Acetic acid bacteria (AAB) produce phosphatidylcholine (PC) as a major membrane component. PC has long been considered important for acetic acid tolerance in AAB, yet direct experimental support remains limited, and its physiological roles under diverse environmental stresses are not well defined. In this study, we constructed PC-deficient mutants of Acetobacter pasteurianus by deleting the phosphatidylethanolamine N-methyltransferase gene. PC deficiency resulted in phosphatidylglycerol accumulation and a tendency toward acyl-chain shortening. Phenotypic analysis showed that PC deficiency impaired growth under ionic, heat, and acidic stresses, indicating that PC supports membrane integrity under these stress conditions. Heterologous expression of PC synthase from Pseudomonas aeruginosa enabled choline-dependent regulation of PC biosynthesis. This system revealed that even low PC levels are sufficient to restore normal growth and acetic acid fermentation. These findings suggest that PC has diverse physiological roles in AAB and its function does not necessarily depend on its abundance in the membrane.

AIM:To conduct a postmarketing surveillance study of patients with Dravet syndrome in Japan to investigate the safety and effectiveness of long-term, real-world, clinical use of stiripentol (STP). METHOD:This prospective study was conducted over 156 weeks in all patients with Dravet syndrome who started STP treatment from its launch in Japan in November 2012 until August 2017. Adverse drug reactions (ADRs) were investigated by degree of seriousness. Effectiveness was determined based on a comprehensive assessment by the physician in charge as well as on the percentage change in the number of seizures from the pretreatment period. RESULTS:In total, 520 patients (266 males, 254 females; mean age [SD] 10 years 6 months [9 years 10 months]; age range 0-50 years) were included in the safety analysis set, and 515 patients in the effectiveness analysis set. ADRs occurred in 69.2%, including somnolence, decreased appetite, dizziness, in order of frequency. Twelve deaths occurred, the rate of which was not higher than the reported rates. No new safety concerns were identified. The rate of overall improvement (marked or moderate) after 156 weeks or at treatment discontinuation was 37.7%. Decreases in the number of all seizure types over the long term were confirmed. INTERPRETATION:In real-world clinical settings, long-term STP treatment can be safe and effective in patients with Dravet syndrome.

β-Aspartyl compounds, such as β-aspartyl hydroxamate (serine racemase inhibitor), β-aspartyl-l-lysine (moisture retention), and β-aspartyl-l-tryptophan (immunomodulator) are physiologically active compounds. There is limited literature on the development of effective methods of production of β-aspartyl compounds. In this study, we describe the biochemical characterization of asparagine synthetase (AS) from Streptococcus thermophilus NBRC 13957 (StAS) and the enzymatic synthesis of β-aspartyl compounds using StAS. Recombinant StAS was expressed in Escherichia coli BL21(DE3) and it displayed activity towards hydroxylamine, methylamine, ethylamine, and ammonia, as acceptors of the β-aspartyl moiety. StAS exhibited higher activity toward hydroxylamine and ethylamine as acceptor substrates compared with the enzymes from Lactobacillus delbrueckii NBRC 13953, Lactobacillus reuteri NBRC 15892, and E. coli. The coupling of the synthesis of β-aspartyl compounds by StAS with an ATP-regeneration system using polyphosphate kinase from Deinococcus proteoliticus NBRC 101906 displayed an approximately 2.5-fold increase in the production of β-aspartylhydroxamate from 1.06 mM to 2.53 mM after a 76-h reaction.

Biodegradable nanocarriers based on polysaccharide-derived amphiphilic copolymers are promising candidates to enhance drug solubility and stability. This study aimed to design a novel amphiphilic carrier based on enzymatic polymerization-derived exopolysaccharides, α-1,3-glucan. Glycosyltransferase I from Streptococcus mutans was used to synthesize α-1,3-glucan, and the amphiphilic α-1,3-glucan-graft-poly(ε-caprolactone) (Glucan-g-PCL) copolymer was synthesized via a homogeneous ring-opening polymerization (ROP) in ionic liquid, 1-butyl-3-methylimidazolium chloride. The chemical structures and physical properties of Glucan-g-PCL copolymer were characterized by FT-IR, 1H NMR, XRD, and TGA. The self-assembly behavior of the amphiphilic α-1,3-glucan derivative was investigated by fluorescence probe. The results showed that Glucan-g-PCL exhibited a low critical aggregation concentration (CAC) and formed core-shell structured nanostructure via self-assembly. Quercetin (Qu), a hydrophobic active component, was successfully encapsulated within the Glucan-g-PCL micelle-like nanostructure, showing efficient encapsulation and dispersion in water. Qu/Glucan-g-PCL micelle-like nanostructure (Qu/M) was characterized by DLS, TEM, FT-IR, and XRD. FT-IR and XRD analyses showed that Qu was present in an amorphous state in the formulation and without any chemical reactions during the sample preparation procedures. In addition, the antioxidant properties of the Qu/M were investigated using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method, and significantly improved antioxidant activity was observed for Qu/M compared to Qu/water. The utilization of Glucan-g-PCL nanostructure encapsulation opens up new possibilities for enhancing and expanding the practical applications of quercetin and α-1,3-glucan.

