1
|
Wiriyasermkul P, Moriyama S, Suzuki M, Kongpracha P, Nakamae N, Takeshita S, Tanaka Y, Matsuda A, Miyasaka M, Hamase K, Kimura T, Mita M, Sasabe J, Nagamori S. <sc>A</sc> multi-hierarchical approach reveals <sc>d</sc>-serine as a hidden substrate of sodium-coupled monocarboxylate transporters. eLife 2024; 12:RP92615. [PMID: 38650461 PMCID: PMC11037918 DOI: 10.7554/elife.92615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Transporter research primarily relies on the canonical substrates of well-established transporters. This approach has limitations when studying transporters for the low-abundant micromolecules, such as micronutrients, and may not reveal physiological functions of the transporters. While d-serine, a trace enantiomer of serine in the circulation, was discovered as an emerging biomarker of kidney function, its transport mechanisms in the periphery remain unknown. Here, using a multi-hierarchical approach from body fluids to molecules, combining multi-omics, cell-free synthetic biochemistry, and ex vivo transport analyses, we have identified two types of renal d-serine transport systems. We revealed that the small amino acid transporter ASCT2 serves as a d-serine transporter previously uncharacterized in the kidney and discovered d-serine as a non-canonical substrate of the sodium-coupled monocarboxylate transporters (SMCTs). These two systems are physiologically complementary, but ASCT2 dominates the role in the pathological condition. Our findings not only shed light on renal d-serine transport, but also clarify the importance of non-canonical substrate transport. This study provides a framework for investigating multiple transport systems of various trace micromolecules under physiological conditions and in multifactorial diseases.
Collapse
Affiliation(s)
- Pattama Wiriyasermkul
- Center for SI Medical Research, The Jikei University School of MedicineTokyoJapan
- Department of Laboratory Medicine, The Jikei University School of MedicineTokyoJapan
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical UniversityNaraJapan
| | - Satomi Moriyama
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical UniversityNaraJapan
| | - Masataka Suzuki
- Department of Pharmacology, Keio University School of MedicineTokyoJapan
| | - Pornparn Kongpracha
- Center for SI Medical Research, The Jikei University School of MedicineTokyoJapan
- Department of Laboratory Medicine, The Jikei University School of MedicineTokyoJapan
| | - Nodoka Nakamae
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical UniversityNaraJapan
| | - Saki Takeshita
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical UniversityNaraJapan
| | - Yoko Tanaka
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical UniversityNaraJapan
| | - Akina Matsuda
- Department of Pharmacology, Keio University School of MedicineTokyoJapan
| | - Masaki Miyasaka
- Center for SI Medical Research, The Jikei University School of MedicineTokyoJapan
- Department of Laboratory Medicine, The Jikei University School of MedicineTokyoJapan
| | - Kenji Hamase
- Graduate School of Pharmaceutical Sciences, Kyushu UniversityFukuokaJapan
| | - Tomonori Kimura
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
| | | | - Jumpei Sasabe
- Department of Pharmacology, Keio University School of MedicineTokyoJapan
| | - Shushi Nagamori
- Center for SI Medical Research, The Jikei University School of MedicineTokyoJapan
- Department of Laboratory Medicine, The Jikei University School of MedicineTokyoJapan
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical UniversityNaraJapan
| |
Collapse
|
2
|
Miyamoto T, Fushinobu S, Saitoh Y, Sekine M, Katane M, Sakai-Kato K, Homma H. Novel tetrahydrofolate-dependent d-serine dehydratase activity of serine hydroxymethyltransferases. FEBS J 2024; 291:308-322. [PMID: 37700610 DOI: 10.1111/febs.16953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/12/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
d-Serine plays vital physiological roles in the functional regulation of the mammalian brain, where it is produced from l-serine by serine racemase and degraded by d-amino acid oxidase. In the present study, we identified a new d-serine metabolizing activity of serine hydroxymethyltransferase (SHMT) in bacteria as well as mammals. SHMT is known to catalyze the conversion of l-serine and tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate, respectively. In addition, we found that human and Escherichia coli SHMTs have d-serine dehydratase activity, which degrades d-serine to pyruvate and ammonia. We characterized this enzymatic activity along with canonical SHMT activity. Intriguingly, SHMT required THF to catalyze d-serine dehydration and did not exhibit dehydratase activity toward l-serine. Furthermore, SHMT did not use d-serine as a substrate in the canonical hydroxymethyltransferase reaction. The d-serine dehydratase activities of two isozymes of human SHMT were inhibited in the presence of a high concentration of THF, whereas that of E. coli SHMT was increased. The pH and temperature profiles of d-serine dehydratase and serine hydroxymethyltransferase activities of these three SHMTs were partially distinct. The catalytic efficiency (kcat /Km ) of dehydratase activity was lower than that of hydroxymethyltransferase activity. Nevertheless, the d-serine dehydratase activity of SHMT was physiologically important because d-serine inhibited the growth of an SHMT deletion mutant of E. coli, ∆glyA, more than that of the wild-type strain. Collectively, these results suggest that SHMT is involved not only in l- but also in d-serine metabolism through the degradation of d-serine.
