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Kalidasan V, Suresh D, Zulkifle N, Hwei YS, Kok Hoong L, Rajasuriar R, Theva Das K. Investigating D-Amino Acid Oxidase Expression and Interaction Network Analyses in Pathways Associated With Cellular Stress: Implications in the Biology of Aging. Bioinform Biol Insights 2024; 18:11779322241234772. [PMID: 38425413 PMCID: PMC10903195 DOI: 10.1177/11779322241234772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
D-amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids by oxidative deamination, producing hydrogen peroxide (H2O2) as a by-product. The generation of intracellular H2O2 may alter the redox-homeostasis mechanism of cells and increase the oxidative stress levels in tissues, associated with the pathogenesis of age-related diseases and organ decline. This study investigates the effect of DAO knockdown using clustered regularly interspaced short palindromic repeats (CRISPR) through an in silico approach on its protein-protein interactions (PPIs) and their potential roles in the process of aging. The target sequence and guide RNA of DAO were designed using the CCTop database, PPI analysis using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, Reactome biological pathway, protein docking using GalaxyTongDock database, and structure analysis. The translated target sequence of DAO lies between amino acids 43 to 50. The 10 proteins that were predicted to interact with DAO are involved in peroxisome pathways such as acyl-coenzyme A oxidase 1 (ACOX1), alanine-glyoxylate and serine-pyruvate aminotransferase (AGXT), catalase (CAT), carnitine O-acetyltransferase (CRAT), glyceronephosphate O-acyltransferase (GNPAT), hydroxyacid oxidase 1 (HAO1), hydroxyacid oxidase 2 (HAO2), trans-L-3-hydroxyproline dehydratase (L3HYPDH), polyamine oxidase (PAOX), and pipecolic acid and sarcosine oxidase (PIPOX). In summary, DAO mutation would most likely reduce activity with its interacting proteins that generate H2O2. However, DAO mutation may result in peroxisomal disorders, and thus, alternative techniques should be considered for an in vivo approach.
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Affiliation(s)
- V Kalidasan
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
| | - Darshinie Suresh
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Nurulisa Zulkifle
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
| | - Yap Siew Hwei
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Leong Kok Hoong
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Reena Rajasuriar
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kumitaa Theva Das
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
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Sakai S, Tanaka Y, Tsukamoto Y, Kimura-Ohba S, Hesaka A, Hamase K, Hsieh CL, Kawakami E, Ono H, Yokote K, Yoshino M, Okuzaki D, Matsumura H, Fukushima A, Mita M, Nakane M, Doi M, Isaka Y, Kimura T. d -Alanine Affects the Circadian Clock to Regulate Glucose Metabolism in the Kidney. KIDNEY360 2024; 5:237-251. [PMID: 38098136 PMCID: PMC10914205 DOI: 10.34067/kid.0000000000000345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/07/2023] [Indexed: 03/01/2024]
Abstract
Key Points d -Alanine affects the circadian clock to regulate gluconeogenesis in the kidney. d -Alanine itself has a clear intrinsic circadian rhythm, which is regulated by urinary excretion, and acts on the circadian rhythm. d -Alanine is a signal activator for circadian rhythm and gluconeogenesis through circadian transcriptional network. Background The aberrant glucose circadian rhythm is associated with the pathogenesis of diabetes. Similar to glucose metabolism in the kidney and liver, d -alanine, a rare enantiomer of alanine, shows circadian alteration, although the effect of d- alanine on glucose metabolism has not been explored. Here, we show that d- alanine acts on the circadian clock and affects glucose metabolism in the kidney. Methods The blood and urinary levels of d -alanine in mice were measured using two-dimensional high-performance liquid chromatography system. Metabolic effects of d -alanine were analyzed in mice and in primary culture of kidney proximal tubular cells from mice. Behavioral and gene expression analyses of circadian rhythm were performed using mice bred under constant darkness. Results d- Alanine levels in blood exhibited a clear intrinsic circadian rhythm. Since this rhythm was regulated by the kidney through urinary excretion, we examined the effect of d -alanine on the kidney. In the kidney, d -alanine induced the expressions of genes involved in gluconeogenesis and circadian rhythm. Treatment of d- alanine mediated glucose production in mice. Ex vivo glucose production assay demonstrated that the treatment of d -alanine induced glucose production in primary culture of kidney proximal tubular cells, where d -amino acids are known to be reabsorbed, but not in that of liver cells. Gluconeogenetic effect of d -alanine has an intraday variation, and this effect was in part mediated through circadian transcriptional network. Under constant darkness, treatment of d- alanine normalized the circadian cycle of behavior and kidney gene expressions. Conclusions d- Alanine induces gluconeogenesis in the kidney and adjusts the period of the circadian clock. Normalization of circadian cycle by d -alanine may provide the therapeutic options for life style–related diseases and shift workers.
