1
|
Leon Kropf V, Albany CJ, Zoccarato A, Green HLH, Yang Y, Brewer AC. TET3 is a positive regulator of mitochondrial respiration in Neuro2A cells. PLoS One 2024; 19:e0294187. [PMID: 38227585 PMCID: PMC10790995 DOI: 10.1371/journal.pone.0294187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/26/2023] [Indexed: 01/18/2024] Open
Abstract
Ten-Eleven-Translocase (TET) enzymes contribute to the regulation of the methylome via successive oxidation of 5-methyl cytosine (5mC) to derivatives which can be actively removed by base-excision-repair (BER) mechanisms in the absence of cell division. This is particularly important in post-mitotic neurons where changes in DNA methylation are known to associate with changes in neural function. TET3, specifically, is a critical regulator of both neuronal differentiation in development and mediates dynamic changes in the methylome of adult neurons associated with cognitive function. While DNA methylation is understood to regulate transcription, little is known of the specific targets of TET3-dependent catalytic activity in neurons. We report the results of an unbiased transcriptome analysis of the neuroblastoma-derived cell line; Neuro2A, in which Tet3 was silenced. Oxidative phosphorylation (OxPhos) was identified as the most significantly down-regulated functional canonical pathway, and these findings were confirmed by measurements of oxygen consumption rate in the Seahorse bioenergetics analyser. The mRNA levels of both nuclear- and mitochondrial-encoded OxPhos genes were reduced by Tet3-silencing, but we found no evidence for differential (hydroxy)methylation deposition at these gene loci. However, the mRNA expression of genes known to be involved in mitochondrial quality control were also shown to be significantly downregulated in the absence of TET3. One of these genes; EndoG, was identified as a direct target of TET3-catalytic activity at non-CpG methylated sites within its gene body. Accordingly, we propose that aberrant mitochondrial homeostasis may contribute to the decrease in OxPhos, observed upon Tet3-downregulation in Neuro2A cells.
Collapse
Affiliation(s)
- Valeria Leon Kropf
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Caraugh J. Albany
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Anna Zoccarato
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Hannah L. H. Green
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Youwen Yang
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Alison C. Brewer
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| |
Collapse
|
2
|
Katane M, Homma H. Biosynthesis and Degradation of Free D-Amino Acids and Their Physiological Roles in the Periphery and Endocrine Glands. Biol Pharm Bull 2024; 47:562-579. [PMID: 38432912 DOI: 10.1248/bpb.b23-00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
It was long believed that D-amino acids were either unnatural isomers or laboratory artifacts, and that the important functions of amino acids were exerted only by L-amino acids. However, recent investigations have revealed a variety of D-amino acids in mammals that play important roles in physiological functions, including free D-serine and D-aspartate that are crucial in the central nervous system. The functions of several D-amino acids in the periphery and endocrine glands are also receiving increasing attention. Here, we present an overview of recent advances in elucidating the physiological roles of D-amino acids, especially in the periphery and endocrine glands.
Collapse
Affiliation(s)
- Masumi Katane
- Medicinal Research Laboratories, Graduate School of Pharmaceutical Sciences, Kitasato University
| | - Hiroshi Homma
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University
| |
Collapse
|
3
|
Weissenbacher A, Huang H, Surik T, Lo Faro ML, Ploeg RJ, Coussios CC, Friend PJ, Kessler BM. Urine recirculation prolongs normothermic kidney perfusion via more optimal metabolic homeostasis-a proteomics study. Am J Transplant 2021; 21:1740-1753. [PMID: 33021021 PMCID: PMC8246941 DOI: 10.1111/ajt.16334] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/27/2020] [Accepted: 09/20/2020] [Indexed: 01/25/2023]
Abstract
We describe a proteomics analysis to determine the molecular differences between normothermically perfused (normothermic machine perfusion, NMP) human kidneys with urine recirculation (URC) and urine replacement (UR). Proteins were extracted from 16 kidney biopsies with URC (n = 8 donors after brain death [DBD], n = 8 donors after circulatory death [DCD]) and three with UR (n = 2 DBD, n = 1 DCD), followed by quantitative analysis by mass spectrometry. Damage-associated molecular patterns (DAMPs) were decreased in kidney tissue after 6 hours NMP with URC, suggesting reduced inflammation. Vasoconstriction was also attenuated in kidneys with URC as angiotensinogen levels were reduced. Strikingly, kidneys became metabolically active during NMP, which could be enhanced and prolonged by URC. For instance, mitochondrial succinate dehydrogenase enzyme levels as well as carbonic anhydrase were enhanced with URC, contributing to pH stabilization. Levels of cytosolic and the mitochondrial phosphoenolpyruvate carboxykinase were elevated after 24 hours of NMP, more prevalent in DCD than DBD tissue. Key enzymes involved in glucose metabolism were also increased after 12 and 24 hours of NMP with URC, including mitochondrial malate dehydrogenase and glutamic-oxaloacetic transaminase, predominantly in DCD tissue. We conclude that NMP with URC permits prolonged preservation and revitalizes metabolism to possibly better cope with ischemia reperfusion injury in discarded kidneys.
Collapse
Affiliation(s)
- Annemarie Weissenbacher
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
- Present address:
Annemarie WeissenbacherDepartment of Visceral, Transplant and Thoracic SurgeryMedical University of InnsbruckInnsbruckAustria
| | - Honglei Huang
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordUK
- Present address:
Honglei HuangOxford BioMedica PlcOxfordUK
| | - Tomas Surik
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Maria L. Lo Faro
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Rutger J. Ploeg
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Constantin C. Coussios
- Institute of Biomedical EngineeringDepartment of Engineering ScienceUniversity of OxfordOxfordUK
| | - Peter J. Friend
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Benedikt M. Kessler
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordUK
| |
Collapse
|
4
|
Identification of an l-serine/l-threonine dehydratase with glutamate racemase activity in mammals. Biochem J 2020; 477:4221-4241. [DOI: 10.1042/bcj20200721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
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.
Collapse
|
5
|
Katane M, Motoda R, Ariyoshi M, Tateishi S, Nakayama K, Saitoh Y, Miyamoto T, Sekine M, Mita M, Hamase K, Matoba S, Sakai-Kato K, Homma H. A colorimetric assay method for measuring d-glutamate cyclase activity. Anal Biochem 2020; 605:113838. [PMID: 32702438 DOI: 10.1016/j.ab.2020.113838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022]
Abstract
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.
Collapse
Affiliation(s)
- Masumi Katane
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Risa Motoda
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Makoto Ariyoshi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Shuhei Tateishi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuki Nakayama
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yasuaki Saitoh
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Tetsuya Miyamoto
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Masae Sekine
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Masashi Mita
- Shiseido Co., Ltd, 1-1-16 Higashi-shimbashi, Minato-ku, Tokyo, 105-0021, Japan
| | - Kenji Hamase
- Department of Drug Discovery and Evolution, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kumiko Sakai-Kato
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Hiroshi Homma
- Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| |
Collapse
|
6
|
Biochemical characterization of d-aspartate oxidase from Caenorhabditis elegans: its potential use in the determination of free d-glutamate in biological samples. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140442. [PMID: 32376478 DOI: 10.1016/j.bbapap.2020.140442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/26/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
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.
Collapse
|