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Errichiello E, Lecca M, Vantaggiato C, Motta Z, Zanotta N, Zucca C, Bertuzzo S, Piubelli L, Pollegioni L, Bonaglia MC. Further evidence supporting the role of GTDC1 in glycine metabolism and neurodevelopmental disorders. Eur J Hum Genet 2024; 32:920-927. [PMID: 38605125 PMCID: PMC11291697 DOI: 10.1038/s41431-024-01603-0] [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: 11/29/2023] [Revised: 02/16/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Copy number variants (CNVs) represent the genetic cause of about 15-20% of neurodevelopmental disorders (NDDs). We identified a ~67 kb de novo intragenic deletion on chromosome 2q22.3 in a female individual showing a developmental encephalopathy characterised by epilepsy, severe intellectual disability, speech delay, microcephaly, and thin corpus callosum with facial dysmorphisms. The microdeletion involved exons 5-6 of GTDC1, encoding a putative glycosyltransferase, whose expression is particularly enriched in the nervous system. In a previous study, a balanced de novo translocation encompassing GTDC1 was reported in a male child with global developmental delay and delayed speech and language development. Based on these premises, we explored the transcriptomic profile of our proband to evaluate the functional consequences of the novel GTDC1 de novo intragenic deletion in relation to the observed neurodevelopmental phenotype. RNA-seq on the proband's lymphoblastoid cell line (LCL) showed expression changes of glycine/serine and cytokine/chemokine signalling pathways, which are related to neurodevelopment and epileptogenesis. Subsequent analysis by ELISA (enzyme-linked immunosorbent assay) and HPLC (high-performance liquid chromatography) revealed increased levels of glycine in the proband's LCL and serum compared to matched controls. Given that an increased level of glycine has been observed in the plasma samples of individuals with Rett syndrome, a condition sharing epilepsy, microcephaly, and intellectual disability with our proband, we proposed that the GTDC1 downregulation is implicated in neurodevelopmental impairment by altering glycine metabolism. Furthermore, our findings expanded the phenotypic spectrum of the novel GTDC1-related condition, including microcephaly and epilepsy among relevant clinical features.
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Affiliation(s)
- Edoardo Errichiello
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, Pavia, Italy.
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.
| | - Mauro Lecca
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Chiara Vantaggiato
- Laboratory of Molecular Biology, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Nicoletta Zanotta
- Unit of Clinical Neurophysiology and Epilepsy Centre, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Claudio Zucca
- Unit of Clinical Neurophysiology and Epilepsy Centre, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Sara Bertuzzo
- Laboratory of Cytogenetics, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Luciano Piubelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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2
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Garofalo M, De Simone G, Motta Z, Nuzzo T, De Grandis E, Bruno C, Boeri S, Riccio MP, Pastore L, Bravaccio C, Iasevoli F, Salvatore F, Pollegioni L, Errico F, de Bartolomeis A, Usiello A. Decreased free D-aspartate levels in the blood serum of patients with schizophrenia. Front Psychiatry 2024; 15:1408175. [PMID: 39050919 PMCID: PMC11266155 DOI: 10.3389/fpsyt.2024.1408175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Schizophrenia (SCZ) and autism spectrum disorder (ASD) are neurodevelopmental diseases characterized by different psychopathological manifestations and divergent clinical trajectories. Various alterations at glutamatergic synapses have been reported in both disorders, including abnormal NMDA and metabotropic receptor signaling. Methods We conducted a bicentric study to assess the blood serum levels of NMDA receptors-related glutamatergic amino acids and their precursors, including L-glutamate, L-glutamine, D-aspartate, L-aspartate, L-asparagine, D-serine, L-serine and glycine, in ASD, SCZ patients and their respective control subjects. Specifically, the SCZ patients were subdivided into treatment-resistant and non-treatment-resistant SCZ patients, based on their responsivity to conventional antipsychotics. Results D-serine and D-aspartate serum reductions were found in SCZ patients compared to controls. Conversely, no significant differences between cases and controls were found in amino acid concentrations in the two ASD cohorts analyzed. Discussion This result further encourages future research to evaluate the predictive role of selected D-amino acids as peripheral markers for SCZ pathophysiology and diagnosis.
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Affiliation(s)
- Martina Garofalo
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Giuseppe De Simone
- Section of Psychiatry, Laboratory of Translational and Molecular Psychiatry and Unit of Treatment-Resistant Psychosis, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University Medical School of Naples “Federico II”, Naples, Italy
| | - Zoraide Motta
- ”The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Varese, Italy
| | - Tommaso Nuzzo
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Elisa De Grandis
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal, and Child Health - DINOGMI, University of Genoa, Genoa, Italy
| | - Claudio Bruno
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal, and Child Health - DINOGMI, University of Genoa, Genoa, Italy
- Center of Translational and Experimental Myology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Silvia Boeri
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal, and Child Health - DINOGMI, University of Genoa, Genoa, Italy
| | - Maria Pia Riccio
- Department of Maternal and Child Health, Unità Operativa semplice di Dipartimento (UOSD) of Child and Adolescent Psychiatry, Azienda Ospedaliera Universitaria (AOU) Federico II, Naples, Italy
| | - Lucio Pastore
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Carmela Bravaccio
- Department of Medical and Translational Sciences, Child Neuropsychiatry, Federico II University, Napoli, Italy
| | - Felice Iasevoli
- Section of Psychiatry, Laboratory of Translational and Molecular Psychiatry and Unit of Treatment-Resistant Psychosis, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University Medical School of Naples “Federico II”, Naples, Italy
| | - Francesco Salvatore
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- Centro Interuniversitario per Malattie Multigeniche e Multifattoriali e loro Modelli Animali (Federico II, Naples; Tor Vergata, Rome and “G. D’Annunzio”, Chieti-Pescara), Naples, Italy
| | - Loredano Pollegioni
- ”The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Varese, Italy
| | - Francesco Errico
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici, Italy
| | - Andrea de Bartolomeis
- Section of Psychiatry, Laboratory of Translational and Molecular Psychiatry and Unit of Treatment-Resistant Psychosis, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University Medical School of Naples “Federico II”, Naples, Italy
| | - Alessandro Usiello
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
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3
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Pollegioni L, Campanini B, Good JM, Motta Z, Murtas G, Buoli Comani V, Pavlidou DC, Mercier N, Mittaz-Crettol L, Sacchi S, Marchesani F. L-serine deficiency: on the properties of the Asn133Ser variant of human phosphoserine phosphatase. Sci Rep 2024; 14:12463. [PMID: 38816452 PMCID: PMC11139964 DOI: 10.1038/s41598-024-63164-y] [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: 01/12/2024] [Accepted: 05/26/2024] [Indexed: 06/01/2024] Open
Abstract
The non-essential amino acid L-serine is involved in a number of metabolic pathways and in the brain its level is largely due to the biosynthesis from the glycolytic intermediate D-3-phosphoglycerate by the phosphorylated pathway (PP). This cytosolic pathway is made by three enzymes proposed to generate a reversible metabolon named the "serinosome". Phosphoserine phosphatase (PSP) catalyses the last and irreversible step, representing the driving force pushing L-serine synthesis. Genetic defects of the PP enzymes result in strong neurological phenotypes. Recently, we identified the homozygous missense variant [NM_004577.4: c.398A > G p.(Asn133Ser)] in the PSPH, the PSP encoding gene, in two siblings with a neurodevelopmental syndrome and a myelopathy. The recombinant Asn133Ser enzyme does not show significant alterations in protein conformation and dimeric oligomerization state, as well as in enzymatic activity and functionality of the reconstructed PP. However, the Asn133Ser variant is less stable than wild-type PSP, a feature also apparent at cellular level. Studies on patients' fibroblasts also highlight a strong decrease in the level of the enzymes of the PP, a partial nuclear and perinuclear localization of variant PSP and a stronger perinuclear aggregates formation. We propose that these alterations contribute to the formation of a dysfunctional serinosome and thus to the observed reduction of L-serine, glycine and D-serine levels (the latter playing a crucial role in modulating NMDA receptors). The characterization of patients harbouring the Asn133Ser PSP substitution allows to go deep into the molecular mechanisms related to L-serine deficit and to suggest treatments to cope with the observed amino acids alterations.
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Affiliation(s)
- Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy.
