyacetone phosphate (DHAP)-dependent aldolase. Biosynthesis is a more energy-efficient process, producing fewer harmful by-products and pollutants, and significantly reducing negative environmental impacts. Furthermore, the specific catalytic activity of enzymes facilitates the production of compounds of higher purity, thereby facilitating the isolation and purification of the products. It has thus become the main method for producing D-allulose. This article reviews the progress in research on the biosynthetic production of D-allulose, focusing on the enzymes involved and their enzymatic properties, and discusses the production prospects for D-allulose.

Simple enzymatic depolymerization process based on rapid ball milling pretreatment for high-crystalline polyethylene terephthalate fibers

The high crystallinity (30 %–50 %) of discarded polyester textile waste limits the industrialization of its clean enzymatic depolymerization. In this study, a simple process based on ball milling pretreatment was developed to achieve effective enzymatic hydrolysis of high-crystalline polyester fiber. Ball milling was selected for its short, mild, and chemical-free process, which achieved a remarkable 23.8-fold (60.9 %) increase in terephthalic acid (TPA) yield from waste polyethylene terephthalate (PET) degradation, along with high TPA purity in the released soluble compounds. Just 30 min of ball milling at room temperature induced polyester amorphization, resulting in polyester with 12 % lower crystallinity compared with untreated polyester (51 %), while simultaneously increasing the surface roughness of polyester, thereby enhancing the efficiency of enzymatic hydrolysis. The simple process for effective enzymatic-depolymerization of waste polyester fiber developed in this study has potential industrial applications

Critical analysis of enhanced microbial bioremediation strategies of PAHs contaminated sites: Toxicity and techno-economic analysis

Polycyclic aromatic hydrocarbons (PAHs) pose significant threats to environmental integrity and public health due to their high toxicity, persistence, and potential for bioaccumulation. In contaminated soils, PAH concentrations typically range from 1 to 100 mg/kg, with severely polluted areas reaching up to 1000 mg/kg. Conventional bioremediation techniques, limited to 30–50% efficiency, underscore the need for more effective solutions. This review highlights recent advancements in microbial bioremediation strategies, demonstrating removal efficiencies of 80–90% through the utilization of functional microorganisms, which metabolize PAHs into non-toxic compounds. Innovative techniques such as genetic engineering, microbial immobilization, and nanotechnology are shown to achieve over 90% pollutant removal. The review discusses key metabolic pathways and enzymatic processes driving PAH degradation, such as ring-hydroxylation and oxygenation. Techno-economic assessments indicate up to 40% cost savings and improved energy efficiency compared to conventional methods, facilitating scalability for large-scale environmental restoration projects. Microbial solutions for groundwater pollution, where PAH levels often exceed the maximum contaminant level (MCL) of 0.2 μg/L, are found to be highly effective in mitigating ecological risks and protecting public health. This comprehensive analysis highlights the promising role of advanced microbial bioremediation techniques in addressing PAH contamination across diverse ecosystems, including soils, sediments, and aquatic environments.

Xylose Acetals - a New Class of Sustainable Solvents and Their Application in Enzymatic Polycondensation.

The use of organic solvents in academic research and industry applications is facing increasing regulatory pressure due to environmental and health concerns. Consequently, there is a growing demand for sustainable solvents, particularly in the enzymatic synthesis and processing of polyesters. Biocatalysts offer a sustainable method for producing these materials; however, achieving high molecular weights often necessitates use of solvents. In this work, we introduce a new class of alternative aprotic solvents with medium polarity produced directly from agricultural waste biomass in up to 83 mol% yield (on xylan basis). The new solvents have a largely unmodified xylose core and acetal functionality, yet they show no peroxide formation and provide reduced flammability risk. We also demonstrate their successful application in enzymatic polycondensation reactions with Candida antarctica lipase B (CaLB). In particular, the solvent dibutylxylose (DBX) outperformed the hazardous solvent diphenyl ether and facilitated polycondensation of the lignin-derived diester pyridine-2,4-dicarboxylate, yielding polyesters with a Mn of >15 kDa. Computational modelling studies provided further insight into the molecular structure and dynamics of CaLB in the presence of new solvents. Lastly, up to 98 wt% of the new xylose acetals were successfully recovered and recycled, further contributing to the sustainability of the overall process.

