Analysis of free d-serine in mammals and its biological relevance

Development of a two-dimensional LC-MS/MS system for the determination of proline and 4-hydroxyproline enantiomers in biological and food samples

A two-dimensional LC-MS/MS system has been developed for the enantioselective determination of proline (Pro), cis-4-hydroxyproline (cis-4-Hyp) and trans-4-hydroxyproline (trans-4-Hyp) in a variety of biological samples. The amino acids were pre-column derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), and the NBD-derivatives were separated by a reversed-phase column (Singularity RP18) as their D plus L mixtures in the first dimension. The collected target fractions were then introduced into the second dimension where the enantiomers were separated by a Pirkle-type enantioselective column (Singularity CSP-001S) and determined by a tandem mass spectrometer (Triple Quad™ 5500). The method was validated by the standard amino acids and also by human plasma, and sufficient results were obtained for the calibration, precision and accuracy. The method was applied to human plasma and urine, bivalve tissues and fermented food/beverages. D-Pro was widely found in the human physiological fluids, bivalves and several fermented products. Although trans-4-D-Hyp was not found in all the tested samples, cis-4-D-Hyp was present in human urine and tissues of the ark shell, and further studies focusing on the origin and physiological significance of these D-enantiomers are expected.

Evaluation of Individual Variation of d-Amino Acids in Human Plasma by a Two-Dimensional LC-MS/MS System and Application to the Early Diagnosis of Chronic Kidney Disease

For the discovery of sensitive biomarkers of kidney function focusing on chiral amino acids, a multiple heart-cutting two-dimensional (2D) liquid chromatography-mass spectrometry (LC-MS)/MS system has been designed/developed. As the target analytes, alanine (Ala), aspartic acid, glutamic acid (Glu), leucine (Leu), lysine, methionine, phenylalanine (Phe), proline (Pro), serine (Ser), and valine were selected considering the presence of their d-forms in mammals. The 2D LC-MS/MS system consisted of the nonenantioselective reversed-phase separation of the target amino acids, the separations of the d- and l-enantiomers, and detection using MS/MS. Using the method, the plasma chiral amino acids, precolumn derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole, were isolated from other intrinsic substances, then determined without losing sensitivity by the fully automated whole-peak volume transfer operation from first to second dimension. In all of the tested plasma samples obtained from five healthy individuals and 15 patients with chronic kidney disease (CKD), the target chiral amino acids were determined without interference. In healthy individuals, the levels of all the tested d-amino acids were regulated in the low ranges. In contrast, the % d values of Glu, Leu, and Phe significantly increased with the progress of kidney dysfunction, besides the previously reported values of d-Ala, Pro, and Ser. Concerning Phe, the significant increase of the % d values (p < 0.05) was reported for the first time even in the mild CKD group compared to those of the healthy group; d-Phe might be a more sensitive marker than the previously reported d-forms. These results demonstrated the potential of these d-forms as the sensitive biomarkers of kidney function for the early diagnosis of CKD.

Two-dimensional LC-MS/MS and three-dimensional LC analysis of chiral amino acids and related compounds in real-world matrices

Amino acids normally have a chiral carbon and d/l-enantiomers are present. Due to the homochirality features on the present Earth, l-enantiomers are predominant in the living beings and the d-enantiomers are rare. Along with the progress and development of cutting edge analytical methods, several d-amino acids were found even in the higher animals including humans, and their biological functions and diagnostic values have also been reported. However, the amounts of these d-amino acids are much lower than the l-forms, and development/utilization of highly sensitive and selective methods are practically essential to avoid the disturbance from uncountable intrinsic substances. In the present review, multi-dimensional HPLC methods for the determination of chiral amino acids, especially two-dimensional LC-MS/MS and three-dimensional LC methods, and their applications to a variety of real-world matrices are summarized.

Integrated Microbiota and Metabolome Analysis to Assess the Effects of the Solid-State Fermentation of Corn-Soybean Meal Feed Using Compound Strains

Solid-state fermentation is known to improve plant-based feed nutritional quality; however, the association between microbes and metabolite production in fermented feed remains unclear. We inoculated corn-soybean-wheat bran (CSW) meal feed with Bacillus licheniformis Y5-39, Bacillus subtilis B-1, and lactic acid bacteria RSG-1. Then, 16S rDNA sequencing and untargeted metabolomic profiling were applied to investigate changes in the microflora and metabolites, respectively, and their integrated correlations during fermentation were assessed. The results indicated that trichloroacetic acid soluble protein levels showed a sharp increase, while glycinin and β-conglycinin levels showed a sharp decrease in the fermented feed, as confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Pediococcus, Enterococcus, and Lactobacillus were predominant in the fermented feed. Overall, 699 significantly different metabolites were identified before and after fermentation. Arginine and proline, cysteine and methionine, and phenylalanine and tryptophan metabolism were the key pathways, with arginine and proline metabolism being the most important pathway in the fermentation process. By analyzing the correlation between the microbiota and metabolite production, lysyl-valine and lysyl-proline levels were found to be positively correlated with Enterococcus and Lactobacillus abundance. However, Pediococcus was positively correlated with some metabolites contributing to nutritional status and immune function. According to our data, Pediococcus, Enterococcus, and Lactobacillus mainly participate in protein degradation, amino acid metabolism, and lactic acid production in fermented feed. Our results provide new insights into the dynamic changes in metabolism that occurred during the solid-state fermentation of corn-soybean meal feed using compound strains and should facilitate the optimization of fermentation production efficiency and feed quality.