Successful implementation of enzymes in practical application hinges on the development of efficient mass production techniques. However, in a heterologous expression system, the protein is often unable to fold correctly and, thus, forms inclusion bodies, resulting in the loss of its original activity. In this study, we present a new and more accurate model for predicting amino acids associated with an increased L-amino acid oxidase (LAO) solubility. Expressing LAO from Rhizoctonia solani in Escherichia coli and combining random mutagenesis and statistical logistic regression, we modified 108 amino acid residues by substituting hydrophobic amino acids with serine and hydrophilic amino acids with alanine. Our results indicated that specific mutations in Euclidean distance, glycine, methionine, and secondary structure increased LAO expression. Furthermore, repeated mutations were performed for LAO based on logistic regression models. The mutated LAO displayed a significantly increased solubility, with the 6-point and 58-point mutants showing a 2.64- and 4.22-fold increase, respectively, compared with WT-LAO. Ultimately, using recombinant LAO in the biotransformation of α-keto acids indicates its great potential as a biocatalyst in industrial production.

Polysaccharide-based amphiphilic copolymers self-assemble in water to form micelle-like structures. They are expected to be used as nanocarriers in the biomedical field owing to their biocompatibility, biodegradability, and low toxicity. α-1,3-Glucan is a water-insoluble glucose homopolymer that can be generated through environmentally friendly enzymatic polymerization and easily purified without using organic solvents. Thus, it has attracted attention as a new bio-based material. In this study, we developed new nanomicelles based on α-1,3-glucan. Glycosyltransferase I from Streptococcus mutans was used to synthesize α-1,3-glucan, and a series of amphiphilic α-1,3-glucan-based graft copolymers (α-1,3-glucan- g -PLA) were synthesized with different L-Lactide supply ratios in the ionic liquid BmimCl. The results of FT-IR, 1 H NMR, 13 C NMR, XRD, and TGA verified that the reaction proceeded successfully. These amphiphilic α-1,3-glucan derivatives with low critical micelle concentrations can self-assemble to form core–shell structural micelles of various sizes (approximately 57–125 nm) in water. Furthermore, the self-assembled micelles were investigated as drug carriers using prednisone acetate (PA) as a model drug, and their sustained drug release behavior for 9 days was confirmed. These results revealed that the synthesized self-assembled micelles have promising potential as new carriers for the efficient delivery of hydrophobic drugs.

The high stereo- and substrate specificities of enzymes have been utilized for microdetermination of amino acids. Here, I review the discovery of l-Arg oxidase from Pseudomonas sp. TPU 7192, l-Lys oxidase/decarboxylase from Burkholderia sp. AIU 395, and enzymes showing apparent l-His oxidase activity from Achromobacter sp. TPU 5009. I also discuss screening and uses of the selective enzymes for microdetermination of amino acids. In addition, functional modifications of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813, l-Trp dehydrogenase from Nostoc punctiforme ATCC 29133, and l-Lys ε-oxidase from Marinomonas mediterranea NBRC 103028 by directed evolution are reviewed. Finally, I review the rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity-this process enables the wider use of natural enzymes.