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | | | - Despina-Christina Pavlidou
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Noëlle Mercier
- Department of Epileptology, Institution of Lavigny, Lavigny, Switzerland
| | - Laureane Mittaz-Crettol
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy
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4
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Vanella R, Küng C, Schoepfer AA, Doffini V, Ren J, Nash MA. Understanding activity-stability tradeoffs in biocatalysts by enzyme proximity sequencing. Nat Commun 2024; 15:1807. [PMID: 38418512 PMCID: PMC10902396 DOI: 10.1038/s41467-024-45630-3] [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: 03/24/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024] Open
Abstract
Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we present the development of enzyme proximity sequencing, a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We use enzyme proximity sequencing to analyze how 6399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase from Rhodotorula gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. Enzyme proximity sequencing can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.
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Affiliation(s)
- Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
| | - Christoph Küng
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Alexandre A Schoepfer
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- National Center for Competence in Research (NCCR), Catalysis, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Vanni Doffini
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Jin Ren
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
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5
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Murtas G, Zerbini E, Rabattoni V, Motta Z, Caldinelli L, Orlando M, Marchesani F, Campanini B, Sacchi S, Pollegioni L. Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels. Biofactors 2024; 50:181-200. [PMID: 37650587 DOI: 10.1002/biof.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
In the brain, the non-essential amino acid L-serine is produced through the phosphorylated pathway (PP) starting from the glycolytic intermediate 3-phosphoglycerate: among the different roles played by this amino acid, it can be converted into D-serine and glycine, the two main co-agonists of NMDA receptors. In humans, the enzymes of the PP, namely phosphoglycerate dehydrogenase (hPHGDH, which catalyzes the first and rate-limiting step of this pathway), 3-phosphoserine aminotransferase, and 3-phosphoserine phosphatase are likely organized in the cytosol as a metabolic assembly (a "serinosome"). The hPHGDH deficiency is a pathological condition biochemically characterized by reduced levels of L-serine in plasma and cerebrospinal fluid and clinically identified by severe neurological impairment. Here, three single-point variants responsible for hPHGDH deficiency and Neu-Laxova syndrome have been studied. Their biochemical characterization shows that V261M, V425M, and V490M substitutions alter either the kinetic (both maximal activity and Km for 3-phosphoglycerate in the physiological direction) and the structural properties (secondary, tertiary, and quaternary structure, favoring aggregation) of hPHGDH. All the three variants have been successfully ectopically expressed in U251 cells, thus the pathological effect is not due to hindered expression level. At the cellular level, mistargeting and aggregation phenomena have been observed in cells transiently expressing the pathological protein variants, as well as a reduced L-serine cellular level. Previous studies demonstrated that the pharmacological supplementation of L-serine in hPHGDH deficiencies could ameliorate some of the related symptoms: our results now suggest the use of additional and alternative therapeutic approaches.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elena Zerbini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | | | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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6
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Wang L, Tang H, Zhu H, Xue Y, Zheng Y. Enhancement of the substrate specificity of D-amino acid oxidase based on tunnel-pocket engineering. Biotechnol Bioeng 2023; 120:3557-3569. [PMID: 37650151 DOI: 10.1002/bit.28541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/11/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
D-Amino acid oxidase (DAAO) selectively catalyzes the oxidative deamination of D-amino acids, making it one of the most promising routes for synthesizing optically pure L-amino acids, including L-phosphinothricin ( L-PPT), a chiral herbicide with significant market potential. However, the native DAAOs that have been reported have low activity against unnatural acid substrate D-PPT. Herein, we designed and screened a DAAO from Rhodotorula taiwanensis (RtwDAAO), and improved its catalytic potential toward D-PPT through protein engineering. A semirational design approach was employed to create a mutation library based on the tunnel-pocket engineering. After three rounds of iterative saturation mutagenesis, the optimal variant M3rd -SHVG was obtained, exhibiting a >2000-fold increase in relative activity. The kinetic parameters showed that M3rd -SHVG improved the substrate binding affinity and turnover number. This is the optimal parameter reported so far. Further, molecular dynamics simulation revealed that the M3rd -SHVG reshapes the tunnel-pocket and corrects the direction of enzyme-substrate binding, allowing efficiently catalyze unnatural substrates. Our strategy demonstrates that the redesign of tunnel-pockets is effective in improving the activity and kinetic efficiency of DAAO, which provides a valuable reference for enzymatic catalysis. With the M3rd -SHVG as biocatalyst, 500 mM D, L-PPT was completely converted and the yield reached 98%. The results laid the foundation for further industrial production.
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Affiliation(s)
- Liuyu Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Heng Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Hongli Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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7
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Tripodi F, Motta Z, Murtas G, Rabattoni V, Nonnis S, Grassi Scalvini F, Rinaldi AM, Rizzi R, Bearzi C, Badone B, Sacchi S, Tedeschi G, Maffioli E, Coccetti P, Pollegioni L. Serine metabolism during differentiation of human iPSC-derived astrocytes. FEBS J 2023; 290:4440-4464. [PMID: 37166453 DOI: 10.1111/febs.16816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/05/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Astrocytes are essential players in development and functions, being particularly relevant as regulators of brain energy metabolism, ionic homeostasis and synaptic transmission. They are also the major source of l-serine in the brain, which is synthesized from the glycolytic intermediate 3-phosphoglycerate through the phosphorylated pathway. l-Serine is the precursor of the two main co-agonists of the N-methyl-d-aspartate receptor, glycine and d-serine. Strikingly, dysfunctions in both l- and d-serine metabolism are associated with neurological and psychiatric disorders. Here, we exploited a differentiation protocol, based on the generation of human mature astrocytes from neural stem cells, and investigated the modification of the proteomic and metabolomic profile during the differentiation process. We show that differentiated astrocytes are more similar to mature rather than to reactive ones, and that axogenesis and pyrimidine metabolism increase up to 30 days along with the folate cycle and sphingolipid metabolism. Consistent with the proliferation and cellular maturation processes that are taking place, also the intracellular levels of l-serine, glycine, threonine, l- and d-aspartate (which level is unexpectedly higher than that of d-serine) show the same biosynthetic time course. A significant utilization of l-serine from the medium is apparent while glycine is first consumed and then released with a peak at 30 days, parallel to its intracellular level. These results underline how metabolism changes during astrocyte differentiation, highlight that d-serine synthesis is restricted in differentiated astrocytes and provide a valuable model for developing potential novel therapeutic approaches to address brain diseases, especially the ones related to serine metabolism alterations.
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Affiliation(s)
- Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Simona Nonnis
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, Italy
| | | | | | - Roberto Rizzi
- Fondazione Istituto Nazionale di Genetica Molecolare, Milan, Italy
- Department of Medical-Surgical Science and Biotechnologies, University of Rome La Sapienza, Italy
| | - Claudia Bearzi
- Fondazione Istituto Nazionale di Genetica Molecolare, Milan, Italy
- Institute for Biomedical Technologies, National Research Council of Italy (ITB-CNR), Milan, Italy
| | - Beatrice Badone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Gabriella Tedeschi
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, Italy
- CIMAINA, University of Milano, Italy
| | - Elisa Maffioli
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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8
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Küng C, Vanella R, Nash MA. Directed evolution of Rhodotorula gracilisd-amino acid oxidase using single-cell hydrogel encapsulation and ultrahigh-throughput screening. REACT CHEM ENG 2023; 8:1960-1968. [PMID: 37496730 PMCID: PMC10366730 DOI: 10.1039/d3re00002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/15/2023] [Indexed: 07/28/2023]
Abstract
Engineering catalytic and biophysical properties of enzymes is an essential step en route to advanced biomedical and industrial applications. Here, we developed a high-throughput screening and directed evolution strategy relying on single-cell hydrogel encapsulation to enhance the performance of d-Amino acid oxidase from Rhodotorula gracilis (RgDAAOx), a candidate enzyme for cancer therapy. We used a cascade reaction between RgDAAOx variants surface displayed on yeast and horseradish peroxidase (HRP) in the bulk media to trigger enzyme-mediated crosslinking of phenol-bearing fluorescent alginate macromonomers, resulting in hydrogel formation around single yeast cells. The fluorescent hydrogel capsules served as an artificial phenotype and basis for pooled library screening by fluorescence activated cell sorting (FACS). We screened a RgDAAOx variant library containing ∼106 clones while lowering the d-Ala substrate concentration over three sorting rounds in order to isolate variants with low Km. After three rounds of FACS sorting and regrowth, we isolated and fully characterized four variants displayed on the yeast surface. We identified variants with a more than 5-fold lower Km than the parent sequence, with an apparent increase in substrate binding affinity. The mutations we identified were scattered across the RgDAAOx structure, demonstrating the difficulty in rationally predicting allosteric sites and highlighting the advantages of scalable library screening technologies for evolving catalytic enzymes.