Development and evaluation of a novel fluorescent chiral derivatization reagent DBD-S-M-Pro: first observation of four chiral amino acids in human hair

This study reports a novel fluorescent chiral derivatization reagent, 4-(N,N-dmethylaminosulfonyl)-2,1,3-benzoxadiazole-(2-succinimidoxy)-trans-2-methyl-L-proline (DBD-S-M-Pro), with a benzoxadiazole structure containing an N-hydroxysuccinimide activation group. DBD-S-M-Pro targets chiral amino-functional compounds under alkaline conditions without a condensation agent. Gradient elution was performed on a BEH C18 (100 × 2.1 mm, 1.7 μm) column with a mobile phase of 0.05% formic acid (FA) in 10 mM ammonium acetate (CH₃COONH₄) and 0.1% FA in acetonitrile or methanol. The efficiency of the chiral resolution was evaluated under excitation and emission wavelengths of 450 nm and 560 nm, respectively. The 19 chiral amino acids were separated in the range of 1.45-14.84. The resolutions of almost all DL-amino acids exceeded 1.5; the exceptions were serine (Ser) and lysine (Lys), with resolutions of 1.45 and 1.46, respectively. In addition, a new approach was devised for the simultaneous analysis of four chiral amino acids (DL-Glu, DL-Ala, DL-Val, and DL-Phe) in human hair. These amino acids were analyzed in the range of 12.5-400 pmol, with R² ≥ 0.9990, limits of detection (S/N = 3) of 4-10 pmol, and intraday and interday precisions of 0.57-6.23%. The average spikes in the hair recoveries were 89.76-111.54%, and the matrix effects were 92.47-102.40%. Next, the contents of free chiral amino acids in the hair samples of 10 healthy volunteers (five males and five females) were analyzed with this method, and the differences were compared. The developed DBD-S-M-Pro provides a novel strategy for the sensitive determination of free chiral amino acids in living organisms.

Isatoic anhydrides as novel inhibitors of monoamine oxidase

The monoamine oxidase (MAO) enzymes metabolise neurotransmitter amines in the central and peripheral tissues, and thereby contribute to the regulation of neurotransmission. Inhibitors of MAO modulate the levels of neurotransmitters in the central nervous system, and have been used for several decades for the treatment of depression and Parkinson's disease, while potential new therapeutic applications in other diseases such as prostate cancer and heart failure may exist. In the interest of discovering new classes of chemical compounds that potently inhibit the MAOs, the present study synthesises a series of ten isatoic anhydrides and evaluates their potential as in vitro inhibitors of human MAO-A and MAO-B. The isatoic anhydrides bear structural similarity to a series of 3,4-dihydro-2(1H)-quinolinones as well as to series of isatins and phthalimides that have been reported to act as potent MAO-B inhibitors. The results document that the isatoic anhydrides inhibit both MAO isoforms with the most potent inhibitors exhibiting IC₅₀ values of 0.010 µM (1b and 1h) and 0.0047 µM (1j) for MAO-A and MAO-B, respectively. Molecular docking suggests that isatoic anhydrides exhibit similar binding modes and interactions with MAO-A and MAO-B, which may explain their potent inhibition of both isoforms. It may be concluded that the isatoic anhydrides represent a new class of MAO inhibitors, while it is interesting to note that very few studies on the pharmacological actions of isatoic anhydrides have been reported. As a secondary aim, the isatoic anhydrides were also evaluated as potential inhibitors of d-amino acid oxidase (DAAO), acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE).

Distribution and evolution of the serine/aspartate racemase family in invertebrates. II. Frequent and widespread parallel evolution of aspartate racemase

Our previous studies showed that invertebrate animal serine racemase (SerR) and aspartate racemase (AspR) evolved from a common ancestral gene and are widely distributed. However, the overall molecular evolutionary background of these genes has remained unclear. In the present study we have cloned, expressed and characterized five SerR and three AspR genes from six invertebrate species. The coexistence of SerR and AspR paralogs has been observed in some species, and the presence of both SerR and AspR is here confirmed in the flatworm Macrostomum lignano, the feather star Anneissia japonica, the ark shell Anadara broughtonii and the sea hare Aplysia californica. Comparison of the gene structures revealed the evolution of SerR and AspR. The ancestral species of metazoans probably had a single SerR gene, and the first gene duplication in the common ancestor species of the eumetazoans occurred after the divergence of porifera and eumetazoans, yielding two SerR genes. Most eumetazoans lost one of the two SerR genes, while the echinoderm Anneissia japonica retained both genes. Furthermore, it is clear that invertebrate AspR genes arose through parallel evolution by duplication of the SerR gene followed by substitution of amino acid residues necessary for substrate recognition in multiple lineages.

Separation and detection of D-/L-serine by conventional HPLC

D-serine has a role as an endogenous allosteric agonist of N-methyl-D-aspartate (NMDA) receptor in the mammalian brain. In this study, we present a detailed description of our method that measures D-/L-serine by using conventional high performance liquid chromatography (HPLC). • We reacted D-serine and L-serine with ortho-phthalaldehyde (OPA) and N-acetyl-L-cysteine (NAC) to form diastereomeric isoindole derivatives, then we separated and detected them by conventional reversed phase HPLC with electrochemical detector (ECD). • We present typical measurement data of rat brain homogenate as an example of a convenient, appropriate method for measuring brain concentrations of D-serine. • Since many peaks appear in biological samples, we confirmed that the peaks were derived from serine by treating the sample with D-amino oxidase and catalase to decompose D-serine. As a results, one peak disappeared, suggesting that it is derived from D-serine.