Collapse
Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Kumiko Sakai-Kato
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| |
Collapse
|
3
|
Kimura T, Sakai S, Isaka Y. D-Serine as a sensor and effector of the kidney. Clin Exp Nephrol 2023; 27:891-900. [PMID: 37498348 PMCID: PMC10582142 DOI: 10.1007/s10157-023-02384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
Abstract
D-Serine, a rare enantiomer of serine, is a biomarker of kidney disease and function. The level of D-serine in the human body is precisely regulated through the urinary clearance of the kidney, and its clearance serves as a new measure of glomerular filtration rate with a lower bias than creatinine clearance. D-Serine also has a direct effect on the kidneys and mediates the cellular proliferation of tubular cells via mTOR signaling and induces kidney remodeling as a compensatory reaction to the loss of kidney mass. In living kidney donors, the removal of the kidney results in an increase in blood D-serine level, which in turn accelerates kidney remodeling and augments kidney clearance, thus reducing blood levels of D-serine. This feedback system strictly controls D-serine levels in the body. The function of D-serine as a biomarker and modulator of kidney function will be the basis of precision medicine for kidney diseases.
Collapse
Affiliation(s)
- Tomonori Kimura
- Reverse Translational Research Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Saito-Asagi 7-6-8, Ibaraki, Osaka, 5670085, Japan.
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Saito-Asagi 7-6-8, Ibaraki, Osaka, 5670085, Japan.
- Department of Nephrology, Osaka University Graduate School of Medicine, Yamada-oka 2-2, Suita, Osaka, 5650871, Japan.
| | - Shinsuke Sakai
- Reverse Translational Research Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Saito-Asagi 7-6-8, Ibaraki, Osaka, 5670085, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Saito-Asagi 7-6-8, Ibaraki, Osaka, 5670085, Japan
- Department of Nephrology, Osaka University Graduate School of Medicine, Yamada-oka 2-2, Suita, Osaka, 5650871, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Yamada-oka 2-2, Suita, Osaka, 5650871, Japan.