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Affiliation(s)
- Christoph Küng
- Institute of Physical Chemistry, Department of Chemistry, University of Basel 4058 Basel Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich 4058 Basel Switzerland
| | - Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel 4058 Basel Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich 4058 Basel Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel 4058 Basel Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich 4058 Basel Switzerland
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9
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Maffioli E, Murtas G, Rabattoni V, Badone B, Tripodi F, Iannuzzi F, Licastro D, Nonnis S, Rinaldi AM, Motta Z, Sacchi S, Canu N, Tedeschi G, Coccetti P, Pollegioni L. Insulin and serine metabolism as sex-specific hallmarks of Alzheimer's disease in the human hippocampus. Cell Rep 2022; 40:111271. [PMID: 36070700 DOI: 10.1016/j.celrep.2022.111271] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 07/01/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
Healthy aging is an ambitious aspiration for humans, but neurodegenerative disorders, such as Alzheimer's disease (AD), strongly affect quality of life. Using an integrated omics approach, we investigate alterations in the molecular composition of postmortem hippocampus samples of healthy persons and individuals with AD. Profound differences are apparent between control and AD male and female cohorts in terms of up- and downregulated metabolic pathways. A decrease in the insulin response is evident in AD when comparing the female with the male group. The serine metabolism (linked to the glycolytic pathway and generating the N-methyl-D-aspartate [NMDA] receptor coagonist D-serine) is also significantly modulated: the D-Ser/total serine ratio represents a way to counteract age-related cognitive decline in healthy men and during AD onset in women. These results show how AD changes and, in certain respects, almost reverses sex-specific proteomic and metabolomic profiles, highlighting how different pathophysiological mechanisms are active in men and women.
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Affiliation(s)
- Elisa Maffioli
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, 20121 Milano, Italy; CIMAINA, University of Milano, 20121 Milano, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Beatrice Badone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Filomena Iannuzzi
- Department of System Medicine, University of Rome "Tor Vergata," 00133 Rome, Italy
| | | | - Simona Nonnis
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, 20121 Milano, Italy; CIMAINA, University of Milano, 20121 Milano, Italy
| | - Anna Maria Rinaldi
- Department of System Medicine, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Nadia Canu
- Department of System Medicine, University of Rome "Tor Vergata," 00133 Rome, Italy; Istituto di Biochimica e Biologia Cellulare (IBBC) CNR, 00015 Monterotondo Scalo, Italy.
| | - Gabriella Tedeschi
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, 20121 Milano, Italy; CIMAINA, University of Milano, 20121 Milano, Italy.
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy.
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy.
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10
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Chemogenetic approaches to dissect the role of H2O2 in redox-dependent pathways using genetically encoded biosensors. Biochem Soc Trans 2022; 50:335-345. [PMID: 35015078 DOI: 10.1042/bst20210506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022]
Abstract
Chemogenetic tools are recombinant enzymes that can be targeted to specific organelles and tissues. The provision or removal of the enzyme substrate permits control of its biochemical activities. Yeast-derived enzyme D-amino acid oxidase (DAAO) represents the first of its kind for a substrate-based chemogenetic approach to modulate H2O2 concentrations within cells. Combining these powerful enzymes with multiparametric imaging methods exploiting genetically encoded biosensors has opened new lines of investigations in life sciences. In recent years, the chemogenetic DAAO approach has proven beneficial to establish a new role for (patho)physiological oxidative stress on redox-dependent signaling and metabolic pathways in cultured cells and animal model systems. This mini-review covers established or emerging methods and assesses newer approaches exploiting chemogenetic tools combined with genetically encoded biosensors.
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11
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Steinhorn B, Eroglu E, Michel T. Chemogenetic Approaches to Probe Redox Pathways: Implications for Cardiovascular Pharmacology and Toxicology. Annu Rev Pharmacol Toxicol 2022; 62:551-571. [PMID: 34530645 PMCID: PMC10507364 DOI: 10.1146/annurev-pharmtox-012221-082339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chemogenetics refers to experimental systems that dynamically regulate the activity of a recombinant protein by providing or withholding the protein's specific biochemical stimulus. Chemogenetic tools permit precise dynamic control of specific signaling molecules to delineate the roles of those molecules in physiology and disease. Yeast d-amino acid oxidase (DAAO) enables chemogenetic manipulation of intracellular redox balance by generating hydrogen peroxide only in the presence of d-amino acids. Advances in biosensors have allowed the precise quantitation of these signaling molecules. The combination of chemogenetic approaches with biosensor methodologies has opened up new lines of investigation, allowing the analysis of intracellular redox pathways that modulate physiological and pathological cell responses. We anticipate that newly developed transgenic chemogenetic models will permit dynamic modulation of cellularredox balance in diverse cells and tissues and will facilitate the identification and validation of novel therapeutic targets involved in both physiological redox pathways and pathological oxidative stress.
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Affiliation(s)
- Benjamin Steinhorn
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Emrah Eroglu
- Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
- Department of Molecular Biology and Biochemistry, Medical University of Graz, 8036 Graz, Austria
| | - Thomas Michel
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;
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12
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Moussa S, Rosini E, Chitsaz D, Pollegioni L, Kennedy TE, Mauzeroll J. High-Throughput Strategy for Glycine Oxidase Biosensor Development Reveals Glycine Release from Cultured Cells. Anal Chem 2021; 93:16504-16511. [PMID: 34843206 DOI: 10.1021/acs.analchem.1c03620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycine is an important biomarker in clinical analysis due to its involvement in multiple physiological processes. As such, the need for low-cost analytical tools for glycine detection is growing. As a neurotransmitter, glycine is involved in inhibitory and excitatory neurochemical transmission in the central nervous system. In this work, we present a 10 μM Pt-based electrochemical enzymatic biosensor based on the flavoenzyme glycine oxidase (GO) for localized real-time measurements of glycine. Among GO variants at position 244, the H244K variant with increased glycine turnover was selected to develop a functional biosensor. This biosensor relies on amperometric readouts and does not require additional redox mediators. The biosensor was characterized and applied for glycine detection from cells, mainly HEK 293 cells and primary rat astrocytes. We have identified an enzyme, GO H244K, with increased glycine turnover using mutagenesis but which can be developed into a functional biosensor. Noteworthy, a glycine release of 395.7 ± 123 μM from primary astrocytes was measured, which is ∼fivefold higher than glycine release from HEK 293 cells (75.4 ± 3.91 μM) using the GO H244K biosensor.
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Affiliation(s)
- Siba Moussa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, Varese 21100, Italy
| | - Daryan Chitsaz
- Integrated Program in Neuroscience, McGill University, 1033 Pine Ave. W., Montreal, Quebec H3A 1A1, Canada
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, Varese 21100, Italy
| | - Timothy E Kennedy
- McGill Program in Neuroengineering, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Janine Mauzeroll
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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13
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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.
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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
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14
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Piubelli L, Pollegioni L, Rabattoni V, Mauri M, Princiotta Cariddi L, Versino M, Sacchi S. Serum D-serine levels are altered in early phases of Alzheimer's disease: towards a precocious biomarker. Transl Psychiatry 2021; 11:77. [PMID: 33500383 PMCID: PMC7838302 DOI: 10.1038/s41398-021-01202-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/28/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
D-Serine acts as a co-agonist of N-methyl-D-aspartate receptors (NMDAR) which appear overactivated in AD, while D-aspartate is a modulatory molecule acting on NMDAR as a second agonist. The aim of this work is to clarify whether the levels of these D-amino acids in serum are deregulated in AD, with the final goal to identify novel and precocious biomarkers in AD. Serum levels of L- and D-enantiomers of serine and aspartate were determined by HPLC using a pre-column derivatization procedure and a selective enzymatic degradation. Experimental data obtained from age-matched healthy subjects (HS) and AD patients were statistically evaluated by considering age, gender, and disease progression, and compared. Minor changes were apparent in the serum L- and D-aspartate levels in AD patients compared to HS. A positive correlation for the D-serine level and age was apparent in the AD cohort. Notably, the serum D-serine level and the D-/total serine ratio significantly increased with the progression of the disease. Gender seems to have a minor effect on the levels of all analytes tested. This work proposes that the serum D-serine level and D-/total serine ratio values as novel and valuable biomarkers for the progression of AD: the latter parameter allows to discriminate CDR 2 and CDR 1 patients from healthy (CDR 0) individuals.