Effects of Quinolinate-Induced Lesion of the Medial Prefrontal Cortex on Prefrontal and Striatal Concentrations of D-Serine in the Rat

D-Serine has been shown to play an important role in the expression and control of a variety of brain functions by acting as the endogenous coagonist for the N-methyl-D-aspartate type glutamate receptor (NMDAR), at least, in the forebrain. To obtain further insight into the still debatable cellular localization of the D-amino acid, we have examined the effects of the selective destruction of the neuronal cell bodies by quinolinate on the tissue or extracellular D-serine concentrations in the medial prefrontal cortex of the rat. A local quinolinate infusion into the bilateral medial prefrontal cortex produced a cortical lesion with a marked (- 65%) and non-significant alteration (- 5%) in the cortical and striatal tissue D-serine concentrations, respectively, 7 days post-infusion. In vivo microdialysis experiments in the right prefrontal lesion site 9 days after the quinolinate application revealed that the basal extracellular D-serine levels were also dramatically reduced (- 64%). A prominent reduction in the tissue levels of GABA in the interneurons of the prefrontal cortex (- 78%) without significant changes in those in the striatum (+ 12%) verified that a major lesion part was confined to the cortical portion. The lack of a significant influence of the prefrontal quinolinate lesion on its dopamine concentrations in the mesocortical dopamine projections suggests that the nerve terminals and axons in the lesion site may be spared. These findings are consistent with the perikarya-selective nature of the present quinolinate-induced lesion and further support the view that neuronal cell bodies of intrinsic neurons in the prefrontal cortical region contain substantial amounts of D-serine, which may sustain the basal extracellular concentrations of D-serine.

Serine Racemase Expression by Striatal Neurons

D-serine is synthesized by serine racemase (SR) and is a co-agonist at forebrain N-methyl-D-aspartate receptors (NMDARs). D-serine and SR are expressed primarily in neurons, but not in quiescent astrocytes. In this study, we examined the localization of D-serine and SR in the mouse striatum and the effects of genetically silencing SR expression in GABAergic interneurons (iSR-/-). iSR-/- mice had substantially reduced SR expression almost exclusively in striatum, but only exhibited marginal D-serine reduction. SR positive cells in the striatum showed strong co-localization with dopamine- and cyclic AMP-regulated neuronal phosphoprotein (DARPP32) in wild type mice. Transgenic fluorescent reporter mice for either the D1 or D2 dopamine receptors exhibited a 65:35 ratio for co-localization with D1and D2 receptor positive cells, respectively. These results indicate that GABAergic medium spiny neurons receiving dopaminergic inputs in striatum robustly and uniformly express SR. In behavioral tests, iSR-/- mice showed a blunted response to the hedonic and stimulant effects of cocaine, without affecting anxiety-related behaviors. Because the cocaine effects have been shown in the constitutive SR-/- mice, the restriction of the blunted response to cocaine to iSR-/- mice reinforces the conclusion that D-serine in striatal GABAergic neurons plays an important role in mediating dopaminergic stimulant effects. Results in this study suggest that SR in striatal GABAergic neurons is synthesizing D-serine, not as a glutamatergic co-transmitter, but rather as an autocrine whereby the GABAergic neurons control the excitability of their NMDARs by determining the availability of the co-agonist, D-serine.

d-Serine induces distinct transcriptomes in diverse Escherichia coli pathotypes

Appropriate interpretation of environmental signals facilitates niche specificity in pathogenic bacteria. However, the responses of niche-specific pathogens to common host signals are poorly understood. d-Serine (d-ser) is a toxic metabolite present in highly variable concentrations at different colonization sites within the human host that we previously found is capable of inducing changes in gene expression. In this study, we made the striking observation that the global transcriptional response of three Escherichia coli pathotypes - enterohaemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC) and neonatal meningitis-associated E. coli (NMEC) - to d-ser was highly distinct. In fact, we identified no single differentially expressed gene common to all three strains. We observed the induction of ribosome-associated genes in extraintestinal pathogens UPEC and NMEC only, and the induction of purine metabolism genes in gut-restricted EHEC, and UPEC indicating distinct transcriptional responses to a common signal. UPEC and NMEC encode dsdCXA - a genetic locus required for detoxification and hence normal growth in the presence of d-ser. Specific transcriptional responses were induced in strains accumulating d-ser (WT EHEC and UPEC/NMEC mutants lacking the d-ser-responsive transcriptional activator DsdC), corroborating the notion that d-ser is an unfavourable metabolite if not metabolized. Importantly, many of the UPEC-associated transcriptome alterations correlate with published data on the urinary transcriptome, supporting the hypothesis that d-ser sensing forms a key part of urinary niche adaptation in this pathotype. Collectively, our results demonstrate distinct pleiotropic responses to a common metabolite in diverse E. coli pathotypes, with important implications for niche selectivity.

Simultaneous Determination of D-amino Acids in Rat Urine by Highperformance Liquid Chromatography-tandem Mass Spectrometry Method: Application to Investigate the Clinical Value of D-amino Acids in the Early Diagnosis of Alzheimer’s Disease

Background:

D-amino acids are closely related to the development and progression of Alzheimer's disease (AD) and are expected as the novel biomarkers for AD diagnosis.