| |
Collapse
|
4
|
Bai Y, Huang W, Jiang X, Xu W, Li Y, Wang Y, Huang S, Wu K, Hu L, Chen C. Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9504. [PMID: 36918294 DOI: 10.1002/rcm.9504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 05/16/2023]
Abstract
RATIONALE Cardiac surgery-associated acute kidney injury (CSA-AKI) is a prevalent complication of cardiac surgery, which may be associated with a great risk of developing chronic kidney disease and mortality. This study aimed to investigate the possible links between gut microbiota metabolism and CSA-AKI. METHODS A prospective cohort of patients who underwent cardiac surgery was continuously recruited, who were further divided into CSA-AKI group and Non-AKI group based on clinical outcomes. Their faecal and plasma samples were collected before surgery and were separately analysed by nontargeted and targeted metabolomics. The differential metabolites related to CSA-AKI were screened out using statistical methods, and altered metabolic pathways were determined by examining the Kyoto Encyclopedia of Genes and Genomes database. RESULTS Nearly 1000 faecal metabolites were detected through high-resolution mass spectrometry (MS) and bioinformatics at high and mid confidence levels, and 49 differential metabolites at high confidence level may perform essential biological functions and provide potential diagnostic indicators. Compared with the Non-AKI group, the patients in the CSA-AKI group displayed dramatic changes in gut microbiota metabolism, including amino acid metabolism, nicotinate and nicotinamide metabolism, purine metabolism and ATP-binding cassette (ABC) transporters. Meanwhile, 188 plasma metabolites were identified and quantified by tandem MS, and 34 differential plasma metabolites were screened out between the two groups using univariate statistical analysis. These differential plasma metabolites were primarily enriched in the following metabolic pathways: sulphur metabolism, amino acid biosynthesis, tryptophan metabolism and ABC transporters. Furthermore, the content of indole metabolites in the faecal and plasma samples of the CSA-AKI group was higher than that of the Non-AKI group. CONCLUSIONS Patients with CSA-AKI may have dysbiosis of their intestinal microbiota and metabolic abnormalities in their gut system before cardiac surgery. Thus, some metabolites and related metabolic pathways may be potential biomarkers and new therapeutic targets for the disease.
Collapse
Affiliation(s)
- Yunpeng Bai
- Center of Scientific Research, Maoming People's Hospital, Maoming, China
- Department of Critical Care Medicine, Maoming People's Hospital, Maoming, China
| | - Wendong Huang
- Center of Scientific Research, Maoming People's Hospital, Maoming, China
| | - Xinyi Jiang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Wang Xu
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ying Li
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yirong Wang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Sumei Huang
- Center of Scientific Research, Maoming People's Hospital, Maoming, China
- Biological Resource Center, Maoming People's Hospital, Maoming, China
| | - Kunyong Wu
- Center of Scientific Research, Maoming People's Hospital, Maoming, China
- Biological Resource Center, Maoming People's Hospital, Maoming, China
| | - Linhui Hu
- Department of Critical Care Medicine, Maoming People's Hospital, Maoming, China
| | - Chunbo Chen
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
- Department of Emergency Medicine, Maoming People's Hospital, Maoming, China
| |
Collapse
|
5
|
Yuan D, Li J, Guo M, Yang Q, Huang J, Nie J, Li R, Li Q. Correlation study of FGF23/D-serine in maintenance hemodialysis patients with combined hearing impairment. PLoS One 2023; 18:e0280378. [PMID: 36649363 PMCID: PMC9844913 DOI: 10.1371/journal.pone.0280378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Recent studies have reported an association between chronic renal failure and hearing impairment. Yet, the exact mechanism of action is still not fully understood. In this study, we investigated the expression of fibroblast growth factor 23 (FGF23) and D-serine in maintenance hemodialysis (MHD) patients with end-stage renal disease (ESRD) complicated with hearing impairment and further investigated the correlation between FGF23/D-serine and hearing impairment. METHODS A total of 90 subjects, including 30 MHD patients complicated with hearing impairment, 30 MHD patients with normal hearing, and 30 controls, were included in this case-control study. Relevant data were obtained by questionnaire survey, audiometric test, enzyme-linked immunosorbent assay (ELISA) to determine FGF23 level, and high-performance liquid chromatography to determine D-serine level. RESULTS MHD patients showed abnormally high expression of FGF23 and D-serine, where FGF23 and D-serine levels were significantly higher in the group with hearing impairment than in the group with normal hearing and normal controls (all P<0.01). Also, elevated FGF23 and D-serine were identified as risk factors for hearing impairment in ESRD, with ORs of 16.54 (95%CI, 2.75-99.55) and 15.22 (95%CI, 2.59-89.51), respectively. Further Person correlation analysis showed a moderate positive correlation between FGF23 and D-serine (r = 0.683, P<0.001). CONCLUSION This study provides potential biomarkers for the early detection of hearing impairment complicated by chronic renal failure, and the reduction of FGF23/D-serine may provide a potential target for the treatment of hearing impairment complicated by chronic renal failure.