The Pseudomonas aeruginosa strain, PAO1, has three putative γ-glutamyltranspeptidase (GGT) genes: ggtI, ggtII, and ggtIII. In this study, the expression of each of these genes in P. aeruginosa PAO1 was analyzed, and the properties of the corresponding GGT proteins were investigated. This is the first report on biochemical characterization of GGT paralogs from Pseudomonas species. The crude extracts prepared from P. aeruginosa PAO1 exhibited hydrolysis and transpeptidation activities of 17.3 and 65.0 mU/mg, respectively, and the transcription of each gene to mRNA was confirmed by RT-PCR. All genes were cloned, and the expression plasmids constructed were introduced into an Escherichia coli expression system. Enzyme activity of the expressed protein of ggtI (PaGGTI) was not detected in the system, while the enzyme activities of the expressed proteins derived from ggtII and ggtIII (PaGGTII and PaGGTIII, respectively) were detected. However, the enzyme activity of PaGGTII was very low and easily decreased. PaGGTII with C-terminal his-tag (PaGGTII25aa) showed increased activity and stability, and the purified enzyme consisted of a large subunit of 40 kDa and a small subunit of 28 kDa. PaGGTIII consisted of a large subunit of 37 kDa and a small subunit of 24 kDa. The maximum hydrolysis and transpeptidation activities of PaGGTII25aa were obtained at 40ºC-50ºC, and the maximum hydrolysis and transpeptidation activities of PaGGTIII were obtained at 50ºC-60ºC. These enzymes retained approximately 80% of their hydrolysis and transpeptidation activities after incubation at 50ºC for 10 min, reflecting good stability. Both PaGGTII25aa and PaGGTIII showed higher activities of hydrolysis and transpeptidation in the alkali range than in the acidic range. However, they were highly stable at a wide pH range (5-10.5).

The gene encoding gamma-glutamyltranspeptidase II (PaGGTII) from Pseudomonas aeruginosa PAO1 was cloned in Escherichia coli. Recombinant PaGGTII showed a weak activity (0.0332 U/mg), and it can be easily inactivated. Multiple alignment of microbial GGTs showed the redundancy of the C-terminal of the small subunit of PaGGTII in length. The truncation of eight amino acid residues at the C-terminal of PaGGTII remarkably improved the activity and stability of the enzyme (PaGGTII Delta 8; 0.388 U/mg). Further truncation at the C-terminal also provided the enzyme relatively higher activity (PaGGTII Delta 9, -Delta 10, -Delta 11, and -Delta 12). Among C-terminal truncated mutants, we focused on PaGGTII Delta 8 and examined the effect of C-terminal amino acid residues on the properties of PaGGTII Delta 8 because the activity of PaGGTII was found to be greatly improved when 8 amino acid residues were truncated. Various mutant enzymes with different C-terminal amino acid residues were constructed. They were expressed in E. coli and purified to homogeneity by ion-exchange chromatography. The properties of PaGGTII Delta 8 and the mutants obtained from mutation at E569 were characterized. K-m and k(cat) of PaGGTII Delta 8 for gamma-glutamyl-p-nitroanilide (gamma-GpNA) were 8.05 mM and 15.49 s(-1), respectively. PaGGTII Delta 8E569Y showed the highest catalytic efficiency for gamma-GpNA with a k(cat)/K-m of 12.55 mM(-1) s(-1). Mg2+, Ca2+, and Mn2+ exhibited positive effects on the catalytic activity for PaGGTII Delta 8 and its ten E569 mutants.

Aldoxime dehydratase (Oxd) is a heme enzyme that catalyzes aldoxime dehydration to the corresponding nitriles. Unlike many other heme enzymes, Oxd has a unique feature that the substrate binds directly to the heme. Therefore, it is thought that structural differences around the bound heme directly relate to differences in substrate selection. However sufficient structural information to discuss the substrate specificity has not been obtained. Oxd from Bacillus sp. OxB-1 (OxdB) shows unique substrate specificity and enantioselectivity compared to the Oxds whose crystal structures have already been reported. Here, we report the crystal structure of OxdB, which has not been reported previously. Although the crystallization of OxdB has been difficult, by adding a site-specific mutation to Glu85 located on the surface of the protein, we succeeded in crystallizing OxdB without reducing the enzyme activity. The catalytic triad essential for Oxd activity were structurally conserved in OxdB. In addition, the crystal structure of the Michaelis complex of OxdB and the diastereomerically pure substrate Z-2-(3-bromophenyl)-propanal oxime implied the importance of several hydrophobic residues for substrate specificity. Mutational analysis implicated Ala12 and Ala14 in the E/Z selectivity of bulky compounds. The N-terminal region of OxdB was shown to be shorter than those of Oxds from Pseudomonas chlororaphis and Rhodococcus sp. N-771, and have high flexibility. These structural differences possibly result in distinct preferences for aldoxime substrates based on factors such as substrate size.