Multi-frequency power ultrasound (MFPU) pretreatment of crayfish (Procambarus clarkii): Effect on the enzymatic hydrolysis process and subsequent Maillard reaction

Crayfish, as a new consumer trend, has become one of the most popular freshwater aquatic foods in China, and its processed product output has been increasing year by year. In this study, the effect of multi-frequency power ultrasound (MFPU) pretreatment in various working modes including mono-, dual- and tri-frequency on the enzymatic hydrolysis and Maillard reaction of crayfish was investigated. Additionally, the underlying mechanism was also explored. Results showed that the degree of hydrolysis (DH) of crayfish was 23.89 %, while it increased to 40.78 % after MFPU pretreatment at 20/40 kHz dual-frequency, indicating that MFPU pretreatment significantly (p < 0.05) enhanced the enzymatic hydrolysis of crayfish. The crayfish protein after MFPU pretreatment exhibited a decrease in α-helix and increase in β-fold content, and the occurrence in the unfolding of the protein structure and alteration of tertiary structure. According to scanning electron microscopy (SEM) and atomic force microscopy (AFM) analyses, the MFPU pretreatment resulted in the fragmentation of crayfish protein. During the analyses of subsequent Maillard reaction, the composition and quantity of volatiles detected by the electronic nose and GC–MS indicated that MFPU pretreatment enhanced flavor of the Maillard reaction products. In conclusion, MFPU pretreatment is a promising technology for improving the degree of hydrolysis of crayfish protein and enhancing the flavor of Maillard reaction products.

Maximizing microbial activity and synergistic interaction to boost biofuel production from lignocellulosic biomass.

Addressing global environmental challenges and meeting the escalating energy demands stand as two pivotal issues in the current landscape. Lignocellulosic biomass emerges as a promising renewable bio-energy source capable of fulfilling the world's energy requirements on a large scale. One of the most important steps in lowering reliance on fossil fuel and lessening environmental effect is turning lignocellulosic biomass into biofuel. As carbon-neutral substitutes for traditional fuel, biofuel offer a solution to environmental concerns compared to conventional fuel. Effective utilization of lignocellulosic biomass is imperative for sustainable development. Ongoing research focuses on exploring the potential of various microorganisms and their co-interactions to synthesize diverse biofuels from different starting materials, including lignocellulosic biomass. Co-culture techniques demonstrate resilience to nutrient scarcity and environmental fluctuations. By utilising a variety of carbon sources, microbes can enhance their adaptability to environmental stressors and potentially increase productivity through their symbiotic interactions. Furthermore, compared to single organism involvement, co-interactions allow faster execution of multistep processes. Lignocellulosic biomass serves as a primary substrate for pre-treatment, fermentation, and enzymatic hydrolysis processes. This review primarily delves into the pretreatment, enzymatic hydrolysis process and the biochemical pathways involved in converting lignocellulosic biomass into bioenergy.

Decomposition and Changes in InVivo Post-HA Filler Injection: A Review.

Hyaluronic acid (HA) fillers are widely used in aesthetic medicine, but their invivo behavior and long-term effects are not fully understood. To review the decomposition and changes occurring in the body following HA filler injections, focusing on crosslinking agents, degradation processes, and tissue responses. This review analyzed oxidative and enzymatic degradation processes of HA fillers, evaluated the impact of 1,4-Butanediol Diglycidyl Ether (BDDE) crosslinking, and examined histological changes post-injection. Uncrosslinked HA degrades rapidly due to endogenous hyaluronidase, while crosslinked HA undergoes slower degradation via free radicals and hyaluronidase. Complete cross-linking (C-MoD) showed better durability compared to partially cross-linked BDDE (P-MoD). The concept of modification efficiency (MoE) was proposed to optimize filler safety and viscoelastic properties. Histological analysis revealed collagen capsule formation and autologous tissue replacement, affecting long-term outcomes. The degree of chemical modification (MoD) influences filler durability and safety, with concerns raised about potential delayed immune reactions from accumulated pendent BDDE. Clinicians should consider injection site, tissue conditions, and filler properties for safe and effective HA filler use. Emphasizing thorough BDDE removal and optimal crosslinking can enhance treatment safety and efficacy. The balance between achieving desired viscoelastic properties and minimizing potential risks is crucial. Future studies should include diverse ethnic groups to validate findings and further explore long-term tissue responses to HA fillers.

