Development of a rapid and simple glycine analysis method using a stable glycine oxidase mutant

Metabolomic analysis reveals the biological characteristics of giant congenital melanocytic nevi

Giant congenital melanocytic nevi (GCMN) is a congenital cutaneous developmental deformity tumor that usually occurs at birth or in the first few weeks after birth, but its pathogenesis is still unclear. In this study, nuclear magnetic resonance-based metabolomics strategy was employed to evaluate the metabolic variations in serum and urine of the GCMN patients in order to understand its underlying biochemical mechanism and provide a potential intervention idea. Twenty-nine metabolites were observed to change significantly in serum and urine metabolomes, which are mainly involved in a variety of metabolic pathways including glyoxylate and dicarboxylate metabolism, TCA cycle and metabolisms of amino acids. The substantial cores of all the disturbed metabolic pathways are related to amino acid metabolism and carbohydrate metabolism and regulate the physiological state of the GCMN patients. Our results provide the physiological basis and physiological responses of GCMN and will be helpful for better understanding the molecular mechanisms of GCMN in future research.

Development of a plasma-free amino acid-based risk score for the incidence of cardiovascular diseases in a general population: The Nagahama study

BACKGROUND & AIMS

Levels of circulating amino acids (AAs) have been suggested to be associated with cardiovascular diseases (CVDs). This study aimed to develop a plasma-free amino acid (PFAA)-based CVD risk-prediction model in a general population.

METHODS

The study participants consisted of 9220 community residents (mean age, 53.2 years; standard deviation, 13.3 years). Circulating levels of 19 PFAAs were measured via high-performance liquid chromatography/electrospray ionization mass spectrometry. The incidence of CVDs was determined by reviewing participants' clinical records. The prediction model was developed using the Cox proportional hazards model with the brute force variable selection and then cross-validated.

RESULTS

During the 8.5-year follow-up, 220 CVD events were observed. Six AAs (alanine, citrulline, glycine, histidine, serine, and tyrosine) were identified as components of the prediction model, of which the C-index was 0.72. The association between the fourth quartile of the risk score calculated using the prediction model and the CVD events was independent of conventional risk factors (adjusted hazard ratio [HR], 1.9; 95 % confidence interval, 1.1-3.3). When examining crude relationships between conventional risk factors and the PFAA-based risk score by subgroup analyses, the association was significant for most subpopulations, men [crude HR = 6.4 (2.0-20.2)] and women [crude HR = 4.9 (2.6-9.3)], and individuals with [crude HR = 4.7 (2.5-8.9)] and without [crude HR = 7.2 (2.7-18.9)] lifestyle-related diseases, but not for older (≥70 years) participants [crude HR = 3.3 (0.8-13.5)]. The risk score successfully identified at-risk individuals [HR = 2.1 (1.2-3.5)] from participants who were classified as low risk by a conventional CVD risk score.

CONCLUSIONS

The PFAA-based risk score predicted CVD events independently of conventional risk factors.

Functional Characterization and Structural Modeling of a Novel Glycine Oxidase from Variovorax paradoxus Iso1

The N-acyl-d-amino acid amidohydrolase (N-d-AAase) of Variovorax paradoxus Iso1 can enantioselectively catalyze the zinc-assisted deacetylation of N-acyl-d-amino acids to yield consistent d-amino acids. A putative FAD-binding glycine/d-amino acid oxidase was located immediately upstream of the N-d-AAase gene. The gene encoding this protein was cloned into Escherichia coli BL21 (DE3)pLysS and overexpressed at 25°C for 6 h with 0.5 mM isopropyl β-d-1-thiogalactopyranoside induction. After purification, the tag-free recombinant protein was obtained. The enzyme could metabolize glycine, sarcosine, and d-alanine, but not l-amino acids or bulky d-amino acids. Protein modeling further supported these results, demonstrating that glycine, sarcosine, and d-alanine could fit into the pocket of the enzyme's activation site, while l-alanine and d-threonine were out of position. Therefore, this protein was proposed as a glycine oxidase, and we designated it VpGO. Interestingly, VpGO showed low sequence similarity to other well-characterized glycine oxidases. We found that VpGO and N-d-AAase were expressed on the same mRNA and could be transcriptionally induced by various N-acetyl-d-amino acids. Western blotting and zymography showed that both proteins had similar expression patterns in response to different types of inducers. Thus, we have identified a novel glycine oxidase that is co-regulated with N-d-AAase in an operon, and metabolizes N-acyl-d-amino acids in the metabolically versatile V. paradoxus Iso1. IMPORTANCE The Gram-negative bacterium Variovorax paradoxus has numerous metabolic capabilities, including the association with important catabolic processes and the promotion of plant growth. We had previously identified and characterized an N-acyl-d-amino-acid amidohydrolase (N-d-AAase) gene from the strain of V. paradoxus Iso1. The aim of this study was to isolate and characterize (both in vitro and in vivo) another potential gene found in the promoter region of this N-d-AAase gene. The protein was identified as a glycine oxidase, and the gene existed in an operon with N-d-AAase. The structural basis for its FAD-binding potential and substrate stereo-specificity were also elucidated. This study first reported a novel glycine oxidase from V. paradoxus. We believe that our study makes a significant contribution to the literature, because this enzyme has great potential for use as an industrial catalysis, as a biosensor, and in agricultural biotechnology.

Why Not Glycine Electrochemical Biosensors?

Glycine monitoring is gaining importance as a biomarker in clinical analysis due to its involvement in multiple physiological functions, which results in glycine being one of the most analyzed biomolecules for diagnostics. This growing demand requires faster and more reliable, while affordable, analytical methods that can replace the current gold standard for glycine detection, which is based on sample extraction with subsequent use of liquid chromatography or fluorometric kits for its quantification in centralized laboratories. This work discusses electrochemical sensors and biosensors as an alternative option, focusing on their potential application for glycine determination in blood, urine, and cerebrospinal fluid, the three most widely used matrices for glycine analysis with clinical meaning. For electrochemical sensors, voltammetry/amperometry is the preferred readout (10 of the 13 papers collected in this review) and metal-based redox mediator modification is the predominant approach for electrode fabrication (11 of the 13 papers). However, none of the reported electrochemical sensors fulfill the requirements for direct analysis of biological fluids, most of them lacking appropriate selectivity, linear range of response, and/or capability of measuring at physiological conditions. Enhanced selectivity has been recently reported using biosensors (with an enzyme element in the electrode design), although this is still a very incipient approach. Currently, despite the benefits of electrochemistry, only optical biosensors have been successfully reported for glycine detection and, from all the inspected works, it is clear that bioengineering efforts will play a key role in the embellishment of selectivity and storage stability of the sensing element in the sensor.