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Affiliation(s)
- Luciano Piubelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Mauri
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Neurology Unit, Ospedale di Circolo and Fondazione Macchi, ASST Settelaghi, Varese, Italy
| | - Lucia Princiotta Cariddi
- Center of Research in Medical Pharmacology, University of Insubria, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Maurizio Versino
- Neurology Unit, Ospedale di Circolo and Fondazione Macchi, ASST Settelaghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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15
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Shimekake Y, Hirato Y, Funabashi R, Okazaki S, Goto M, Furuichi T, Suzuki H, Kera Y, Takahashi S. X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA. Acta Crystallogr F Struct Biol Commun 2020; 76:517-523. [PMID: 33135670 PMCID: PMC7605106 DOI: 10.1107/s2053230x20013333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/05/2020] [Indexed: 11/11/2022] Open
Abstract
D-Amino-acid oxidases (DAAOs) catalyze the oxidative deamination of neutral and basic D-amino acids. The DAAO from the thermophilic fungus Rasamsonia emersonii strain YA (ReDAAO) has a high thermal stability and a unique broad substrate specificity that includes the acidic D-amino acid D-Glu as well as various neutral and basic D-amino acids. In this study, ReDAAO was crystallized by the hanging-drop vapor-diffusion method and its crystal structure was determined at a resolution of 2.00 Å. The crystal structure of the enzyme revealed that unlike other DAAOs, ReDAAO forms a homotetramer and contains an intramolecular disulfide bond (Cys230-Cys285), suggesting that this disulfide bond is involved in the higher thermal stability of ReDAAO. Moreover, the structure of the active site and its vicinity in ReDAAO indicates that Arg97, Lys99, Lys114 and Ser231 are candidates for recognizing the side chain of D-Glu.
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Affiliation(s)
- Yuya Shimekake
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuki Hirato
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Rikako Funabashi
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Sayoko Okazaki
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takehiro Furuichi
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Hideyuki Suzuki
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yoshio Kera
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Shouji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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16
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Rosini E, D’Antona P, Pollegioni L. Biosensors for D-Amino Acids: Detection Methods and Applications. Int J Mol Sci 2020; 21:E4574. [PMID: 32605078 PMCID: PMC7369756 DOI: 10.3390/ijms21134574] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
D-enantiomers of amino acids (D-AAs) are only present in low amounts in nature, frequently at trace levels, and for this reason, their biological function was undervalued for a long time. In the past 25 years, the improvements in analytical methods, such as gas chromatography, HPLC, and capillary electrophoresis, allowed to detect D-AAs in foodstuffs and biological samples and to attribute them specific biological functions in mammals. These methods are time-consuming, expensive, and not suitable for online application; however, life science investigations and industrial applications require rapid and selective determination of D-AAs, as only biosensors can offer. In the present review, we provide a status update concerning biosensors for detecting and quantifying D-AAs and their applications for safety and quality of foods, human health, and neurological research. The review reports the main challenges in the field, such as selectivity, in order to distinguish the different D-AAs present in a solution, the simultaneous assay of both L- and D-AAs, the production of implantable devices, and surface-scanning biosensors. These innovative tools will push future research aimed at investigating the neurological role of D-AAs, a vibrant field that is growing at an accelerating pace.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; (P.D.); (L.P.)
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17
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d-Aspartate oxidase: distribution, functions, properties, and biotechnological applications. Appl Microbiol Biotechnol 2020; 104:2883-2895. [DOI: 10.1007/s00253-020-10439-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022]
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18
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Shimekake Y, Furuichi T, Abe K, Kera Y, Takahashi S. A novel thermostable D-amino acid oxidase of the thermophilic fungus Rasamsonia emersonii strain YA. Sci Rep 2019; 9:11948. [PMID: 31420577 PMCID: PMC6697736 DOI: 10.1038/s41598-019-48480-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022] Open
Abstract
d-Amino acid oxidase (DAAO) is a valuable flavoenzyme capable of being used in various practical applications, such as in determining d-amino acids and producing a material for semisynthetic cephalosporins, requiring higher thermal stability, higher catalytic activity, and broad substrate specificity. In this study, we isolated the thermophilic fungus Rasamsonia emersonii strain YA, which can grow on several d-amino acids as the sole nitrogen source, from a compost and characterized DAAO (ReDAAO) of the fungus. ReDAAO expressed in Escherichia coli exhibited significant oxidase activity against various neutral and basic d-amino acids, in particular hydrophobic d-amino acids. In addition, the enzyme also significantly acted on cephalosporin C, a starting material for semisynthetic antibiotics, and d-Glu, a general substrate for d-aspartate oxidase but not for DAAO, showing its unique and practically useful substrate specificity. The apparent kcat and Km values of the enzyme toward good substrates were comparable to those of higher catalytic fungal DAAOs, and the thermal stability (T50 value of ~60 °C) was comparable to that of a thermophilic bacterial DAAO and significantly higher than that of other eukaryotic DAAOs. These results highlight the great potential of ReDAAO for use in practical applications.
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Affiliation(s)
- Yuya Shimekake
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Takehiro Furuichi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Katsumasa Abe
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yoshio Kera
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Shouji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.
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19
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Free d-aspartate triggers NMDA receptor-dependent cell death in primary cortical neurons and perturbs JNK activation, Tau phosphorylation, and protein SUMOylation in the cerebral cortex of mice lacking d-aspartate oxidase activity. Exp Neurol 2019; 317:51-65. [PMID: 30822420 DOI: 10.1016/j.expneurol.2019.02.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/19/2019] [Accepted: 02/24/2019] [Indexed: 11/23/2022]
Abstract
In mammals, free d-aspartate (D-Asp) is abundant in the embryonic brain, while levels remain very low during adulthood as a result of the postnatal expression and activity of the catabolizing enzyme d-aspartate oxidase (DDO). Previous studies have shown that long-lasting exposure to nonphysiological, higher D-Asp concentrations in Ddo knockout (Ddo-/-) mice elicits a precocious decay of synaptic plasticity and cognitive functions, along with a dramatic age-dependent expression of active caspase 3, associated with increased cell death in different brain regions, including hippocampus, prefrontal cortex, and substantia nigra pars compacta. Here, we investigate the yet unclear molecular and cellular events associated with the exposure of abnormally high D-Asp concentrations in cortical primary neurons and in the brain of Ddo-/- mice. For the first time, our in vitro findings document that D-Asp induces in a time-, dose-, and NMDA receptor-dependent manner alterations in JNK and Tau phosphorylation levels, associated with pronounced cell death in primary cortical neurons. Moreover, observations obtained in Ddo-/- animals confirmed that high in vivo levels of D-Asp altered cortical JNK signaling, Tau phosphorylation and enhanced protein SUMOylation, indicating a robust indirect role of DDO activity in regulating these biochemical NMDA receptor-related processes. Finally, no gross modifications in D-Asp concentrations and DDO mRNA expression were detected in the cortex of patients with Alzheimer's disease when compared to age-matched healthy controls.
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20
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Ball J, Gannavaram S, Gadda G. Structural determinants for substrate specificity of flavoenzymes oxidizing d-amino acids. Arch Biochem Biophys 2018; 660:87-96. [PMID: 30312594 DOI: 10.1016/j.abb.2018.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022]
Abstract
The oxidation of d-amino acids is relevant to neurodegenerative diseases, detoxification, and nutrition in microorganisms and mammals. It is also important for the resolution of racemic amino acid mixtures and the preparation of chiral building blocks for the pharmaceutical and food industry. Considerable biochemical and structural knowledge has been accrued in recent years on the enzymes that carry out the oxidation of the Cα-N bond of d-amino acids. These enzymes contain FAD as a required coenzyme, share similar overall three-dimensional folds and highly conserved active sites, but differ in their specificity for substrates with neutral, anionic, or cationic side-chains. Here, we summarize the current biochemical and structural knowledge regarding substrate specificity on d-amino acid oxidase, d-aspartate oxidase, and d-arginine dehydrogenase for which a wealth of biochemical and structural studies is available.