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Affiliation(s)
- Shinsuke Sakai
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Youichi Tanaka
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Tsukamoto
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Shihoko Kimura-Ohba
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Atsushi Hesaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Kenji Hamase
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Chin-Ling Hsieh
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Eiryo Kawakami
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Advanced Data Science (ADSP), RIKEN Information R&D and Strategy Headquarters, Yokohama, Kanagawa, Japan
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
| | - Hiraku Ono
- Department of Endocrinology, Hematology and Gerontorogy, Graduate School of Medicine, Chiba University,Chiba, Japan
| | - Kotaro Yokote
- Department of Endocrinology, Hematology and Gerontorogy, Graduate School of Medicine, Chiba University,Chiba, Japan
| | - Mitsuaki Yoshino
- Laboratory of Rare Disease Information and Resource library, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Disease, Osaka University, Suita, Osaka, Japan
| | - Hiroyo Matsumura
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Atsuko Fukushima
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | | | | | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tomonori Kimura
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Reverse Translational Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
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3
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Park H, Kim E, Jun T, Pyo SH, Kim SH. Colorimetric Detection of Furfural with Enhanced Visible Absorption of Furfural-DNPH in Basic Conditions. ACS OMEGA 2024; 9:2519-2527. [PMID: 38250383 PMCID: PMC10795146 DOI: 10.1021/acsomega.3c07025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Furfural is an intermediary toxic aldehyde compound produced during heat-induced food processing and storage. Furfural is also formed by the degradation of cellulosic insulation in oil-immersed electric potential transformers, whose level is an important indicator of aging for replacement. In this study, we report a new means to detect the trace level of furfural in a colorimetric manner. Furfural is reacted with dinitrophenylhydrazine (DNPH) in acid solutions. The colorless furfural-DNPH compound turns orange-colored as the solution changes to basic. The delocalization of the π-electron in the DNPH-aldehyde derivatives at the basic condition causes the shift of the absorption peak from 318 to 470 nm, which renders the solution orange-colored. The color and absorbance are saturated in 20 min of incubation. There is high linearity between the absorbance and the concentration of furfural in the range of 0-0.2 mM, which enables the quantitative detection of furfural. The limit of detection is estimated to be as low as 1.76 μM for the absorbance analysis and 10 μM for the naked eyes. The colorimetric assay protocol is applicable to the detection of various aromatic aldehydes, which show strong π-electron delocalization and is not applicable to aliphatic aldehydes due to lack of delocalization. This simple assay can be conducted in typical 96-well microplates using a microplate reader, which provides a low-cost and high-throughput screening. Therefore, we believe that our method is potentially applicable for the quantitative detection of aromatic aldehydes in various samples from foods, electronic devices, and so on.