Objective:

The aim was to investigate the potential clinical value of D-amino acids for Alzheimer's disease.

Methods:

A simple and sensitive HPLC/MS-MS method was developed for the simultaneous determination of D-alanine, D-glutamine, D-proline and D-serine in rat urine. The samples were firstly pretreated by methanol, then derivatized by 7-chloro-4-nitrobenzoxadiazole with Fudosteine as internal standard, enantioseparated on Sumichiral OA-2500S column, using a mobile phase composed of acetonitrile- methanol (50:50, v/v) containing 0.5% formic acid, and detected with 4000 Qtrap MS/MS in electrospray-ionization source by negative ion mode.

Results:

The established method was successfully applied to determine the D-amino acid levels in rat urine from 20 Alzheimer's disease rats and 20 age-matched normal controls. The mean levels of Damino acids in the urine of Alzheimer's disease rats were all significantly lower than those in normal controls. Based on the contents of D-amino acids, the distinction model between Alzheimer's disease rats and normal controls was established by the Bayesian discriminant analysis.

Conclusion:

The relationship between Alzheimer's disease and D-amino acids revealed that D-amino acids would be potential biomarkers for Alzheimer’s disease.

Genetic variation of rs12918566 affects GRIN2A expression and is associated with spontaneous movement response during sevoflurane anesthesia induction

N-methyl-D-aspartate (NMDA) receptors mediate excitatory neurotransmission in the nervous system and are preferentially inhibited by general anesthetics such as sevoflurane. Spontaneous movement is a common complication during sevoflurane anesthesia induction and seriously affects operations. In this study, we investigated the relationship between NMDA polymorphisms and spontaneous movement during sevoflurane induction. This prospective clinical study enrolled 393 patients undergoing sevoflurane anesthesia as part of their surgical routine. In the GRIN1, GRIN2A, and GRIN2B genes, 13 polymorphisms that form a heteromeric complex as part of the NMDA receptor were selected using Haploview and genotyped using matrix-assisted laser desorption ionization-time of flight mass spectrometry MassARRAY. Both RNAfold and Genotype-Tissue Expression portals were used to identify gene expression profiles. Our data showed that 35.8% of subjects exhibited spontaneous movement. The GRIN2A rs12918566 polymorphism was associated with spontaneous movement during sevoflurane induction. A logistic regression analysis of additive, dominant, and recessive models indicated a significant association (odds ratio [OR] (95% confidence limit [CI]): 0.58 (0.42-0.80), p = .00086; OR (95% CI): 0.51 (0.31-0.84), p = .0075, and OR (95% CI): 0.47 (0.27-0.81), p = .0060, respectively). After false discovery rate (FDR) correction, the additive model was still significant with a P_FDR =0.010. Bioinformatics demonstrated that the rs12918566 genomic variation affected GRIN2A expression in brain tissue. We also revealed that GRIN2A rs12918566 was significantly associated with spontaneous movement during sevoflurane induction. We believe the NMDA receptor plays an important role in regulating the anesthetic effects of sevoflurane.

Identification of an l-serine/l-threonine dehydratase with glutamate racemase activity in mammals

Recent investigations have shown that multiple d-amino acids are present in mammals and these compounds have distinctive physiological functions. Free d-glutamate is present in various mammalian tissues and cells and in particular, it is presumably correlated with cardiac function, and much interest is growing in its unique metabolic pathways. Recently, we first identified d-glutamate cyclase as its degradative enzyme in mammals, whereas its biosynthetic pathway in mammals is unclear. Glutamate racemase is a most probable candidate, which catalyzes interconversion between d-glutamate and l-glutamate. Here, we identified the cDNA encoding l-serine dehydratase-like (SDHL) as the first mammalian clone with glutamate racemase activity. This rat SDHL had been deposited in mammalian databases as a protein of unknown function and its amino acid sequence shares ∼60% identity with that of l-serine dehydratase. Rat SDHL was expressed in Escherichia coli, and the enzymatic properties of the recombinant were characterized. The results indicated that rat SDHL is a multifunctional enzyme with glutamate racemase activity in addition to l-serine/l-threonine dehydratase activity. This clone is hence abbreviated as STDHgr. Further experiments using cultured mammalian cells confirmed that d-glutamate was synthesized and l-serine and l-threonine were decomposed. It was also found that SDHL (STDHgr) contributes to the homeostasis of several other amino acids.

Factors regulating serine racemase and d-amino acid oxidase expression in the mouse striatum

d-Serine plays an important role in modulating N-methyl-d-aspartate receptor (NMDAR) neurotransmission in the mammalian brain by binding to the receptor's glycine modulatory site (GMS). The cytosolic enzyme serine racemase (SR) converts L-serine to d-serine, while the peroxisomal enzyme d-amino acid oxidase (DAAO) catalyzes the breakdown of d-serine. Although it is important to understand how the activities of SR and DAAO regulate d-serine levels, very little is known about the mechanisms that regulate the expression of SR and DAAO. In this study, we investigated whether the different centrally active drugs affect the expression of SR and DAAO in adult mouse brain. We found that the NMDAR antagonist, MK801, and cocaine, psychotropic drugs that both augment glutamate release, reduce the expression of SR and DAAO. This regulation is brain region selective, and in the case of cocaine, is reversed in part byα-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) antagonist 2,3-dihydroxy-6-nitro-7-sulfamoyl-benzo[f]quinoxaline-2,3-dione (NBQX). However, d-serine and antipsychotics do not regulate SR and DAAO protein levels. In a genetic model of SR disruption, we found that DAAO expression was unaltered in SR conditional knockout mice, in which tissue d-serine content remains fairly stable despite marked reduction in SR expression. This study reveals a new mechanism by which AMPAR activity could regulate NMDAR function via d-serine availability.