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Affiliation(s)
- Jacob Ball
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Swathi Gannavaram
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Giovanni Gadda
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA; Departments of Biology, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302-3965, USA.
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21
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Subramanian K, Góra A, Spruijt R, Mitusińska K, Suarez-Diez M, Martins dos Santos V, Schaap PJ. Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS One 2018; 13:e0198990. [PMID: 29906280 PMCID: PMC6003678 DOI: 10.1371/journal.pone.0198990] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 11/28/2022] Open
Abstract
D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.
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Affiliation(s)
- Kalyanasundaram Subramanian
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
| | - Ruud Spruijt
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
- Department of Chemistry, Silesian University of Technology, ks. Marcina Strzody, Gliwice, Poland
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
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22
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Zhang N, Tian M, Liu X, Yang L. Enzyme assay for d -amino acid oxidase using optically gated capillary electrophoresis-laser induced fluorescence detection. J Chromatogr A 2018; 1548:83-91. [DOI: 10.1016/j.chroma.2018.03.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
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Chatard C, Meiller A, Marinesco S. Microelectrode Biosensors forin vivoAnalysis of Brain Interstitial Fluid. ELECTROANAL 2018. [DOI: 10.1002/elan.201700836] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Charles Chatard
- INSERM U1028, CNRS UMR5292; Lyon Neuroscience Research Center, Team TIGER
- Université Claude Bernard Lyon 1; Lyon France
| | - Anne Meiller
- AniRA-Neurochem Technological Platform; Lyon France
- Université Claude Bernard Lyon 1; Lyon France
| | - Stéphane Marinesco
- INSERM U1028, CNRS UMR5292; Lyon Neuroscience Research Center, Team TIGER
- AniRA-Neurochem Technological Platform; Lyon France
- Université Claude Bernard Lyon 1; Lyon France
- Lyon Neuroscience Research Center, Team TIGER; Faculty of Medicine; 8 Avenue Rockefeller 69373 Lyon Cedex 08 France
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Molla G. Competitive Inhibitors Unveil Structure/Function Relationships in Human D-Amino Acid Oxidase. Front Mol Biosci 2017; 4:80. [PMID: 29250527 PMCID: PMC5715370 DOI: 10.3389/fmolb.2017.00080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 02/02/2023] Open
Abstract
D-amino acid oxidase (DAAO) catalyzes the oxidative deamination of several neutral D-amino acids and is the enzyme mainly responsible (together with serine racemase) for degrading D-serine (D-Ser) in the central nervous system of mammals. This D-amino acid, which binds the coagonist site of the N-methyl-D-aspartate receptor, is thus a key neuromodulator of glutamatergic neurotransmission. Altered D-Ser metabolism results in several pathological conditions (e.g., amylotrophic lateral sclerosis or schizophrenia, SZ) for which effective "broad spectrum" pharmaceutical drugs are not yet available. In particular, the correlation between reduced D-Ser concentration and SZ led to a renaissance of biochemical interest in human DAAO (hDAAO). In the last 10 years, public and corporate research laboratories undertook huge efforts to study the structural, enzymatic, and physiological properties of the human flavoenzyme and to identify novel effective inhibitors which, acting as pharmaceutical drugs, could decrease hDAAO activity, thus restoring the physiological concentration of D-Ser. Although, none of the identified hDAAO inhibitors has reached the market yet, from a biochemical point of view, these compounds turned out to be invaluable for gaining a detailed understanding of the structure/function relationships at the molecular level in the mammalian DAAO, in particular of the interaction between ligand and the enzyme. This detailed knowledge, together with several recent studies concerning the interaction of the human enzyme with other protein regulative partners, its subcellular localization, and in vivo degradation, contributed to gaining comprehensive knowledge of the structure, function, and physiopathological role of this important human enzyme.
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Affiliation(s)
- Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,The Protein Factory Research Center, Politecnico of Milano and University of Insubria, Milan, Italy
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Decreased free d-aspartate levels are linked to enhanced d-aspartate oxidase activity in the dorsolateral prefrontal cortex of schizophrenia patients. NPJ SCHIZOPHRENIA 2017; 3:16. [PMID: 28560262 PMCID: PMC5441530 DOI: 10.1038/s41537-017-0015-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/10/2017] [Accepted: 02/22/2017] [Indexed: 01/02/2023]
Abstract
It is long acknowledged that the N-methyl d-aspartate receptor co-agonist, d-serine, plays a crucial role in several N-methyl d-aspartate receptor-mediated physiological and pathological processes, including schizophrenia. Besides d-serine, another free d-amino acid, d-aspartate, is involved in the activation of N-methyl d-aspartate receptors acting as an agonist of this receptor subclass, and is abundantly detected in the developing human brain. Based on the hypothesis of N-methyl d-aspartate receptor hypofunction in the pathophysiology of schizophrenia and considering the ability of d-aspartate and d-serine to stimulate N-methyl d-aspartate receptor-dependent transmission, in the present work we assessed the concentration of these two d-amino acids in the post-mortem dorsolateral prefrontal cortex and hippocampus of patients with schizophrenia and healthy subjects. Moreover, in this cohort of post-mortem brain samples we investigated the spatiotemporal variations of d-aspartate and d-serine. Consistent with previous work, we found that d-aspartate content was selectively decreased by around 30% in the dorsolateral prefrontal cortex, but not in the hippocampus, of schizophrenia-affected patients, compared to healthy subjects. Interestingly, such selective reduction was associated to greater (around 25%) cortical activity of the enzyme responsible for d-aspartate catabolism, d-aspartate oxidase. Conversely, no significant changes were found in the methylation state and transcription of DDO gene in patients with schizophrenia, compared to control individuals, as well as in the expression levels of serine racemase, the major enzyme responsible for d-serine biosynthesis, which also catalyzes aspartate racemization. These results reveal the potential involvement of altered d-aspartate metabolism in the dorsolateral prefrontal cortex as a factor contributing to dysfunctional N-methyl d-aspartate receptor-mediated transmission in schizophrenia. Altered metabolism of an amino acid activator of ion channels in the brain could explain dysfunctional nerve signaling in schizophrenia. Researchers in Italy led by Alessandro Usiello from Ceinge Biotecnologie Avanzate and Loredano Pollegioni from the University of Insubria measured the levels of two amino acids—D-aspartate and D-serine—in post-mortem tissues taken from two brain regions of patients with and without schizophrenia. Both amino acids activate the N-methyl D-aspartate receptor, which is known to be less active in people with schizophrenia. The researchers found a mild increase in D-serine levels but a major decrease in D-aspartate in the schizophrenia patients’ dorsolateral prefrontal cortex (DLPFC), a memory and reasoning part of the brain, but not in the hippocampus. They also documented a greater activity of the enzyme responsible for D-aspartate breakdown in the DLPFC.
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Age-Related Changes in D-Aspartate Oxidase Promoter Methylation Control Extracellular D-Aspartate Levels and Prevent Precocious Cell Death during Brain Aging. J Neurosci 2016; 36:3064-78. [PMID: 26961959 DOI: 10.1523/jneurosci.3881-15.2016] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The endogenous NMDA receptor (NMDAR) agonist D-aspartate occurs transiently in the mammalian brain because it is abundant during embryonic and perinatal phases before drastically decreasing during adulthood. It is well established that postnatal reduction of cerebral D-aspartate levels is due to the concomitant onset of D-aspartate oxidase (DDO) activity, a flavoenzyme that selectively degrades bicarboxylic D-amino acids. In the present work, we show that d-aspartate content in the mouse brain drastically decreases after birth, whereas Ddo mRNA levels concomitantly increase. Interestingly, postnatal Ddo gene expression is paralleled by progressive demethylation within its putative promoter region. Consistent with an epigenetic control on Ddo expression, treatment with the DNA-demethylating agent, azacitidine, causes increased mRNA levels in embryonic cortical neurons. To indirectly evaluate the effect of a putative persistent Ddo gene hypermethylation in the brain, we used Ddo knock-out mice (Ddo(-/-)), which show constitutively suppressed Ddo expression. In these mice, we found for the first time substantially increased extracellular content of d-aspartate in the brain. In line with detrimental effects produced by NMDAR overstimulation, persistent elevation of D-aspartate levels in Ddo(-/-) brains is associated with appearance of dystrophic microglia, precocious caspase-3 activation, and cell death in cortical pyramidal neurons and dopaminergic neurons of the substantia nigra pars compacta. This evidence, along with the early accumulation of lipufuscin granules in Ddo(-/-) brains, highlights an unexpected importance of Ddo demethylation in preventing neurodegenerative processes produced by nonphysiological extracellular levels of free D-aspartate.