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Affiliation(s)
- Hyunjoo Park
- Korea
Electric Power Research Institute, 105 Munji-Ro, Yuseong-Gu, Daejeon 34056, Republic of Korea
- Department
of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Yuseong-Gu, Daehak-Ro, Daejeon 34141, Republic of Korea
| | - Eunyoung Kim
- Korea
Electric Power Research Institute, 105 Munji-Ro, Yuseong-Gu, Daejeon 34056, Republic of Korea
| | - Taehyun Jun
- Korea
Electric Power Research Institute, 105 Munji-Ro, Yuseong-Gu, Daejeon 34056, Republic of Korea
| | - Sang-Hyun Pyo
- Biotechnology,
Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Shin-Hyun Kim
- Department
of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Yuseong-Gu, Daehak-Ro, Daejeon 34141, Republic of Korea
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Zangelmi E, Ruffolo F, Dinhof T, Gerdol M, Malatesta M, Chin JP, Rivetti C, Secchi A, Pallitsch K, Peracchi A. Deciphering the role of recurrent FAD-dependent enzymes in bacterial phosphonate catabolism. iScience 2023; 26:108108. [PMID: 37876809 PMCID: PMC10590968 DOI: 10.1016/j.isci.2023.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/30/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Phosphonates-compounds containing a direct C-P bond-represent an important source of phosphorus in some environments. The most common natural phosphonate is 2-aminoethylphosphonate (AEP). Many bacteria can break AEP down through specialized "hydrolytic" pathways, which start with the conversion of AEP into phosphonoacetaldehyde (PAA), catalyzed by the transaminase PhnW. However, the substrate scope of these pathways is very narrow, as PhnW cannot process other common AEP-related phosphonates, notably N-methyl AEP (M1AEP). Here, we describe a heterogeneous group of FAD-dependent oxidoreductases that efficiently oxidize M1AEP to directly generate PAA, thus expanding the versatility and usefulness of the hydrolytic AEP degradation pathways. Furthermore, some of these enzymes can also efficiently oxidize plain AEP. By doing so, they surrogate the role of PhnW in organisms that do not possess the transaminase and create novel versions of the AEP degradation pathways in which PAA is generated solely by oxidative deamination.
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Affiliation(s)
- Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Francesca Ruffolo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Tamara Dinhof
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, 1090 Vienna, Austria
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Jason P. Chin
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, BT9 5DL Belfast, UK
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Katharina Pallitsch
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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5
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Du S, Wey M, Armstrong DW. d-Amino acids in biological systems. Chirality 2023; 35:508-534. [PMID: 37074214 DOI: 10.1002/chir.23562] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/20/2023]
Abstract
Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.
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Affiliation(s)
- Siqi Du
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Michael Wey
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
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6
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Rosini E, Boreggio M, Verga M, Caldinelli L, Pollegioni L, Fasoli E. The D-amino acid oxidase-carbon nanotubes: evaluation of cytotoxicity and biocompatibility of a potential anticancer nanosystem. 3 Biotech 2023; 13:243. [PMID: 37346390 PMCID: PMC10279611 DOI: 10.1007/s13205-023-03568-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/19/2023] [Indexed: 06/23/2023] Open
Abstract
The 'enzyme prodrug therapy' represents a promising strategy to overcome limitations of current cancer treatments by the systemic administration of prodrugs, converted by a foreign enzyme into an active anticancer compound directly in tumor sites. One example is D-amino acid oxidase (DAAO), a dimeric flavoenzyme able to catalyze the oxidative deamination of D-amino acids with production of hydrogen peroxide, a reactive oxygen species (ROS), able to favor cancer cells death. A DAAO variant containing five aminoacidic substitutions (mDAAO) was demonstrated to possess a better therapeutic efficacy under low O2 concentration than wild-type DAAO (wtDAAO). Recently, aiming to design promising nanocarriers for DAAO, multi-walled carbon nanotubes (MWCNTs) were functionalized with polyethylene glycol (PEG) to reduce their tendency to aggregation and to improve their biocompatibility. Here, wtDAAO and mDAAO were adsorbed on PEGylated MWCNTs and their activity and cytotoxicity were tested. While PEG-MWCNTs-DAAOs have shown a higher activity than pristine MWCNTs-DAAO (independently on the DAAO variant used), PEG-MWCNTs-mDAAO showed a higher cytotoxicity than PEG-MWCNTs-wtDAAO at low O2 concentration. In order to evaluate the nanocarriers' biocompatibility, PEG-MWCNTs-DAAOs were incubated in human serum and the composition of protein corona was investigated via nLC-MS/MS, aiming to characterize both soft and hard coronas. The mDAAO variant has influenced the bio-corona composition in both number of proteins and presence of opsonins and dysopsonins: notably, the soft corona of PEG-MWCNTs-mDAAO contained less proteins and was more enriched in proteins able to inhibit the immune response than PEG-MWCNTs-wtDAAO. Considering the obtained results, the PEGylated MWCNTs conjugated with the mDAAO variant seems a promising candidate for a selective antitumor oxidative therapy: under anoxic-like conditions, this novel drug delivery system showed a remarkable cytotoxic effect controlled by the substrate addition, against different tumor cell lines, and a bio-corona composition devoted to prolong its blood circulation time, thus improving the drug's biodistribution. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03568-1.