d-Serine and d-Alanine Regulate Adaptive Foraging Behavior in Caenorhabditis elegans via the NMDA Receptor

d-Serine (d-Ser) is a coagonist for NMDA-type glutamate receptors and is thus important for higher brain function. d-Ser is synthesized by serine racemase and degraded by d-amino acid oxidase. However, the significance of these enzymes and the relevant functions of d-amino acids remain unclear. Here, we show that in the nematode Caenorhabditis elegans, the serine racemase homolog SERR-1 and d-amino acid oxidase DAAO-1 control an adaptive foraging behavior. Similar to many organisms, C. elegans immediately initiates local search for food when transferred to a new environment. With prolonged food deprivation, the worms exhibit a long-range dispersal behavior as the adaptive foraging strategy. We found that serr-1 deletion mutants did not display this behavior, whereas daao-1 deletion mutants immediately engaged in long-range dispersal after food removal. A quantitative analysis of d-amino acids indicated that d-Ser and d-alanine (d-Ala) are both synthesized and suppressed during food deprivation. A behavioral pharmacological analysis showed that the long-range dispersal behavior requires NMDA receptor desensitization. Long-term pretreatment with d-Ala, as well as with an NMDA receptor agonist, expanded the area searched by wild-type worms immediately after food removal, whereas pretreatment with d-Ser did not. We propose that d-Ser and d-Ala are endogenous regulators that cooperatively induce the long-range dispersal behavior in C. elegans through actions on the NMDA receptor.SIGNIFICANCE STATEMENT In mammals, d-serine (d-Ser) functions as an important neuromodulator of the NMDA-type glutamate receptor, which regulates higher brain functions. In Caenorhabditis elegans, previous studies failed to clearly define the physiological significance of d-Ser, d-alanine (d-Ala), and their metabolic enzymes. In this study, we found that these d-amino acids and their associated enzymes are active during food deprivation, leading to an adaptive foraging behavior. We also found that this behavior involved NMDA receptor desensitization.

Determination of phenylalanine enantiomers in the plasma and urine of mammals and ᴅ-amino acid oxidase deficient rodents using two-dimensional high-performance liquid chromatography

A two-dimensional (2D) HPLC system focusing on the determination of phenylalanine (Phe) enantiomers in mammalian physiological fluids has been developed. ᴅ-Phe is indicated to have potential values as a disease biomarker and therapeutic molecule in several neuronal and metabolic disorders, thus the regulation of ᴅ-Phe in mammals is a matter of interest. However, the precise determination of amino acid enantiomers is difficult in complex biological samples, and the development of an analytical method with practically acceptable sensitivity, selectivity and throughput is expected. In the present study, a 2D-HPLC system equipped with a reversed-phase column in the 1st dimension and an enantioselective column in the 2nd dimension has been designed, following the fluorescence derivatization of the target amino acid enantiomers with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F). The analytical method was validated using both plasma and urine samples, and successfully applied to human, rat and mouse fluids. Trace levels of ᴅ-Phe were determined in the plasma, and the %ᴅ values were around 0.1% for all species. In the urine, relatively large amounts of ᴅ-Phe were observed, and the %ᴅ values for humans, rats and mice were 3.99, 1.76 and 5.25%, respectively. The relationships between the enzymatic activity of ᴅ-amino acid oxidase (DAO) and the amounts of intrinsic ᴅ-Phe have also been clarified, and high ᴅ-Phe amounts were observed (around 0.3% in the plasma and around 50% in the urine) in the DAO deficient rats and mice.

A colorimetric assay method for measuring d-glutamate cyclase activity

In mammals, metabolism of free d-glutamate is regulated by d-glutamate cyclase (DGLUCY), which reversibly converts d-glutamate to 5-oxo-d-proline and H₂O. Metabolism of these d-amino acids by DGLUCY is thought to regulate cardiac function. In this study, we established a simple, accurate, and sensitive colorimetric assay method for measuring DGLUCY activity. To this end, we optimized experimental procedures for derivatizing 5-oxo-d-proline with 2-nitrophenylhydrazine hydrochloride. 5-Oxo-d-proline was derivatized with 2-nitrophenylhydrazine hydrochloride in the presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide as a catalyst to generate the acid hydrazides, whose levels were then determined using a colorimetric method. Under optimized conditions, we examined the sensitivity and accuracy of the colorimetric method and compared our technique with other methods by high-performance liquid chromatography with ultraviolet-visible or fluorescence detection. Moreover, we assessed the suitability of this colorimetric method for measuring DGLUCY activity in biological samples. Our colorimetric method could determine DGLUCY activity with adequate validity and reliability. This method will help to elucidate the relationship among DGLUCY activity, the physiological and pathological roles of d-glutamate and 5-oxo-d-proline, and cardiac function.

Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes

Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.