Collapse
Affiliation(s)
- Dunlu Yuan
- Department of Nephrology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiaqing Li
- Department of Nephrology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Min Guo
- Department of Otolaryngology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qing Yang
- Department of Nephrology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jingjing Huang
- Department of Medical Record, The Third People’s Hospital of Kunming, Kunming, China
| | - Jingwen Nie
- Department of Nephrology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruomei Li
- Department of Otolaryngology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qing Li
- Department of Nephrology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- * E-mail:
| |
Collapse
|
6
|
Bogos LG, Pralea IE, Moldovan RC, Iuga CA. Indirect Enantioseparations: Recent Advances in Chiral Metabolomics for Biomedical Research. Int J Mol Sci 2022; 23:ijms23137428. [PMID: 35806433 PMCID: PMC9267260 DOI: 10.3390/ijms23137428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
Chiral metabolomics is starting to become a well-defined research field, powered by the recent advances in separation techniques. This review aimed to cover the most relevant advances in indirect enantioseparations of endogenous metabolites that were published over the last 10 years, including improvements and development of new chiral derivatizing agents, along with advances in separation methodologies. Moreover, special emphasis is put on exciting advances in separation techniques combined with mass spectrometry, such as chiral discrimination by ion-mobility mass spectrometry together with untargeted strategies for profiling of chiral metabolites in complex matrices. These advances signify a leap in chiral metabolomics technologies that will surely offer a solid base to better understand the specific roles of enantiomeric metabolites in systems biology.
Collapse
Affiliation(s)
- Luisa-Gabriela Bogos
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania; (L.-G.B.); (I.-E.P.); (C.-A.I.)
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania
| | - Ioana-Ecaterina Pralea
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania; (L.-G.B.); (I.-E.P.); (C.-A.I.)
| | - Radu-Cristian Moldovan
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania; (L.-G.B.); (I.-E.P.); (C.-A.I.)
- Correspondence:
| | - Cristina-Adela Iuga
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania; (L.-G.B.); (I.-E.P.); (C.-A.I.)
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania
| |
Collapse
|
7
|
Iwata Y, Okushima H, Hesaka A, Kawamura M, Imamura R, Takahara S, Horio M, Tanaka Y, Ikeda T, Nakane M, Mita M, Hayashi T, Isaka Y, Kimura T. Identification of Diabetic Nephropathy in Patients Undergoing Kidney Biopsy through Blood and Urinary Profiles of d-Serine. KIDNEY360 2021; 2:1734-1742. [PMID: 35372995 PMCID: PMC8785851 DOI: 10.34067/kid.0004282021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/07/2021] [Indexed: 02/04/2023]
Abstract
Background The diagnosis of diabetic nephropathy (DN), the major cause of ESKD, requires kidney biopsy. d-Serine, present only in trace amounts in humans, is a biomarker for kidney diseases and shows potential to distinguish the origin of kidney diseases, whose diagnoses usually require kidney biopsy. We extended this concept and examined the potential of d-serine in the diagnosis of DN. Methods We enrolled patients with biopsy sample-proven DN and primary GN (minimal change disease and IgA nephropathy) and participants without kidney disease. A total of 388 participants were included in this study, and d-serine levels in blood and urine were measured using two-dimensional high-performance liquid chromatography, and urinary fractional excretion (FE) of d-serine was calculated. Using data from 259 participants, we developed prediction models for detecting DN by logistic regression analyses, and the models were validated in 129 participants. Results A d-serine blood level of >2.34 μM demonstrated a high specificity of 83% (95% CI, 70% to 93%) for excluding participants without kidney diseases. In participants with a d-serine blood level >2.34 μM, the threshold of 47% in FE of d-serine provided an optimal threshold for the detection of DN (AUC, 0.85 [95% CI, 0.76 to 0.95]; sensitivity, 79% [95% CI, 61% to 91%]; specificity, 83% [95% CI, 67% to 94%]). This plasma-high and FE-high profile of d-serine in combination with clinical factors (age, sex, eGFR, and albuminuria) correctly predicted DN with a sensitivity of 91% (95% CI, 72% to 99%) and a specificity of 79% (95% CI, 63% to 80%), and outperformed the model based on clinical factors alone in the validation dataset (P<0.02). Conclusions Analysis of d-serine in blood and urinary excretion is useful in identifying DN in patients undergoing kidney biopsy. Profiling of d-serine in patients with kidney diseases supports the suitable treatment through the auxial diagnosis of the origins of kidney diseases.