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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
| | - Marta Boreggio
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Matteo Verga
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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7
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Sakamoto T, Odera K, Onozato M, Sugasawa H, Takahashi R, Fujimaki Y, Fukushima T. Direct Fluorescence Evaluation of d-Amino Acid Oxidase Activity Using a Synthetic d-Kynurenine Derivative. Anal Chem 2022; 94:14530-14536. [PMID: 36222234 DOI: 10.1021/acs.analchem.2c00775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
d-Amino acid oxidase (DAO) has been suggested to be associated with the central nervous system diseases, such as schizophrenia. We newly synthesized a nonfluorescent 5-methylthio-d-kynurenine (MeS-d-KYN), which was converted to blue-fluorescent 6-MeS-kynurenic acid (MeS-KYNA, λex = 364 nm, λem = 450 nm) through a one-step reaction by incubation with DAO. It was revealed that fluorescence intensity increased accompanied by commercial porcine kidney DAO activity (unit) with a good correlation (R2 = 0.9972), suggesting that the fluorometric evaluation of DAO activity using MeS-d-KYN is feasible. MeS-d-KYN was applied to fluorescent DAO imaging in cultured LLC-PK1 cells, and the blue fluorescence of MeS-KYNA overlapped considerably with the location of peroxisomes, which was suggested to be the location of DAO in the cells. Because fluorescence was diminished in the presence of 6-chloro-1,2-benzisoxazol-3(2H)-one (CBIO), a DAO inhibitor, it was considered that DAO activity in cells could be directly evaluated using MeS-d-KYN as the substrate.
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Affiliation(s)
- Tatsuya Sakamoto
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba274-8510, Japan
| | - Keiko Odera
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba274-8510, Japan
| | - Mayu Onozato
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba274-8510, Japan
| | - Hiroshi Sugasawa
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba274-8510, Japan
| | - Ryoya Takahashi
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba274-8510, Japan
| | - Yasuto Fujimaki
- Tokyo Metropolitan Industrial Technology Research Institute, Jonan Branch, 1-20-20 minamikamata, Ota-ku, Tokyo144-0035, Japan
| | - Takeshi Fukushima
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba274-8510, Japan
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8
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Taheri P. Crosstalk of nitro-oxidative stress and iron in plant immunity. Free Radic Biol Med 2022; 191:137-149. [PMID: 36075546 DOI: 10.1016/j.freeradbiomed.2022.08.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022]
Abstract
Accumulation of oxygen and nitrogen radicals and their derivatives, known as reactive oxygen species (ROS) and reactive nitrogen species (RNS), occurs throughout various phases of plant growth in association with biotic and abiotic stresses. One of the consequences of environmental stresses is disruption of homeostasis between production and scavenging of ROS and RNS, which leads to nitro-oxidative burst and affects other defense-related mechanisms, such as polyamines levels, phenolics, lignin and callose as defense components related to plant cell wall reinforcement. Although this subject has attracted huge interest, the cross-talk between these signaling molecules and iron, as a main metal element involved in the activity of various enzymes and numerous vital processes in the living cells, remains largely unexplored. Therefore, it seems necessary to pay more in depth attention to the mechanisms of plant resistance against various environmental stimuli for designing novel and effective plant protection strategies. This review is focused on advances in recent knowledge related to the role of ROS, RNS, and association of these signaling molecules with iron in plant immunity. Furthermore, the role of cell wall fortification as a main physical barrier involved in plant defense have been discussed in association with reactive species and iron ions.
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Affiliation(s)
- Parissa Taheri
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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9
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Lee CJ, Qiu TA, Hong Z, Zhang Z, Min Y, Zhang L, Dai L, Zhao H, Si T, Sweedler JV. Profiling of d-alanine production by the microbial isolates of rat gut microbiota. FASEB J 2022; 36:e22446. [PMID: 35816159 DOI: 10.1096/fj.202101595r] [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: 11/03/2021] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
d-alanine (d-Ala) and several other d-amino acids (d-AAs) act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized d-serine in animals, d-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce d-Ala and other d-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their d-AA production in vitro, focusing on d-Ala. Serial dilutions of intestinal contents from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial d-AA production, combining a d-amino acid oxidase-based enzymatic assay for rapid assessment of non-acidic d-AA amount and chiral LC-MS/MS to quantify individual d-AAs, revealing 19 out of the 38 isolated strains as d-AA producers. LC-MS/MS analysis of the eight top d-AA producers showed high levels of d-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from the enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of d-glutamate and d-aspartate, which are poor substrates for this enzymatic assay. We observed large inter- and intra-species variation of d-AA production profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology.