The effect of L-theanine and S-ketamine on d-serine cellular uptake

Decreased extracellular level of d-Serine (D-Ser), a co-agonist of the N-methyl-d-aspartate (NMDA) receptors was connected to receptor hypofunction in the brain and the related deficit of cognitive functions. Extracellular D-Ser concentration is modulated by ASCT neutral amino acid transporters. L-Theanine (L-Tea), a neutral amino acid component of green tea was reported to improve cognitive functions. We thus intended to investigate the possible inhibitory effect of L-Tea on the D-Ser uptake of SH-SY5Y neuroblastoma cells, which was previously found as a good model of D-Ser transport into astrocytes. Cells were incubated with D-Ser and various concentrations of L-Tea or the reference compound S-ketamine (S-Ket). The effect on the uptake was assessed by measuring the intracellular D-Ser concentration using a capillary electrophoresis - laser induced fluorescence detection method. L-Tea competitively inhibited D-Ser uptake into SH-SY5Y cells with an IC50 value of 9.68 mM. Having previously described as an inhibitor of ASCT-2 transporter, S-Ket was intended to be used as a positive control. However, no acute inhibition of D-Ser transport by S-Ket was observed. Its long-term effect on the transport was also examined. No significant difference in D-Ser uptake in control and S-Ket-treated cells was found after 72 h treatment, although the intracellular D-Ser content of the 50 μM S-Ket pre-treated cells was significantly higher. L-Tea was found to be a weak competitive inhibitor of the ASCT transporters, while S-Ket did not directly affect D-Ser uptake or modify the uptake kinetics after a long-term incubation period.

Mechanism of eukaryotic serine racemase-catalyzed serine dehydration

Eukaryotic serine racemase (SR) is a pyridoxal 5'-phosphate enzyme belonging to the Fold-type II group, which catalyzes serine racemization and is responsible for the synthesis of D-Ser, a co-agonist of the N-methyl-d-aspartate receptor. In addition to racemization, SR catalyzes the dehydration of D- and L-Ser to pyruvate and ammonia. The bifuctionality of SR is thought to be important for D-Ser homeostasis. SR catalyzes the racemization of D- and L-Ser with almost the same efficiency. In contrast, the rate of L-Ser dehydration catalyzed by SR is much higher than that of D-Ser dehydration. This has caused the argument that SR does not catalyze the direct D-Ser dehydration and that D-Ser is first converted to L-Ser, then dehydrated. In this study, we investigated the substrate and solvent isotope effect of dehydration of D- and L-Ser catalyzed by SR from Dictyostelium discoideum (DdSR) and demonstrated that the enzyme catalyzes direct D-Ser dehydration. Kinetic studies of dehydration of four Thr isomers catalyzed by D. discoideum and mouse SRs suggest that SR discriminates the substrate configuration at C3 but not at C2. This is probably the reason for the difference in efficiency between L- and D-Ser dehydration catalyzed by SR.

Biochemical characterization of d-aspartate oxidase from Caenorhabditis elegans: its potential use in the determination of free d-glutamate in biological samples

d-Aspartate oxidase (DDO) is a flavin adenine dinucleotide (FAD)-containing flavoprotein that stereospecifically acts on acidic d-amino acids (i.e., free d-aspartate and d-glutamate). Mammalian DDO, which exhibits higher activity toward d-aspartate than d-glutamate, is presumed to regulate levels of d-aspartate in the body and is not thought to degrade d-glutamate in vivo. By contrast, three DDO isoforms are present in the nematode Caenorhabditis elegans, DDO-1, DDO-2, and DDO-3, all of which exhibit substantial activity toward d-glutamate as well as d-aspartate. In this study, we optimized the Escherichia coli culture conditions for production of recombinant C. elegans DDO-1, purified the protein, and showed that it is a flavoprotein with a noncovalently but tightly attached FAD. Furthermore, C. elegans DDO-1, but not mammalian (rat) DDO, efficiently and selectively degraded d-glutamate in addition to d-aspartate, even in the presence of various other amino acids. Thus, C. elegans DDO-1 might be a useful tool for determining these acidic d-amino acids in biological samples.

Decreased d-Serine Levels Prevent Retinal Ganglion Cell Apoptosis in a Glaucomatous Animal Model

Purpose

The purpose of this study was to determine d-Serine and d-Serine synthetase serine racemase (SR) expression and whether decreased d-Serine expression has protective effects on retinal ganglion cells (RGCs) in a glaucomatous animal model.

Methods

The rat chronic intraocular hypertension (COH) model was generated as a glaucomatous animal model by cauterizing three episcleral veins. Quantitative analysis of RGC survival was determined by the counting of retrograde FluoroGold-labeled RGCs. The level of d-Serine in the retinas and aqueous humor was determined by Ultra High Performance Liquid Chromatography coupled to triple-quadrupole Mass Spectrometry (UHPLC-MS/MS). Retinal expression of serine racemase (SR) protein was determined by immunohistochemistry and Western blot analysis. The TUNEL assay was used to detect cell apoptosis.

Results

The content of d-Serine increased significantly in the glaucomatous retina of the COH model 2 weeks after surgery compared with the control retina. d-Serine synthetase SR expression in the right glaucomatous eye increased slightly after surgery compared with that in the left control eye and remained at this high level for 6 weeks after surgery. SR-positive cells were located mainly in the ganglion cell layer (GCL) of the retina. d-Amino acid oxidase (DAAO) treatment significantly increased RGC survival in the glaucomatous eyes, and the TUNEL assay was used to confirm that DAAO reduced the number of TUNEL-positive cells in glaucomatous eyes. However, excess d-Serine could not exacerbate RGC loss in the COH model.

Conclusions

Increased d-Serine and SR expressions in the retina of the COH model were detected. DAAO treatment significantly increased RGC survival in the glaucomatous eyes. These results suggest that decreased d-Serine expression has protective effects on RGCs.