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Hopkins SC, Heffernan MLR, Saraswat LD, Bowen CA, Melnick L, Hardy LW, Orsini MA, Allen MS, Koch P, Spear KL, Foglesong RJ, Soukri M, Chytil M, Fang QK, Jones SW, Varney MA, Panatier A, Oliet SHR, Pollegioni L, Piubelli L, Molla G, Nardini M, Large TH. Structural, Kinetic, and Pharmacodynamic Mechanisms of d-Amino Acid Oxidase Inhibition by Small Molecules. J Med Chem 2013; 56:3710-24. [DOI: 10.1021/jm4002583] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Seth C. Hopkins
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | | | - Lakshmi D. Saraswat
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Carrie A. Bowen
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Laurence Melnick
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Larry W. Hardy
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Michael A. Orsini
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | | | - Patrick Koch
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Kerry L. Spear
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | | | | | - Milan Chytil
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Q. Kevin Fang
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Steven W. Jones
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Mark A. Varney
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Aude Panatier
- Neurocentre Magendie, Inserm U862 and Université de Bordeaux, Bordeaux, F-33077, France
| | - Stephane H. R. Oliet
- Neurocentre Magendie, Inserm U862 and Université de Bordeaux, Bordeaux, F-33077, France
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie
e Scienze della Vita, Università degli Studi dell’Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
- The Protein Factory, Politecnico di Milano, ICRM-CNR and Università degli Studi dell’Insubria, Via Mancinelli 7,
20131 Milano, Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie
e Scienze della Vita, Università degli Studi dell’Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
- The Protein Factory, Politecnico di Milano, ICRM-CNR and Università degli Studi dell’Insubria, Via Mancinelli 7,
20131 Milano, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie
e Scienze della Vita, Università degli Studi dell’Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
- The Protein Factory, Politecnico di Milano, ICRM-CNR and Università degli Studi dell’Insubria, Via Mancinelli 7,
20131 Milano, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milan, I-20133 Milano, Italy
| | - Thomas H. Large
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
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Jiang T, Gao C, Dou P, Ma C, Kong J, Xu P. Rationally re-designed mutation of NAD-independent L-lactate dehydrogenase: high optical resolution of racemic mandelic acid by the engineered Escherichia coli. Microb Cell Fact 2012; 11:151. [PMID: 23176608 PMCID: PMC3526519 DOI: 10.1186/1475-2859-11-151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/04/2012] [Indexed: 11/18/2022] Open
Abstract
Background NAD-independent l-lactate dehydrogenase (l-iLDH) from Pseudomonas stutzeri SDM can potentially be used for the kinetic resolution of small aliphatic 2-hydroxycarboxylic acids. However, this enzyme showed rather low activity towards aromatic 2-hydroxycarboxylic acids. Results Val-108 of l-iLDH was changed to Ala by rationally site-directed mutagenesis. The l-iLDH mutant exhibited much higher activity than wide-type l-iLDH towards l-mandelate, an aromatic 2-hydroxycarboxylic acid. Using the engineered Escherichia coli expressing the mutant l-iLDH as a biocatalyst, 40 g·L-1 of dl-mandelic acid was converted to 20.1 g·L-1 of d-mandelic acid (enantiomeric purity higher than 99.5%) and 19.3 g·L-1 of benzoylformic acid. Conclusions A new biocatalyst with high catalytic efficiency toward an unnatural substrate was constructed by rationally re-design mutagenesis. Two building block intermediates (optically pure d-mandelic acid and benzoylformic acid) were efficiently produced by the one-pot biotransformation system.
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Affiliation(s)
- Tianyi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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Structure–function relationships in human d-amino acid oxidase. Amino Acids 2012; 43:1833-50. [DOI: 10.1007/s00726-012-1345-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/16/2012] [Indexed: 01/01/2023]
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Abstract
The presence of D-amino acids in foods is promoted by harsh technological processes (e.g., high temperature or extreme pH values) or can be the consequence of adulteration or microbial contamination (D-amino acids are major components of the bacterial cell wall). For this reason, quality control is becoming more and more important both for the industry (as a cost factor) and for consumer protection. For routine food analysis and quality control, simple and easily applicable analytical methods are needed: biosensors can often satisfy these requirements. The use of an enzymatic, stereospecific reaction could confer selectivity to a biosensor for detecting and quantifying D-amino acids in foodstuffs. The flavoenzyme D-amino acid oxidase from the yeast Rhodotorula gracilis is an ideal biocatalyst for this kind of application because of its absolute stereospecificity, very high turnover number with various substrates, tight binding with the FAD cofactor, and broad substrate specificity. Furthermore, alterations in the local brain concentrations of D-serine (predominantly D-amino acid in the mammalian central nervous system) have been related to several neurological and psychiatric diseases. Therefore, quantifying this neuromodulator represents an important task in biological, medical, and pharmaceutical research. Recently, an enzymatic microbiosensor, also using R. gracilis D-amino acid oxidase as biocatalyst, was developed for detecting D-serine in vivo.
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Yano S, Ozaki H, Matsuo S, Ito M, Wakayama M. Production, purification and characterization of D-aspartate oxidase from the fungus <i>Trichoderma harzianum</i> SKW-36. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/abb.2012.31002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
D: -Amino acids play several key roles and are widely diffused in living organisms, from bacteria (in which D-alanine is a component of the cell wall) to mammals (where D-serine is involved in glutamatergic neurotransmission in the central nervous system). The study of the biological processes involving D-amino acids and their use as clinical or biotechnological biomarkers requires reliable methods of quantifying them. Although "traditional" analytical techniques have been (and still are) employed for such tasks, enzymatic assays based on enzymes which possess a strict stereospecificity (i.e., that are only active on the D-enantiomers of amino acids) allowed the set-up of low-cost protocols with a high sensitivity and selectivity and suitable for determining the D-amino acid content of complex biological samples. The most exploited enzyme in these assays is D-amino acid oxidase, a flavoenzyme that exclusively oxidizes D-amino acids and possesses with a broad substrate specificity and a high kinetic efficiency.
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Hawkes T, Pline-Srnic W, Dale R, Friend E, Hollinshead T, Howe P, Thompson P, Viner R, Greenland A. D-glufosinate as a male sterility agent for hybrid seed production. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:301-14. [PMID: 20678098 DOI: 10.1111/j.1467-7652.2010.00549.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A chemical male sterility system based on anther-localized conversion of the inactive D-enantiomer of the herbicide, glufosinate (2-amino-4-(methylphosphinyl)-butanoate) to the phytotoxic L is described. Highly pure D-glufosinate was isolated in >98% enantiomeric excess from the racemate via fermentation with a strain of Escherichia coli expressing the PAT (L-glufosinate N-acetyl transferase) gene and purification of the unreacted D-enantiomer from the broth by ion exchange. A modified (F58K, M213S) form of the D-amino acid oxidase (DAAO) (EC 1.4.3.3) from Rhodosporidium toruloides was designed, tested in vitro and found to efficiently oxidize D-glufosinate to its 2-oxo derivative [2-oxo-4-(methylphosphinyl)-butanoic acid]. Tobacco (Nicotiana tabacum) plants were transformed to express this modified oxidase under control of the TAP1 tapetum-specific promoter. A number of the resultant transgenic lines exhibited complete male sterility that persisted for two or more weeks immediately following foliar treatment with 75 or 200 g/ha of D-glufosinate without exhibiting obvious phytotoxic symptoms or any measurable decline in female fertility. Similarly, plants containing the same construct and, additionally, a PAT gene expressed from a plastocyanin promoter exhibited significantly reduced male fertility and no reduction in female fertility following foliar application of racemic glufosinate. Thus, foliar application of d-glufosinate either purified or as the commercial herbicide, combined with anther expression of a modified DAAO promises to provide a cost-effective conditional chemical male sterility system with the characteristics necessary for practical F₁ hybrid seed production.