Recently, the program INTMSAlign_HiSol for identifying aggregation hotspots in proteins only requiring secondary structure data was introduced. We explored the utility of this program further and applied it for engineering of the aldoxime dehydratase from Bacillus sp. OxB-1. Towards this end, the effect of inverting the hydropathy at selected positions of the amino acid sequence on the enzymatic activity was studied leading to 60% of our constructed variants, which showed improved activity. In part, this activity increase can be rationalised by an improved heme incorporation of the variants. For example, a single mutation gave a 1.8 fold increased enzymatic activity and 30% improved absolute heme incorporation.

Background: A post-marketing surveillance study is investigating the safety and effectiveness of stiripentol during real-world clinical use in Japanese patients with Dravet syndrome (DS). Methods: The safety and effectiveness of stiripentol were prospectively investigated over 104 weeks in all patients with DS who were administered the drug from November 2012 through July 2019 in Japan. Patients administered stiripentol for the first time after its approval were defined as "new patients," and those who continued to take the drug after participating in domestic clinical studies were defined as "continuous-use patients." The responder rate was defined as the proportion of patients with a >= 50 % decrease in seizure episodes at the time of assessment of stiripentol effectiveness compared with the 4 weeks before starting stiripentol. Overall improvement was evaluated by the physician in charge based on the comprehensive assessment of the patient's condition after stiripentol treatment. Results: Of 411 patients whose information was collected, 410 patients (376 new and 34 continuous-use) were included in the safety analysis set, and 409 (376 new and 33 continuous-use) were included in the effectiveness analysis set. The median age of new patients was 7 years (range: 0.5-50 years) at the time of stiripentol initiation; 99 % of patients were taking concomitant sodium valproate and 93 % clobazam. Adverse drug reactions occurred in 70 % of new patients; the most common were somnolence (39 %) and loss of appetite (25 %). No new safety concerns due to stiripentol were observed. The responder rate in new patients was 43 % (110/257 patients) for convulsive seizures (tonic-clonic and/or clonic convulsions), 55 % (58/105 patients) for focal impaired awareness seizures, and 62 % (56/90 patients) for generalized myoclonic seizures and/or generalized atypical absence seizures. Overall improvement (after 104 weeks or at the time of drug discontinuation) was rated as marked or moderate in 160/353 of new patients (45 %). Conclusion: Stiripentol is safe and effective during long-term use in patients with DS in routine clinical practice.

The formation of amide bonds is important in many areas of chemistry, and the ligation by condensation of N-hydroxylamine and an alpha-keto acid has been attracting increasing attention. Porcine kidney D-amino acid oxidase, which catalyzes the oxidative deamination of amino acids to yield alpha-keto acids, ammonia, and hydrogen peroxide, and native chemical ligation were used to access alpha-keto acids, and amides were synthesized with Nhydroxylamine. D-Phenylalanine was converted to phenylpyruvic acid obtained by recombinant pig D-amino acid oxidase in high yield (97%). The alpha-keto acid was ligated with N-benzylhydroxylamine and N-hydroxylphenylalanine in N,N-dimethylformamide, and benzyl-2-phenylacetamide and (2-phenylacetyl)phenylalanine in 82% and 79% yields, respectively. Other amide compounds were also obtained via this synthesis.

An enzyme showing l-histidine oxidase (HisO) activity by the formation of hydrogen peroxide was newly purified from Achromobacter sp. TPU 5009. This enzyme was found to be a heterodimer of two proteins (molecular mass, 53.8 and 58.3 kDa), the partial determination of which indicated they are homologs of l-histidine ammonia-lyase (AchHAL) and urocanate hydratase (AchURO). The enzyme was stable in a pH range of 5.0-11.0, with >90% of the original activity maintained below 60°C at pH 7.0. To characterize AchHAL and AchURO, each of their genes was cloned and expressed in a heterologous expression system. Heterologous AchHAL catalyzed the elimination of the α-amino group of l-histidine to urocanate and ammonia, while heterologous AchURO catalyzed the hydration of urocanate to imidazolone propionate. Since imidazolone propionate is highly unstable in the presence of oxygen at neutral pH, it was immediately decomposed and hydrogen peroxide was non-enzymatically produced. Our results indicate that this natural enzyme showing apparent HisO activity is composed of AchHAL and AchURO, which formed hydrogen peroxide after the spontaneous decomposition of imidazolone propionate.