High-Throughput LC-MS/MS Method for Chiral Amino Acid Analysis Without Derivatization

D-Amino acids have recently attracted much attention in various research fields including medical, clinical, and food industry due to their important biological functions that differ from L-amino acid. Most chiral amino acid separation techniques require complicated derivatization procedures in order to achieve the desirable chromatographic behavior and detectability. This chapter describes a highly sensitive analytical method for the enantioseparation of chiral amino acids without any derivatization process using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The method allows the simultaneous analysis of 18 D-amino acids with high sensitivity and reproducibility. Additionally, this chapter also focuses on the application of the method to real samples for the quantification of targeted amino acids.

Artificial Thermostable D-Amino Acid Dehydrogenase: Creation and Application

Many kinds of NAD(P)⁺-dependent L-amino acid dehydrogenases have been so far found and effectively used for synthesis of L-amino acids and their analogs, and for their sensing. By contrast, similar biotechnological use of D-amino acid dehydrogenase (D-AADH) has not been achieved because useful D-AADH has not been found from natural resources. Recently, using protein engineering methods, an NADP⁺-dependent D-AADH was created from meso-diaminopimelate dehydrogenase (meso-DAPDH). The artificially created D-AADH catalyzed the reversible NADP⁺-dependent oxidative deamination of D-amino acids to 2-oxo acids. The enzyme, especially thermostable one from thermophiles, was efficiently applicable to synthesis of D-branched-chain amino acids (D-BCAAs), with high yields and optical purity, and was useful for the practical synthesis of ¹³C- and/or ¹⁵N-labeled D-BCAAs. The enzyme also made it possible to assay D-isoleucine selectively in a mixture of isoleucine isomers. Analyses of the three-dimensional structures of meso-DAPDH and D-AADH, and designed mutations based on the information obtained made it possible to markedly enhance enzyme activity and to create D-AADH homologs with desired reactivity profiles. The methods described here may be an effective approach to artificial creation of biotechnologically useful enzymes.

Structural and enzymatic properties of mammalian d-glutamate cyclase

d-Glutamate cyclase (DGLUCY) is a unique enzyme that reversibly converts free d-glutamate to 5-oxo-d-proline and H₂O. Mammalian DGLUCY is highly expressed in the mitochondrial matrix in the heart, and its downregulation disrupts d-glutamate and/or 5-oxo-d-proline levels, contributing to the onset and/or exacerbation of heart failure. However, detailed characterisation of DGLUCY has not yet been performed. Herein, the structural and enzymatic properties of purified recombinant mouse DGLUCY were examined. The results revealed a dimeric oligomerisation state, and both d-glutamate-to-5-oxo-d-proline and 5-oxo-d-proline-to-d-glutamate reactions were catalysed in a stereospecific manner. Catalytic activity is modulated by divalent cations and nucleotides including ATP and ADP. Interestingly, the presence of Mn²⁺ completely abolished the 5-oxo-d-proline-to-d-glutamate reaction but stimulated the d-glutamate-to-5-oxo-d-proline reaction. The optimum pH is ∼8.0, similar to that in the mitochondrial matrix, and the catalytic efficiency for d-glutamate is markedly higher than that for 5-oxo-d-proline. These findings suggest that DGLUCY functions as a metalloenzyme that degrades d-glutamate in the mitochondrial matrix in mammalian cells. The results also provide insight into the correlation between DGLUCY enzyme activity and the physiological and pathological roles of d-glutamate and 5-oxo-d-proline in cardiac function, which is of relevance to the risk of onset of heart failure.

Enantioselective micellar electrokinetic chromatography of dl-amino acids using (+)-1-(9-fluorenyl)-ethyl chloroformate derivatization and UV-induced fluorescence detection

Chiral analysis of dl-amino acids was achieved by micellar electrokinetic chromatography coupled with UV-excited fluorescence detection. The fluorescent reagent (+)-1-(9-fluorenyl)ethyl chloroformate was employed as chiral amino acid derivatizing agent and sodium dodecyl sulfate served as pseudo-stationary phase for separating the formed amino acid diastereomers. Sensitive analysis of (+)-1-(9-fluorenyl)ethyl chloroformate-amino acids was achieved applying a xenon-mercury lamp for ultraviolet excitation, and a spectrograph and charge-coupled device for wavelength-resolved emission detection. Applying signal integration over a 30 nm emission wavelength interval, signal-to-noise ratios for derivatized amino acids were up to 23 times higher as obtained using a standard photomultiplier for detection. The background electrolyte composition (electrolyte, pH, sodium dodecyl sulfate concentration, and organic solvent) was studied in order to attain optimal chemo- and enantioseparation. Enantioseparation of 12 proteinogenic dl-amino acids was achieved with chiral resolutions between 1.2 and 7.9, and detection limits for most derivatized amino acids in the 13-60 nM range (injected concentration). Linearity (coefficients of determination > 0.985) and peak-area and migration-time repeatabilities (relative standard deviations lower than 2.6 and 1.9%, respectively) were satisfactory. The employed fluorescence detection system provided up to 100-times better signal-to-noise ratios for (+)-1-(9-fluorenyl)ethyl chloroformate-amino acids than ultraviolet absorbance detection, showing good potential for d-amino acid analysis.