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Affiliation(s)
- Tim Hawkes
- Syngenta, Jealott's Hill Research Centre, Bracknell, Berks, UK.
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New biotech applications from evolved D-amino acid oxidases. Trends Biotechnol 2011; 29:276-83. [PMID: 21397351 DOI: 10.1016/j.tibtech.2011.01.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/24/2011] [Accepted: 01/27/2011] [Indexed: 11/20/2022]
Abstract
D-Amino acid oxidase (DAAO) is a well-known flavoenzyme that catalyzes the oxygen-dependent oxidative deamination of amino acid D-isomers with absolute stereospecificity, which results in α-keto acids, ammonia and hydrogen peroxide. Recently, the extraordinary functional plasticity of DAAO has become evident; in turn, boosting research on this flavoprotein. Protein engineering has allowed for a redesign of DAAO substrate specificity, oxygen affinity, cofactor binding, stability, and oligomeric state. We review recent developments in utilizing DAAO, including as a biocatalyst for resolving racemic amino acid mixtures, as a tool for biosensing, and as a new mechanism of herbicide resistance. Perspectives for future biotechnological applications of this oxidative biocatalyst are also outlined.
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Analyzing the D-amino acid content in biological samples by engineered enzymes. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3235-9. [PMID: 21419721 DOI: 10.1016/j.jchromb.2011.02.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 02/16/2011] [Accepted: 02/22/2011] [Indexed: 11/23/2022]
Abstract
The aim of our present research is to produce mutant forms of D-amino acid oxidase from Rhodotorula gracilis in order to determine D-amino acid content in different biological samples. During the past few years, our group has produced yeast D-amino acid oxidase variants with altered substrate specificity (e.g., active on acidic, or hydrophobic, or on all D-amino acids) both by rational design and directed evolution methods. Now, the kinetic constants for a number of amino acids (even for unnatural ones) of the most relevant D-amino acid oxidase variants have been investigated. This information constitutes the basis for considering potential analytical applications in this important field.
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Rosini E, Molla G, Ghisla S, Pollegioni L. On the reaction of d-amino acid oxidase with dioxygen: O2 diffusion pathways and enhancement of reactivity. FEBS J 2010; 278:482-92. [DOI: 10.1111/j.1742-4658.2010.07969.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Study on the decrease of renal d-amino acid oxidase activity in the rat after renal ischemia by chiral ligand exchange capillary electrophoresis. Amino Acids 2010; 42:337-45. [DOI: 10.1007/s00726-010-0811-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/08/2010] [Indexed: 01/25/2023]
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Katane M, Saitoh Y, Maeda K, Hanai T, Sekine M, Furuchi T, Homma H. Role of the active site residues arginine-216 and arginine-237 in the substrate specificity of mammalian D-aspartate oxidase. Amino Acids 2010; 40:467-76. [PMID: 20567862 DOI: 10.1007/s00726-010-0658-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022]
Abstract
D-aspartate oxidase (DDO) and D-amino acid oxidase (DAO) are flavin adenine dinucleotide-containing flavoproteins that catalyze the oxidative deamination of D-amino acids. Unlike DAO, which acts on several neutral and basic D-amino acids, DDO is highly specific for acidic D-amino acids. Based on molecular modeling and simulated annealing docking analyses, a recombinant mouse DDO carrying two substitutions (Arg-216 to Leu and Arg-237 to Tyr) was generated (R216L-R237Y variant). This variant and two previously constructed single-point mutants of mouse DDO (R216L and R237Y variants) were characterized to investigate the role of Arg-216 and Arg-237 in the substrate specificity of mouse DDO. The R216L-R237Y and R216L variants acquired a broad specificity for several neutral and basic D-amino acids, and showed a considerable decrease in activity against acidic D-amino acids. The R237Y variant, however, did not show any additional specificity for neutral or basic D-amino acids and its activity against acidic D-amino acids was greatly reduced. The kinetic properties of these variants indicated that the Arg-216 residue is important for the catalytic activity and substrate specificity of mouse DDO. However, Arg-237 is, apparently, only marginally involved in substrate recognition, but is important for catalytic activity. Notably, the substrate specificity of the R216L-R237Y variant differed significantly from that of the R216L variant, suggesting that Arg-237 has subsidiary effects on substrate specificity. Additional experiments using several DDO and DAO inhibitors also suggested the involvement of Arg-216 in the substrate specificity and catalytic activity of mouse DDO and that Arg-237 is possibly involved in substrate recognition by this enzyme. Collectively, these results indicate that Arg-216 and Arg-237 play crucial and subsidiary role(s), respectively, in the substrate specificity of mouse DDO.
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Affiliation(s)
- Masumi Katane
- Laboratory of Biomolecular Science, Department of Pharmaceutical Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
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D-Aspartate Oxidase: The Sole Catabolic Enzyme Acting on Free D-Aspartate in Mammals. Chem Biodivers 2010; 7:1435-49. [DOI: 10.1002/cbdv.200900250] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Takahashi S, Matsumoto S, Maruyama K, Wakaizumi A, Abe K, Kera Y, Yamada RH. An active-site mutation enhances the catalytic activity of the yeast Cryptococcus humicola d-aspartate oxidase. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Habl G, Zink M, Petroianu G, Bauer M, Schneider-Axmann T, von Wilmsdorff M, Falkai P, Henn FA, Schmitt A. Increased D-amino acid oxidase expression in the bilateral hippocampal CA4 of schizophrenic patients: a post-mortem study. J Neural Transm (Vienna) 2009; 116:1657-65. [PMID: 19823762 PMCID: PMC2776935 DOI: 10.1007/s00702-009-0312-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 09/04/2009] [Indexed: 01/15/2023]
Abstract
An important risk gene in schizophrenia is d-amino acid oxidase (DAAO). To establish if expression of DAAO is altered in cortical, hippocampal or thalamic regions of schizophrenia patients, we measured gene expression of DAAO in a post-mortem study of elderly patients with schizophrenia and non-affected controls in both hemispheres differentiating between gray and white matter. We compared cerebral post-mortem samples (granular frontal cortex BA9, middle frontal cortex BA46, superior temporal cortex BA22, entorhinal cortex BA28, sensoric cortex BA1–3, hippocampus (CA4), mediodorsal nucleus of the thalamus) from 10 schizophrenia patients to 13 normal subjects investigating gene expression of DAAO in the gray and white matter of both hemispheres of the above-mentioned brain regions by in situ-hybridization. We found increased expression of DAAO-mRNA in the hippocampal CA4 of schizophrenic patients. Compared to the control group, both hemispheres of the hippocampus of schizophrenic patients showed an increased expression of 46% (right, P = 0.013) and 54% (left, P = 0.019), respectively. None of the other regions examined showed statistically significant differences in DAAO expression. This post-mortem study demonstrated increased gene expression of DAAO in the left and right hippocampus of schizophrenia patients. This increased expression could be responsible for a decrease in local d-serine levels leading to a NMDA-receptor hypofunction that is hypothesized to play a major role in the pathophysiology of schizophrenia. However, our study group was small and results should be verified using larger samples.