A large number of protein sequences are registered in public databases such as PubMed. Functionally uncharacterized enzymes are included in these databases, some of which likely have potential for industrial applications. However, assignment of the enzymes remained difficult tasks for now. In this study, we assigned a total of 28 original sequences to uncharacterized enzymes in the FAD-dependent oxidase family expressed in some species of bacteria including Chryseobacterium, Flavobacterium, and Pedobactor. Progenitor sequence of the assigned 28 sequences was generated by ancestral sequence reconstruction, and the generated sequence exhibited L-lysine oxidase activity; thus, we named the enzyme AncLLysO. Crystal structures of ligand-free and ligand-bound forms of AncLLysO were determined, indicating that the enzyme recognizes L-Lys by hydrogen bond formation with R76 and E383. The binding of L-Lys to AncLLysO induced dynamic structural change at a plug loop formed by residues 251 to 254. Biochemical assays of AncLLysO variants revealed the functional importance of these substrate recognition residues and the plug loop. R76A and E383D variants were also observed to lose their activity, and the kcat/Km value of G251P and Y253A mutations were approximately 800- to 1800-fold lower than that of AncLLysO, despite the indirect interaction of the substrates with the mutated residues. Taken together, our data demonstrate that combinational approaches to sequence classification from database and ancestral sequence reconstruction may be effective not only to find new enzymes using databases of unknown sequences but also to elucidate their functions.

l-Lysine oxidase/monooxygenase (l-LOX/MOG) from Pseudomonas sp. AIU 813 catalyzes the mixed bioconversion of l-amino acids, particularly l-lysine, yielding an amide and carbon dioxide by an oxidative decarboxylation (i.e. apparent monooxygenation), as well as oxidative deamination (hydrolysis of oxidized product), resulting in α-keto acid, hydrogen peroxide (H2O2), and ammonia. Here, using high-resolution MS and monitoring transient reaction kinetics with stopped-flow spectrophotometry, we identified the products from the reactions of l-lysine and l-ornithine, indicating that besides decarboxylating imino acids (i.e. 5-aminopentanamide from l-lysine), l-LOX/MOG also decarboxylates keto acids (5-aminopentanoic acid from l-lysine and 4-aminobutanoic acid from l-ornithine). The reaction of reduced enzyme and oxygen generated an imino acid and H2O2, with no detectable C4a-hydroperoxyflavin. Single-turnover reactions in which l-LOX/MOG was first reduced by l-lysine to form imino acid before mixing with various compounds revealed that under anaerobic conditions, only hydrolysis products are present. Similar results were obtained upon H2O2 addition after enzyme denaturation. H2O2 addition to active l-LOX/MOG resulted in formation of more 5-aminopentanoic acid, but not 5-aminopentamide, suggesting that H2O2 generated from l-LOX/MOG in situ can result in decarboxylation of the imino acid, yielding an amide product, and extra H2O2 resulted in decarboxylation only of keto acids. Molecular dynamics simulations and detection of charge transfer species suggested that interactions between the substrate and its binding site on l-LOX/MOG are important for imino acid decarboxylation. Structural analysis indicated that the flavoenzyme oxidases catalyzing decarboxylation of an imino acid all share a common plug loop configuration that may facilitate this decarboxylation.

α-1,3-Glucan is a homopolymer composed of D-glucose (Glc) and it is an extracellular polysaccharide found in dental plaque due to Streptococcus species. α-1,3-Glucanase from Streptomyces thermodiastaticus strain HF3-3 (Agl-ST) has been identified as a thermostable α-1,3-glucanase, which is classified into glycoside hydrolase family 87 (GH87) and specifically hydrolyzes α-1,3-glucan with an endo-action. The enzyme has a potential to inhibit the production of dental plaque and to be used for biotechnological applications. Here we show the structure of the catalytic unit of Agl-ST determined at 1.16 Å resolution using X-ray crystallography. The catalytic unit is composed of two modules, a β-sandwich fold module, and a right-handed β-helix fold module, which resembles other structural characterized GH87 enzymes from Bacillus circulans str. KA-304 and Paenibacillus glycanilyticus str. FH11, with moderate sequence identities between each other (approximately 27% between the catalytic units). However, Agl-ST is smaller in size and more thermally stable than the others. A disulfide bond that anchors the C-terminal coil of the β-helix fold, which is expected to contribute to thermal stability only exists in the catalytic unit of Agl-ST.