Development of an efficient biocatalytic three-component reaction for synthesizing pyrrole derivatives

Multi-component reactions (MCRs) enable the development of efficient and atom-economic methods for synthesizing pyrrole derivatives. However, the current MCRs methods for synthesizing pyrrole derivatives in the enzymatic process have been unexploited. Herein, we developed a one-pot three-component enzymatic promiscuous catalytic system with green, efficient, and atom-economic to construct pyrrole derivatives. In this system, amines and 1,3-dicarbonyl compounds formed enamines with subsequent Michael addition with nitroolefins catalyzed by trypsin. A series of pyrrole derivatives were successfully obtained with moderate to good yield (up to 92 %). In addition, molecular simulations were conducted to gain insight into the source of differing tolerance of aromatic amides and fatty amines and the intrinsic effect of solvents in this system. This enzymatic catalytic one-pot three-component system has excellent functional tolerance, simple operation, and application potential for industrial production demonstrated by the gram scale experiment.

Ambient temperature-dependent variations in bitter compounds and microbial dynamics in traditional huangjiu fermentation

Huangjiu, a traditional Chinese fermented wine, often develops excessive bitterness under semi-open fermentation conditions. This study examines the impact of ambient temperature on bitterness and microbial composition during Huangjiu fermentation. Using high−performance liquid chromatography (HPLC), gas chromatography−olfactometry (GC−O), and metagenomic sequencing, we identified seven bitter amino acids and eleven bitter volatile substances. Our results indicate that lower ambient temperatures (8.21 ± 0.69 °C to 9.88 ± 0.83 °C) suppress the accumulation of bitter substances, with the total concentration of bitter amino acids reduced by up to 3.94% compared to higher temperatures (16.36 ± 0.97 °C to 4.75 ± 0.74 °C). Partial least squares (PLS) regression established correlations between electronic tongue bitterness values and the presence of bitter compounds, revealing that higher temperatures promote the formation of specific compounds, such as benzaldehyde, furfural, ethyl nonanoate, and phenylalanine, thereby enhancing bitterness perception. Metabolic pathway analysis highlighted the enzymatic processes and intermediates involved in the biosynthesis of these bitter compounds. Correlation analysis showed that Saccharomyces and Lactobacillus are closely linked to the synthesis of bitter amino acids, while Aspergillus and Rhizopus contribute to the formation of furfural and ethyl octanoate. This study offers a theoretical foundation for reducing flavor variations between Huangjiu batches and provides practical guidance for optimizing the traditional fermentation process.

Improved Antioxidant, Antihypertensive, and Antidiabetic Activities and Tailored Emulsion Stability and Foaming Properties of Mixture of Corn Gluten and Soy Protein Hydrolysates Via Enzymatic Processing and Fractionation

ABSTRACTBioactive peptides and protein hydrolysates have gained considerable attention in the food industry and functional food markets due to their diverse health effects, including antioxidant, antihypertensive, and antidiabetic properties. This study aimed to produce combined soy and corn protein hydrolysates using Alcalase (Al), modification of Al‐hydrolysates through sequential hydrolysis using Flavourzyme (Al‐FL), cross‐linking of Al‐hydrolysates using microbial transglutaminase (MTGase) (Al‐TG), and fractionation of Al‐hydrolysates by ultrafiltration (UF) with molecular weight (MW) cut‐off of 100 (Al‐F4), 30 (Al‐F3), 10 (Al‐F2), and 2 kDa (Al‐F1). Notably, the &lt; 2 kDa fraction (Al‐F1) showcased exceptional biological activities, including antioxidant (81.54% DPPH, 98.02% ABTS), antihypertensive (95.45%), and antidiabetic effects (44.72% α‐glucosidase, 77.52% α‐amylase), linked to its high hydrophobic amino acid content and low molecular weights (111 and 263 Da). Conversely, the higher molecular weight fraction (Al‐TG) excelled in emulsion and foam stability, attributed to its balanced amino acid profile and larger peptides (1385–7057 Da). Our findings reveal that specific protein hydrolysate fractions, particularly Al‐F1 and Al‐TG, are promising for applications in food and pharmaceutical formulations due to their enhanced biological and functional properties.

Target-Triggered Ultrafast Chondroitin Gelation Enabled Power-Free and Point-of-Care Bioassays.

Point-of-care (POC) tests increasingly highlight the importance of portable, cost-effective, and visually quantitative detection of biomarkers. Herein, we developed a power-free and visual signal-readout POC sensor based on the target-triggered ultrafast gelation process. In the gelation process, the target triggered the cascade reaction catalyzed by oxidase and ferrous glycinate to produce carbon radicals that immediately initiated the rapid polymerization and cross-linking of acryloylated chondroitin sulfate and dimethylacrylamide. This highly efficient enzymatic polymerization process contributed to the ultrafast generation of chondroitin hydrogel within 1 min at 25 °C. The increase in viscosity of aqueous solution resulted from hydrogel formation was then visually measured according to the distance of solution migration on a tick-labeled pH test strip, which thus realized the quantification of a target. By utilizing glucose oxidase as an oxidase model during the gelation process, this POC sensor was successfully employed in the rapid quantitative detection of glucose without the need for any auxiliary instruments. Benefiting from the specificity and stability of the enzymatic polymerization reaction, the sensor exhibited excellent performance in the detection of glucose in clinical blood samples. Moreover, the sensor was further extended to uric acid detection and enabled accurate assay in clinical urine samples, which indicated the versatility and practicability of this sensor in the POC test.