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Affiliation(s)
- Gregor Habl
- Central Institute of Mental Health, P.O. Box 12 21 20, 68072 Mannheim, Germany
- Department of Radiation Oncology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Mathias Zink
- Central Institute of Mental Health, P.O. Box 12 21 20, 68072 Mannheim, Germany
| | - Georg Petroianu
- Department of Cellular Biology and Pharmacology, Florida International University, 11200 SW 8th Street, GL 495E, Miami, FL 33199 USA
| | - Manfred Bauer
- Department of Neuropathology, University of Leipzig, Liebigstr. 26, 04103 Leipzig, Germany
| | - Thomas Schneider-Axmann
- Department of Psychiatry, University of Goettingen, Von-Siebold Str. 5, 37075 Goettingen, Germany
| | - Martina von Wilmsdorff
- Department of Psychiatry Rheinische Kliniken, University of Duesseldorf, Bergische Landstr. 2, 40629 Duesseldorf, Germany
| | - Peter Falkai
- Department of Psychiatry, University of Goettingen, Von-Siebold Str. 5, 37075 Goettingen, Germany
| | - Fritz A. Henn
- Central Institute of Mental Health, P.O. Box 12 21 20, 68072 Mannheim, Germany
- Present Address: Life Sciences, Brookhaven National Laboratory, Bldg. 490, Upton, NY 11973-5000 USA
| | - Andrea Schmitt
- Central Institute of Mental Health, P.O. Box 12 21 20, 68072 Mannheim, Germany
- Department of Psychiatry, University of Goettingen, Von-Siebold Str. 5, 37075 Goettingen, Germany
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Pedotti M, Ghisla S, Motteran L, Molla G, Pollegioni L. Catalytic and redox properties of glycine oxidase from Bacillus subtilis. Biochimie 2009; 91:604-12. [DOI: 10.1016/j.biochi.2009.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
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43
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Zhang Z. Use of whole cell culture of Aeromonas sp. as enantioselective scavenger: a facile preparation of l-amino acid derivatives in high enantiomeric excess. Bioorg Med Chem Lett 2009; 19:1129-31. [PMID: 19150596 DOI: 10.1016/j.bmcl.2008.12.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Revised: 12/23/2008] [Accepted: 12/25/2008] [Indexed: 11/17/2022]
Abstract
The bacterium Aeromonas sp. (CGMCC 2226) can enantioselectively scavenge D-isomer, making L-amino acid derivatives (AADs) in high ee. The enantioselective scavenger (ES) has shown a broad substrate scope. Eleven L-AADs, Phe derivatives substituted with methyl-, mono- and dichloro-, bromo-, and nitro-group, were produced in high ee from corresponding racemates.
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Affiliation(s)
- Zizhang Zhang
- Department of Chemistry, Zhejiang University, 38 Zheda Road, Hangzhou 310027, PR China.
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44
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Rosini E, Molla G, Rossetti C, Pilone MS, Pollegioni L, Sacchi S. A biosensor for all d-amino acids using evolved d-amino acid oxidase. J Biotechnol 2008; 135:377-84. [DOI: 10.1016/j.jbiotec.2008.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 05/21/2008] [Accepted: 06/02/2008] [Indexed: 10/22/2022]
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45
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Properties and applications of microbial D-amino acid oxidases: current state and perspectives. Appl Microbiol Biotechnol 2008; 78:1-16. [DOI: 10.1007/s00253-007-1282-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 11/09/2007] [Accepted: 11/09/2007] [Indexed: 10/22/2022]
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46
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Caligiuri A, D’Arrigo P, Rosini E, Pedrocchi-Fantoni G, Tessaro D, Molla G, Servi S, Pollegioni L. Activity of yeast d-amino acid oxidase on aromatic unnatural amino acids. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Katane M, Hanai T, Furuchi T, Sekine M, Homma H. Hyperactive mutants of mouse D-aspartate oxidase: mutagenesis of the active site residue serine 308. Amino Acids 2008; 35:75-82. [PMID: 18235994 DOI: 10.1007/s00726-007-0627-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022]
Abstract
The role of Ser-308 of murine D-aspartate oxidase (mDASPO), particularly its side chain hydroxyl group, was investigated through the use of site-specific mutational analysis of Ser-308. Recombinant mDASPO carrying a substitution of Gly, Ala, or Tyr for Ser-308 was generated, and fused to either His (His-mDASPO), or glutathione S-transferase, His, and S (GHS-mDASPO) at its N-terminus. Wild-type His-mDASPO or GHS-mDASPO or their mutant derivatives were expressed in Escherichia coli and purified by affinity chromatography. All purified recombinant proteins had functional DASPO activity. The Gly-308 and Ala-308 mutants had significantly higher catalytic efficiency towards D-Asp and N-methyl-D-Asp, and a higher affinity for flavin adenine dinucleotide (FAD) compared to the wild-type enzyme. The Tyr-308 mutant had lower catalytic efficiency and binding capacity. These results suggest that the side chain hydroxyl group of a critical residue of mDASPO, Ser-308, down-regulates enzymatic activity, substrate binding, and FAD binding. This study provides information on the active site of DASPO that will considerably enhance our understanding of the biological significance of this enzyme.
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Affiliation(s)
- M Katane
- Laboratory of Biomolecular Science, School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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48
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Stability and stabilization of D-amino acid oxidase from the yeast Trigonopsis variabilis. Biochem Soc Trans 2007; 35:1588-92. [DOI: 10.1042/bst0351588] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of DAO (D-amino acid oxidase) for the conversion of cephalosporin C has provided a significant case for the successful implementation of an O2-dependent biocatalyst on an industrial scale. Improvement of the operational stability of the immobilized oxidase is, however, an important goal of ongoing process optimization. We have examined DAO from the yeast Trigonopsis variabilis with the aim of developing a rational basis for the stabilization of the enzyme activity at elevated temperature and under conditions of substrate turnover. Loss of activity in the resting enzyme can occur via different paths of denaturation. Partial thermal unfolding and release of the FAD cofactor, kinetically coupled with aggregation, contribute to the overall inactivation rate of the oxidase at 50°C. Oxidation of Cys108 into a stable cysteine sulfinic acid causes both decreased activity and stability of the enzyme. Strategies to counteract each of the denaturation steps in DAO are discussed. Fusion to a pull-down domain is a novel approach to produce DAO as protein-based insoluble particles that display high enzymatic activity per unit mass of catalyst.
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49
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Martínez-Martínez I, Navarro-Fernández J, García-Carmona F, Takami H, Sánchez-Ferrer A. Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426. Proteins 2007; 70:1429-41. [PMID: 17894345 DOI: 10.1002/prot.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Glycine oxidase from Geobacillus kaustophilus HTA426 (GOXK) is a 43 kDa monomer flavoenzyme containing noncovalently bound FAD. The induction of the enzyme resulted in the expression of a fully soluble protein with higher specific activity than those previously reported for GOX from B. subtilis (GOXB). A study of the kinetic properties of this novel GOXK revealed the lowest KM values for most of the substrates analyzed, with the exception of D-proline which kept a similar value and had the highest Vmax value reported. The Vmax/KM ratio maintained a substrate preference of GOXK for amines of small size, like glycine, sarcosine, N-ethyl-glycine, and glycine-ethyl-ester. GOXK presented good stability at 60-70 degrees C and in alkaline media (pH 6-9.5). The putative tridimensional structure was modeled by sequence alignment and by comparing the changes between GOXK and GOXB, and the residues that could be responsible for the substrate specificity as well as those essential for the catalytic activity were found. The comparison between the possible topology of GOXK with that of GOXB showed changes at the putative interactions between monomers for the building of the tetrameric oligomerization.
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Affiliation(s)
- Irene Martínez-Martínez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Campus Espinardo, E-30071 Murcia, Spain
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50
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Boselli A, Piubelli L, Molla G, Pilone MS, Pollegioni L, Sacchi S. Investigating the role of active site residues of Rhodotorula gracilis d-amino acid oxidase on its substrate specificity. Biochimie 2007; 89:360-8. [PMID: 17145127 DOI: 10.1016/j.biochi.2006.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 10/27/2006] [Indexed: 11/21/2022]
Abstract
D-amino acid oxidase (DAAO) is a flavoprotein that catalyzes stereospecifically the oxidative deamination of D-amino acids. The wild-type DAAO is mainly active on neutral D-amino acids, while basic D-amino acids are poor substrates and the acidic ones are virtually not oxidized. To present a comprehensive picture of how the active site residues can modulate the substrate specificity a number of mutants at position M213, Y223, Y238, R285, S335, and Q339 were prepared in the enzyme from the yeast Rhodotorula gracilis. All DAAO mutants have spectral properties similar to those of the wild-type enzyme and are catalytically active, thus excluding an essential role in catalysis; a lower activity on neutral and basic amino acids was observed. Interestingly, an increase in activity and (k(cat)/K(m))(app) ratio on D-aspartate was observed for all the mutants containing an additional charged residue in the active site. The active site of yeast DAAO appears to be a highly evolved scaffold built up through evolution to optimize the oxidative deamination of neutral D-amino acids without limiting its substrate specificity. It is noteworthy, that introduction of a sole, additional, positively charged residue in the active site is sufficient to optimize the reactivity on acidic D-amino acids, giving rise to kinetic properties similar to those of D-aspartate oxidase.
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Affiliation(s)
- Angelo Boselli
- Department of Biotechnology and Molecular Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
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