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Affiliation(s)
- Cindy J Lee
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tian A Qiu
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhenkun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhao Min
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Linzixuan Zhang
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huimin Zhao
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan V Sweedler
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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10
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Genetically encoded tools for measuring and manipulating metabolism. Nat Chem Biol 2022; 18:451-460. [PMID: 35484256 DOI: 10.1038/s41589-022-01012-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
Over the past few years, we have seen an explosion of novel genetically encoded tools for measuring and manipulating metabolism in live cells and animals. Here, we will review the genetically encoded tools that are available, describe how these tools can be used and outline areas where future development is needed in this fast-paced field. We will focus on tools for direct measurement and manipulation of metabolites. Metabolites are master regulators of metabolism and physiology through their action on metabolic enzymes, signaling enzymes, ion channels and transcription factors, among others. We hope that this Perspective will encourage more people to use these novel reagents or even join this exciting new field to develop novel tools for measuring and manipulating metabolism.
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11
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Boreggio M, Rosini E, Gambarotti C, Pollegioni L, Fasoli E. Unveiling the Bio-corona Fingerprinting of Potential Anticancer Carbon Nanotubes Coupled with D-Amino Acid Oxidase. Mol Biotechnol 2022; 64:1164-1176. [PMID: 35467257 PMCID: PMC9411096 DOI: 10.1007/s12033-022-00488-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/31/2022] [Indexed: 11/27/2022]
Abstract
The oxidation therapy, based on the controlled production of Reactive Oxygen Species directly into the tumor site, was introduced as alternative antitumor approach. For this purpose, d-amino acid oxidase (DAAO) from the yeast Rhodotorula gracilis, an enzyme able to efficiently catalyze the production of hydrogen peroxide from d-amino acids, was adsorbed onto multi-walled carbon nanotubes (MWCNTs), previously functionalized with polylactic-co-glycolic acid (PLGA) or polyethylene glycol (PEG) at different degrees to reduce their toxicity, to be targeted directly into the tumor. In vitro activity and cytotoxicity assays demonstrated that DAAO-functionalized nanotubes (f-MWCNTs) produced H2O2 and induced toxic effects to selected tumor cell lines. After incubation in human plasma, the protein corona was investigated by SDS-PAGE and mass spectrometry analysis. The enzyme nanocarriers generally seemed to favor their biocompatibility, promoting the interaction with dysopsonins. Despite this, PLGA or high degree of PEGylation promoted the adsorption of immunoglobulins with a possible activation of immune response and this effect was probably due to PLGA hydrophobicity and dimensions and to the production of specific antibodies against PEG. In conclusion, the PEGylated MWCNTs at low degree seemed the most biocompatible nanocarrier for adsorbed DAAO, preserving its anticancer activity and forming a bio-corona able to reduce both defensive responses and blood clearance.
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Affiliation(s)
- Marta Boreggio
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varèse, Italy
| | - Cristian Gambarotti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varèse, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy.
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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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Smolyarova DD, Podgorny OV, Bilan DS, Belousov VV. A guide to genetically encoded tools for the study of H 2 O 2. FEBS J 2021; 289:5382-5395. [PMID: 34173331 DOI: 10.1111/febs.16088] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/23/2021] [Accepted: 06/24/2021] [Indexed: 01/09/2023]
Abstract
Cell metabolism heavily relies on the redox reactions that inevitably generate reactive oxygen species (ROS). It is now well established that ROS fluctuations near basal levels coordinate numerous physiological processes in living organisms, thus exhibiting regulatory functions. Hydrogen peroxide, the most long-lived ROS, is a key contributor to ROS-dependent signal transduction in the cell. H2 O2 is known to impact various targets in the cell; therefore, the question of how H2 O2 modulates physiological processes in a highly specific manner is central in redox biology. To resolve this question, novel genetic tools have recently been created for detecting H2 O2 and emulating its generation in living organisms with unmatched spatiotemporal resolution. Here, we review H2 O2 -sensitive genetically encoded fluorescent sensors and opto- and chemogenetic tools for controlled H2 O2 generation.
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Affiliation(s)
- