Extracellular expression of natural cytosolic arginine deiminase from Pseudomonas putida and its application in the production of L-citrulline

Production of Immobilized Arginine Deiminase Using the Self-Assembling Peptide ELK16 for Efficient l-Citrulline Synthesis

Self-assembling peptide (SAP) tags induce protein self-assembly, forming insoluble protein aggregates. Traditional l-citrulline production using arginine deiminase (ADI) is limited by enzyme instability and low reusability. SAP tags were fused with ADI to overcome these challenges, and ADI-ELK16 demonstrated optimal activity at 55 °C and pH 6.0 with enhanced thermal stability. ADI-ELK16 retained 57.34% of its enzyme activity after 10 cycles, with notable reusability. The protein was characterized by scanning electron microscopy (SEM), dynamic light scattering (DLS), and the zeta potential. Additionally, the conversion of 100 g/L l-arginine to 92.3 g/L l-citrulline over batch reactions validated the industrial potential of ADI-ELK16. Compared with traditional immobilization methods, this approach eliminates the need for carrier materials, simplifying the immobilization process and significantly enhancing the catalytic performance and stability, making ADI-ELK16 a highly efficient and reusable system for industrial applications.

Optimization of citrulline production from a Bacillus subtilis BH-01 isolated from raw buffalo milk

The main purpose of this study was to optimize the L-citrulline production process using Plackett-Burman and Box-Behnken designs. L-citrulline-producing bacterium BH-01 was isolated from raw buffalo milk. The isolate was tested for probiotic activities such as tolerance to simulated gastric and intestinal juices, antagonistic activity against six antibiotic-resistant bacteria, and temperature tolerance. L-citrulline production and arginine deiminase (ADI) activity were optimized using statistical designs. The bacterial isolate was molecularly identified as Bacillus subtilis strain AUMC B-498 (accession number PP574248.1). The strain exhibited resistance at pH 2.0 and bile salt 0.5% for a two-hour exposure period. It could inhibit the growth of Escherichia coli, Klebsiella pneumonia, Serratia sp., Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Streptococcus pneumoniae. From the results of statistical optimization, the Plackett-Burman design identified temperature, L-arginine, incubation period, and peptone as the most effective factors among the eight selected variables. Based on these, the Box-Behnken design was used to optimize the factors required to maximize citrulline production. The maximum L-citrulline was 632.5 µg/L, and ADI activity was 1.42 U/mL. Therefore, BH-01 isolated from Buffalo milk might be a promising candidate in food, biotechnological, and pharmaceutical applications due to its dual functionality for citrulline production and probiotic characteristics.

Enhanced thermostability and catalytic activity for arginine deiminase from Enterobacter faecalis SK32.001 via combinatorial mutagenesis

Arginine deiminase (ADI) exhibits potential for clinical and industrial applications, yet its low thermostability and catalytic efficiency under physiological conditions limit its utility. In this work, the ADI of Enterococcus faecalis SK32.001 was rationally designed. A total of 120 combinatorial mutants, ranging from two-point to six-point mutations, were constructed by sequentially stacking single-point positive mutants (F44W, N163P, E220L, N318E, A336G, T340I). Among them, the mutants S604, S700, S601, and S606 exhibited higher Tm values, while the mutants S605, S547, S602, S607, S517, and S557 demonstrated enhanced enzymatic activity. Notably, the five-point mutant S547 (F44W/N163P/E220I/A336G/T340I) exhibited remarkable pH tolerance (pH 4.5-9.5, with over 80 % residual enzyme activity). Its specific enzyme activity reached 131.60 U/mg, which was 2-fold higher than that of wild enzyme. The Tm value of this enzyme increases to 64.04 °C, 11.62 °C higher than that of the wild-type enzyme. The structure predicted by AlphaFold 2 revealed that the increased rigidity, formation of new hydrogen bonds, and an increase in hydrophobic residues may account for the enhanced enzyme activity and thermostability. This research demonstrates that rational design strategies can effectively optimize enzyme properties, providing insights for the development of microbial enzymes with industrial relevance.

Integrated neural network and PSO hybrid approach for production of citrulline using immobilized permeabilized Pseudomonas furukawaii

In the present study, nutraceutical citrulline was produced using immobilization of permeabilized whole cells of Pseudomonas furukawaii, an efficient producer of ADI. Since arginine deiminase (ADI) is intracellularly localized, various additives such as SDS (Sodium dodecyl sulfate), Triton X-100, and EDTA (Ethylenediaminetetraacetic Acid) were used to permeabilize the cell to improve substrate accessibility and ADI activity. The maximum ADI activity was observed with 0.25 mg ml-1 biomass concentration treated with 0.5 mmol l-1 EDTA for 15 min using OFAT (One factor at a time) approach. Optimization of permeabilization conditions of P. furukawaii cells using novel neural networks and particle swarm optimization led to maximum ADI activity with 0.10 mmol l-1 EDTA and 0.30 mg ml-1 biomass. Further, the morphological characterization of immobilized cells was assessed by field emission scanning electron microscopy and FTIR (Fourier transform infrared spectroscopy). An optimal citrulline production of 1.19 mmol l-1 was achieved at 2.5% sodium alginate with 20 mmol l-1 arginine at 38°C, and 180 min of incubation. The immobilized cells retained 90.3% productivity after seven reuse cycles. Thus, the formulated immobilized whole-cell biocatalyst, with higher stability offers cost-effective methods of citrulline production.

Rational design to improve the catalytic efficiency and stability of arginine deiminase

Arginine deiminase (ADI) has garnered significant interest because of its ability to objectively eradicate cancer cells and produce L-citrulline. To meet the production demands, this study focused on enhancing the enzyme activity and thermal stability of ADI. In this study, 24 ADI mutants were obtained through computer aid site-specific mutation in the ADI of Enterobacter faecalis. Notably, the specific enzyme activities of F44W, N163P, E220I, E220L, N318E, A336G, T340I, and N382F increased, reaching 1.33-2.53 times that of the original enzyme. This study confirmed that site-specific mutations are critical for optimizing enzyme function. Additionally, the F44W, N163P, E220I, T340I, and A336G mutants demonstrated good thermal stability. The optimal pH for mutant F44W increased to 8, whereas mutants E220I, I244V, A336G, T340I, and N328F maintained an optimal pH of 7.5. Conversely, the M109L, N163P, E220L, I244L, and N318E mutants shad an optimal pH of 7. This study revealed that mutant enzymes with increased activity were more likely to contain mutation sites situated near the four loops associated with catalytic residues, whereas mutations at the dimer junction sites had a higher tendency to enhance enzyme stability. These findings contribute to the development of ADI industrial applications and its modifications.

Research progress of L-aspartate-α-decarboxylase and its isoenzyme in the β-alanine synthesis

Driven by the massive demand in recent years, the production of β-alanine has significantly progressed in chemical and biological ways. Although the chemical method is relatively mature compared to biological synthesis, its high cost of waste disposal and environmental pollution does not meet the environmental protection standard. Hence, the biological method has become more prevalent as a potential alternative to the chemical synthesis of β-alanine in recent years. As a result, the aspartate pathway from L-aspartate to β-alanine (the most significant rate-limiting step in the β-alanine synthesis) catalyzed by L-aspartate-α-decarboxylase (ADC) has become a research hotspot in recent years. Therefore, it is vital to comprehensively understand the different enzymes that possess a similar catalytic ability to ADC. This review will investigate the exploratory process of unique synthesis features and catalytic properties of ADC/ADC-like enzymes in particular creatures with similar catalytic capacity or high sequence homology. At the same time, we will discuss the different β-alanine production methods which can apply to future industrialization.

Characterization of a recombinant arginine deiminase from Halothermothrix orenii and its application in citrulline production

In recent years, arginine deiminase (ADI, EC 3.5.3.6) has attracted much attention as a biocatalyst that produces the functional amino acid l-citrulline from l-arginine and also as an anticancer enzyme. Here, we identified and characterized a putative ADI from the thermophilic bacterium Halothermothrix orenii. The H. orenii ADI (H-ADI) protein was expressed in Escherichia coli BL21(DE3) with a specific activity of 91.8 U/mg protein at 55°C and pH 6.5. The enzyme remained at 74% relative activity after incubation at 45°C for 180 min, only 25% at 50°C. The melting temperature was 56°C. H-ADI is not a metal-requiring enzyme; Ni²⁺ slightly improved the catalytic activity. The K_m and V_max for l-arginine were 55.5 mM and 156.8 μmol/min/mg protein, respectively. Moreover, three residues (Arg183, Arg237, and His273) were key to the formation of l-citrulline, as analyzed by alanine-scanning mutagenesis. Finally, the enzymatic synthesis of l-citrulline was carried out at 50°C with a conversion ratio reaching 99.03%. Together, these findings show that H-ADI is a promising biocatalyst for the production of l-citrulline.

Microbial arginine deiminase: A multifaceted green catalyst in biomedical sciences

Arginine deiminase is a well-recognized guanidino-modifying hydrolase that catalyzes the conversion of L-arginine to citrulline and ammonia. Their biopotential to regress tumors via amino acid deprivation therapy (AADT) has been well established. PEGylated formulation of recombinant Mycoplasma ADI is in the last-phase clinical trials against various arginine-auxotrophic cancers like hepatocellular carcinoma, melanoma, and mesothelioma. Recently, ADIs have attained immense importance in several other biomedical applications, namely treatment of Alzheimer's, as an antiviral drug, bioproduction of nutraceutical L-citrulline and bio-analytics involving L-arginine detection. Considering the wide applications of this biodrug, the demand for ADI is expected to escalate several-fold in the coming years. However, the sustainable production aspects of the enzyme with improved pharmacokinetics is still limited, creating bottlenecks for effective biopharmaceutical development. To circumvent the lacunae in enzyme production with appropriate paradigms of 'quality-by-design' an explicit overview of its properties with 'biobetter' formulations strategies are required. Present review provides an insight into all the potential biomedical applications of ADI along with the improvements required for its reach to clinics. Recent research advances with special emphasis on the development of ADI as a 'biobetter' enzyme have also been comprehensively elaborated.

l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process

As an important semi-essential amino acid, l-arginine is extensively used in the food and pharmaceutical fields. At present, l-arginine production depends on cost-effective, green, and sustainable microbial fermentation by using a renewable carbon source. To enhance its fermentative production, various metabolic engineering strategies have been employed, which provide valid paths for reducing the cost of l-arginine production. This review summarizes recent advances in molecular biology strategies for the optimization of l-arginine-producing strains, including manipulating the principal metabolic pathway, modulating the carbon metabolic pathway, improving the intracellular biosynthesis of cofactors and energy usage, manipulating the assimilation of ammonia, improving the transportation and membrane permeability, and performing biosensor-assisted high throughput screening, providing useful insight into the current state of l-arginine production.

Arginine Deiminase: Current Understanding and Applications

BACKGROUND

Arginine deiminase (ADI), an arginine catabolizing enzyme, is considered as an anti-tumor agent for the treatment of arginine auxotrophic cancers. However, some obstacles limit its clinical applications.

OBJECTIVE

This review will summarize the clinical applications of ADI, from a brief history to its limitations, and will discuss the different ways to deal with the clinical limitations.

METHOD

The structure analysis, cloning, expression, protein engineering and applications of arginine deiminase enzyme have been explained in this review.

CONCLUSION

Recent patents on ADI are related to ADI engineering to increase its efficacy for clinical application. The intracellular delivery of ADI and combination therapy seem to be the future strategies in the treatment of arginine auxotrophic cancers. Applying ADIs with optimum features from different sources and or ADI engineering, are promising strategies to improve the clinical application of ADI.

High-efficiency expression of Sulfolobus acidocaldarius maltooligosyl trehalose trehalohydrolase in Escherichia coli through host strain and induction strategy optimization

Maltooligosyl trehalose trehalohydrolase (MTHase, EC 3.2.1.141) catalyzes the release of trehalose, a novel food ingredient, by splitting the α-1,4-glucosidic linkage adjacent to the α-1,1-glucosidic linkage of maltooligosyl trehalose. However, the high-yield preparation of recombinant MTHase has not yet been reported. In this study, a codon-optimized synthetic gene encoding Sulfolobus acidocaldarius MTHase was expressed in Escherichia coli. In initial expression experiments conducted using pET-24a (+) and E. coli BL21 (DE3), the MTHase activity was 10.4 U/mL and a large amount of the expression product formed inclusion bodies. The familiar strategies, including addition of additives, co-expression with molecular chaperones, and expression with a fusion partner, failed to enhance soluble MTHase expression. Considering the intermolecular disulfide bond of MTHase, expression was investigated using a system comprising plasmid pET-32a (+) and host E. coli Origami (DE3), which is conducive to cytoplasmic disulfide bond formation. The MTHase activity increased to 55.0 U/mL, a 5.3-fold increase. Optimization of the induction conditions in a 3-L fermentor showed that when the lactose was fed at 0.2 g/L/h beginning at an OD₆₀₀ of 40 and the induction temperature was maintained at 30 °C, the MTHase activity reached a maximum of 204.6 U/mL. This is the first report describing a systematic effort to obtain high-efficiency MTHase production. The high yield obtained using this process provides the basis for the industrial-scale production of trehalose. This report is also expected to be valuable in the production of other enzymes containing disulfide bonds.

Thermostability and Specific-Activity Enhancement of an Arginine Deiminase from Enterococcus faecalis SK23.001 via Semirational Design for l-Citrulline Production

l-Citrulline is a nonessential amino acid with a variety of physiological functions and can be enzymatically produced by arginine deiminase (ADI, EC 3.5.3.6). The enzymatic-production approach is of immense interest because of its mild conditions, high yield, low cost, and environmental benignity. However, the major hindrances of l-citrulline industrialization are the poor thermostability and enzyme activity of ADI. Hence, in this work, directed evolution and site-directed mutagenesis aided with in silico screening, including the use of b-factor values and HoTMuSiC, were applied to a previously identified ADI from Enterococcus faecalis SK23.001 ( EfADI), and a triple-site variant R15K-F269Y-G292P was obtained. The triple-site variant displays a 2.5-fold higher specific enzyme activity (333 U mg^-1), a lower K_m value of 6.4 mM, and a 6.1-fold longer half-life ( t_1/2,45°C = 86.7 min) than wild-type EfADI. This work provides a protein-engineering strategy to improve enzyme activity and thermostability, which might be transferrable to other ADIs and enzymes.

Citrulline metabolism in plants

Citrulline was chemically isolated more than 100 years ago and is ubiquitous in animals, plants, bacteria, and fungi. Most of the research on plant citrulline metabolism and transport has been carried out in Arabidopsis thaliana and the Cucurbitaceae family, particularly in watermelon which accumulates this non-proteinogenic amino acid to very high levels. Industrially, citrulline is produced via specially optimized microbial strains; however, the amounts present in watermelon render it an economically viable source providing that other high-value compounds can be co-extracted. In this review, we provide an overview of our current understanding of citrulline biosynthesis, transport, and catabolism in plants additionally pointing out significant gaps in our knowledge which need to be closed by future experimentation. This includes the identification of further potential enzymes of citrulline metabolism as well as obtaining a far better spatial resolution of both sub-cellular and long-distance partitioning of citrulline. We further discuss what is known concerning the biological function of citrulline in plants paying particular attention to the proposed roles in scavenging of excess NH₄⁺ and as a compatible solute.

Efficient androst-1,4-diene-3,17-dione production by co-expressing 3-ketosteroid-Δ1 -dehydrogenase and catalase in Bacillus subtilis

AIMS

3-ketosteroid-Δ¹ -dehydrogenase (KSDD), a flavin adenine dinucleotide (FAD)-dependent enzyme involved in sterol metabolism, specifically catalyses the conversion of androst-4-ene-3,17-dione (AD) to androst-1,4-diene-3,17-dione (ADD). However, the low KSDD activity and the toxic effects of hydrogen peroxide (H₂ O₂ ) generated during the biotransformation of AD to ADD with FAD regeneration hinder its application on AD conversion. The aim of this work was to improve KSDD activity and eliminate the toxic effects of the generated H₂ O₂ to enhance ADD production.

METHODS AND RESULTS

The ksdd gene obtained from Mycobacterium neoaurum JC-12 was codon-optimized to increase its expression level in Bacillus subtilis, and the KSDD activity reached 12·3 U mg^-1 , which was sevenfold of that of codon-unoptimized gene. To improve AD conversion, catalase was co-expressed with KSDD in B. subtilis 168/pMA5-ksdd^opt -katA to eliminate the toxic effects of H₂ O₂ generated during AD conversion. Finally, under optimized bioconversion conditions, fed-batch strategy was carried out and the ADD yield improved to 8·76 g l^-1 .

CONCLUSIONS

This work demonstrates the potential to improve enzyme activity by codon-optimization and eliminate the toxic effects of H₂ O₂ by co-expressing catalase.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study showed the highest ADD productivity ever reported and provides a promising strain for efficient ADD production in the pharmaceutical industry.