Enantioselective and simultaneous determination of lactate and 3-hydroxybutyrate in human plasma and urine using a narrow-bore online two-dimensional high-performance liquid chromatography system

For the enantioselective and simultaneous analysis of lactate and 3-hydroxybutyrate, a validated online two-dimensional high-performance liquid chromatography system using 4-nitro-7-piperazino-2,1,3-benzoxadiazole as a fluorescent derivatization reagent has been developed. For the reversed-phase separation in the first dimension, a Capcell Pak C18 ACR column (1.5 × 250 mm, particle size 3 μm) was used, and the target fractions were isolated by their hydrophobicity. In the second dimension, a polysaccharide-coated enantioselective column, Chiralpak AD-H (2.0 × 250 mm, 5 μm), was used. The system was validated by the calibration curve, intraday precision, interday precision, and accuracy using standards and real human samples, and satisfactory results were obtained. The present method was applied to human plasma and urine, and in the plasma, trace amounts of d-lactate (8.4 μM) and l-3-hydroxybutyrate (1.0 μM), besides high levels of l-lactate (860.9 μM) and d-3-hydroxybutyrate (59.4 μM), were successfully determined. In urine, trace levels of d-lactate (3.7 μM), d-3-hydroxybutyrate (2.3 μM), and l-3-hydroxybutyrate (3.3 μM) in addition to a relatively large amount of l-lactate (15.4 μM) were observed. The present online two-dimensional high-performance liquid chromatography system is useful for the simultaneous determination of all the lactate and 3-hydroxybutyrate enantiomers in human physiological fluids, and further clinical applications are ongoing.

d-Amino acids in molecular evolution in space - Absolute asymmetric photolysis and synthesis of amino acids by circularly polarized light

Living organisms on the Earth almost exclusively use l-amino acids for the molecular architecture of proteins. The biological occurrence of d-amino acids is rare, although their functions in various organisms are being gradually understood. A possible explanation for the origin of biomolecular homochirality is the delivery of enantioenriched molecules via extraterrestrial bodies, such as asteroids and comets on early Earth. For the asymmetric formation of amino acids and their precursor molecules in interstellar environments, the interaction with circularly polarized photons is considered to have played a potential role in causing chiral asymmetry. In this review, we summarize recent progress in the investigation of chirality transfer from chiral photons to amino acids involving the two major processes of asymmetric photolysis and asymmetric synthesis. We will discuss analytical data on cometary and meteoritic amino acids and their potential impact delivery to the early Earth. The ongoing and future ambitious space missions, Hayabusa2, OSIRIS-REx, ExoMars 2020, and MMX, are scheduled to provide new insights into the chirality of extraterrestrial organic molecules and their potential relation to the terrestrial homochirality. This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.

Detection and quantification of d-amino acid residues in peptides and proteins using acid hydrolysis

Biomolecular homochirality refers to the assumption that amino acids in all living organisms were believed to be of the l-configuration. However, free d-amino acids are present in a wide variety of organisms and d-amino acid residues are also found in various peptides and proteins, being generated by enzymatic or non-enzymatic isomerization. In mammals, peptides and proteins containing d-amino acids have been linked to various diseases, and they act as novel disease biomarkers. Analytical methods capable of precisely detecting and quantifying d-amino acids in peptides and proteins are therefore important and useful, albeit their difficulty and complexity. Herein, we reviewed conventional analytical methods, especially 0h extrapolating method, and the problems of this method. For the solution of these problems, we furthermore described our recently developed, sensitive method, deuterium-hydrogen exchange method, to detect innate d-amino acid residues in peptides and proteins, and its applications to sample ovalbumin. This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.

Involvement of neuronal and glial activities in control of the extracellular d-serine concentrations by the AMPA glutamate receptor in the mouse medial prefrontal cortex

It has been well accepted that d-serine may be an exclusive endogenous coagonist for the N-methyl-d-aspartate (NMDA)-type glutamate receptor in mammalian forebrain regions. We have recently found by using an in vivo dialysis method that an intra-medial prefrontal cortex infusion of S-α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (S-AMPA), a selective AMPA-type glutamate receptor agonist, causes a reduction in the extracellular levels of d-serine in a calcium-permeable AMPA receptor antagonist-sensitive manner. The inhibitory influence by the AMPA receptor on the extracellular d-serine, however, contradicts the data obtained from in vitro experiments that the AMPA receptor stimulation leads to facilitation of the d-serine liberation. This discrepancy appears to be due to the different cell setups between the in vivo and in vitro preparations. From the viewpoints of the previous reports indicating (1) the neuronal presence of d-serine synthesizing enzyme, serine racemase, and d-serine-like immunoreactivity and (2) the same high tissue concentrations of d-serine in the glia-enriched white matter and in the neuron-enriched gray matter of the mammalian neocortex, we have now investigated in the mouse medial prefrontal cortex, the effects of attenuation of neuronal and glial activities, by tetrodotoxin or fluorocitrate, respectively, on the S-AMPA-induced downregulation of the extracellular d-serine contents. In vivo dialysis studies revealed that a local infusion of tetrodotoxin or fluorocitrate eliminated the ability of S-AMPA given intra-cortically to cause a significant decrease in the dialysate concentrations of d-serine without affecting the elevating effects of S-AMPA on those of glycine, another intrinsic coagonist for the NMDA receptor. These findings suggest that the control by the AMPA receptor of the extracellular d-serine levels could be modulated by the neuronal and glial activities in the prefrontal cortex. It cannot be excluded that fluorocitrate would indirectly alter the modulation by changing synaptic neurotransmission via glial activity attenuation as previously reported.