In vitro study of the gel cohesivity and persistence to hyaluronidase degradation of a novel stabilized composition of 26 mg/mL of high molecular weight HA

Aim: Hyaluronic acid (HA) is extensively used in injectable skin quality products due to its documented role in skin rejuvenation. The rapid in vivo degradation of HA by the enzyme hyaluronidase necessitates the development of advanced formulations to ensure the efficacy and longevity of the treatments. In this context, a novel 2.6% high molecular weight HA (H-HA)/3.2% sorbitol composition has been introduced, featuring stabilization through hydrogen bonds rather than traditional crosslinking. Methods: The stabilized composition was evaluated through two in vitro enzymatic degradation tests. In the first test, the efficiency on the gel degradation was followed by rheology and compared with two crosslinked HA products available on the market. In the second test, the effect on the gel structure of a less diluted hyaluronidase dose was followed by rheological and cohesivity measurements. Results: In vitro study demonstrates that, before its complete degradation into a liquid-like state, the stabilized composition exhibits high elasticity and cohesivity during the enzymatic degradation process, surpassing traditional crosslinked HA products. Conclusion: The stabilization provided by the sorbitol in the stabilized composition effectively enhances product properties and protects them during gel degradation. These attributes indicate significant potential for improved clinical outcomes in skin quality treatments.

Agarose Degrading Potential and Whole Genome Sequence Analysis of Marine Bacterium Aliagarivorans sp. Strain DM1 Isolated from the Arabian Sea.

In recent years, agar-degrading bacteria have gained significant interest due to their biotechnological, environmental, microbiological, and industrial applications. Agar poses challenges such as marine waste accumulation, difficult industrial processing, limited natural degradability, and sustainability concerns due to high demand and overharvesting of red algae. The present study addresses the need for efficient agar-degrading microorganisms by isolating Aliagarivorans sp. strain DM1 from biofilm on fabric surfaces in the intertidal regions of the Arabian Sea, India. Phylogenetic analysis revealed that strain DM1 is closely related to Aliagarivorans taiwanensis AAT1T, and it exhibited significant agar-degrading activity on Zobell marine agar plates. Whole genome sequencing of Aliagarivorans sp. strain DM1, conducted using the Illumina NovaSeq platform, yielded a genome size of 4,898,415bp with an average G + C content of 53.3%. The genome includes 4,518 predicted protein-coding genes (CDS), 86 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes, with thirteen predicted agarases identified. The highest enzyme activity recorded was 51.00 U mL-1 on the 6th day of incubation using 10% inoculum, with optimal conditions of pH 8-9, 0.8M NaCl, and temperatures between 50 and 60°C. These findings underscore the promise of Aliagarivorans sp. strain DM1 in developing efficient enzymatic processes that can be applied in various biotechnological and industrial fields, including waste management and agaro-oligosaccharide production. Furthermore, strain DM1 possesses several key characteristics that enhance its adaptability and utility in marine and industrial applications, surpassing closely related strains in enzyme stability, environmental tolerance, and industrial versatility.

HaloClass: Salt-Tolerant Protein Classification with Protein Language Models.

Salt-tolerant proteins, also known as halophilic proteins, have unique adaptations to function in high-salinity environments. These proteins have naturally evolved in extremophilic organisms, and more recently, are being increasingly applied as enzymes in industrial processes. Due to an abundance of salt-tolerant sequences and a simultaneous lack of experimental structures, most computational methods to predict stability are sequence-based only. These approaches, however, are hindered by a lack of structural understanding of these proteins. Here, we present HaloClass, an SVM classifier that leverages ESM-2 protein language model embeddings to accurately identify salt-tolerant proteins. On a newer and larger test dataset, HaloClass outperforms existing approaches when predicting the stability of never-before-seen proteins that are distal to its training set. Finally, on a mutation study that evaluated changes in salt tolerance based on single- and multiple-point mutants, HaloClass outperforms existing approaches, suggesting applications in the guided design of salt-tolerant enzymes.