Collapse
Affiliation(s)
- Yukimasa Iwata
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, Osaka, Japan
| | - Hiroki Okushima
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, Osaka, Japan
| | - Atsushi Hesaka
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Masataka Kawamura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryoichi Imamura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Shiro Takahara
- Department of Renal Transplantation, Kansai Medical Hospital, Toyonaka, Osaka, Japan
| | - Masaru Horio
- Department of Nephrology, Kansai Medical Hospital, Toyonaka, Osaka, Japan
| | - Youko Tanaka
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
| | | | | | | | - Terumasa Hayashi
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, Osaka, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tomonori Kimura
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| |
Collapse
|
8
|
Abstract
Like many biological compounds, proteins are found primarily in their homochiral form. However, homochirality is not guaranteed throughout life. Determining their chiral proteinogenic sequence is a complex analytical challenge. This is because certain d-amino acids contained in proteins play a role in human health and disease. This is the case, for example, with d-Asp in elastin, β-amyloid and α-crystallin which, respectively, have an action on arteriosclerosis, Alzheimer’s disease and cataracts. Sequence-dependent and sequence-independent are the two strategies for detecting the presence and position of d-amino acids in proteins. These methods rely on enzymatic digestion by a site-specific enzyme and acid hydrolysis in a deuterium or tritium environment to limit the natural racemization of amino acids. In this review, chromatographic and electrophoretic techniques, such as LC, SFC, GC and CE, will be recently developed (2018–2020) for the enantioseparation of amino acids and peptides. For future work, the discovery and development of new chiral stationary phases and derivatization reagents could increase the resolution of chiral separations.
Collapse
|
9
|
Moussa S, Murtas G, Pollegioni L, Mauzeroll J. Enhancing Electrochemical Biosensor Selectivity with Engineered d-Amino Acid Oxidase Enzymes for d-Serine and d-Alanine Quantification. ACS APPLIED BIO MATERIALS 2021; 4:5598-5604. [PMID: 35006748 DOI: 10.1021/acsabm.1c00409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
d-Amino acid oxidase (DAAO) enzymes bind a range of d-amino acids with variable affinity. As such, the design of selective DAAO-based enzymatic biosensors remains a challenge for real-world biosensor application. Herein, a methodology for developing biosensors with varying substrate selectivity is presented. First, we address DAAO-based biosensor selectivity toward d-serine by introducing point mutations into DAAO using rational design. Next, the wild-type yeast DAAO (RgDAAO WT) and variants human DAAO W209R and yeast M213G are characterized for their selectivity and activity toward d-serine and d-alanine, the preferred DAAO substrates. The DAAO enzymes have been immobilized for final biosensor design, where they demonstrate selectivity comparable to free DAAO. The cross-linking procedure impacts on DAAO structure and function and the use of a regeneration strategy allows the biosensor response to be improved.
Collapse
Affiliation(s)
- Siba Moussa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Giulia Murtas
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, ltaly
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, ltaly
| | - Janine Mauzeroll
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
10
|
Urinary l-erythro-β-hydroxyasparagine-a novel serine racemase inhibitor and substrate of the Zn2+-dependent d-serine dehydratase. Biosci Rep 2021; 41:228199. [PMID: 33821987 PMCID: PMC8071972 DOI: 10.1042/bsr20210260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 12/24/2022] Open
Abstract
In the present study, we identified l-erythro-β-hydroxyasparagine (l-β-EHAsn) found abundantly in human urine, as a novel substrate of Zn2+-dependent d-serine dehydratase (DSD). l-β-EHAsn is an atypical amino acid present in large amounts in urine but rarely detected in serum or most organs/tissues examined. Quantitative analyses of urinary l-β-EHAsn in young healthy volunteers revealed significant correlation between urinary l-β-EHAsn concentration and creatinine level. Further, for in-depth analyses of l-β-EHAsn, we developed a simple three-step synthetic method using trans-epoxysuccinic acid as the starting substance. In addition, our research revealed a strong inhibitory effect of l-β-EHAsn on mammalian serine racemase, responsible for producing d-serine, a co-agonist of the N-methyl-d-aspartate (NMDA) receptor involved in glutamatergic neurotransmission.
Collapse
|
11
|
Okushima H, Iwata Y, Hesaka A, Sugimori E, Ikeda T, Nakane M, Mita M, Hayashi T, Isaka Y, Kimura T. Intra-body dynamics of D-serine reflects the origin of kidney diseases. Clin Exp Nephrol 2021; 25:893-901. [PMID: 33768329 PMCID: PMC8260539 DOI: 10.1007/s10157-021-02052-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
Introduction d-Serine, present only in trace amounts in humans, is now recognized as a biomarker of chronic kidney disease (CKD). CKD is heterogeneous in its original kidney diseases, whose diagnoses require kidney biopsy. In this study, we examined whether the intra-body dynamics of d-serine, indexed by its blood and urinary levels, reflects the origin of kidney diseases. Methods Patients with six kinds of kidney disease undergoing kidney biopsy were enrolled in a single center. Levels of d- and l-serine were measured using two-dimensional high-performance liquid chromatography. The associations between the origin of kidney diseases and the intra-body dynamics of d-serine were examined using multivariate cluster analyses. Results Unlike the non-CKD profile, patients with CKD showed broadly-distributed profiles of intra-body dynamics of d-serine. The plasma level of d-serine plays a key role in the detection of kidney diseases, whereas a combination of plasma and urinary levels of d-serine distinguished the origin of CKD, especially lupus nephritis. Conclusion Intra-body dynamics of d-serine have the potential to predict the origin of kidney diseases. Monitoring of d-serine may guide specific treatments for the origin of kidney diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s10157-021-02052-5.
Collapse
Affiliation(s)
- Hiroki Okushima
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, 3-1-56 Bandaihigashi, Sumiyoshi, Osaka, 558-8558, Japan
| | - Yukimasa Iwata
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, 3-1-56 Bandaihigashi, Sumiyoshi, Osaka, 558-8558, Japan
| | - Atsushi Hesaka
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- Department of Nephrology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eri Sugimori
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | | | | | | | - Terumasa Hayashi
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, 3-1-56 Bandaihigashi, Sumiyoshi, Osaka, 558-8558, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomonori Kimura
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.
- Reverse Translational Research Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.
- Department of Nephrology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
12
|
Promiscuous enzymes generating d-amino acids in mammals: Why they may still surprise us? Biochem J 2021; 478:1175-1178. [PMID: 33710333 DOI: 10.1042/bcj20200988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/17/2022]
Abstract
Promiscuous catalysis is a common property of enzymes, particularly those using pyridoxal 5'-phosphate as a cofactor. In a recent issue of this journal, Katane et al. Biochem. J. 477, 4221-4241 demonstrate the synthesis and accumulation of d-glutamate in mammalian cells by promiscuous catalysis mediated by a pyridoxal 5'-phosphate enzyme, the serine/threonine dehydratase-like (SDHL). The mechanism of SDHL resembles that of serine racemase, which synthesizes d-serine, a well-established signaling molecule in the mammalian brain. d-Glutamate is present in body fluids and is degraded by the d-glutamate cyclase at the mitochondria. This study demonstrates a biochemical pathway for d-glutamate synthesis in mammalian cells and advances our knowledge on this little-studied d-amino acid in mammals. d-Amino acids may still surprise us by their unique roles in biochemistry, intercellular signaling, and as potential biomarkers of disease.
Collapse
|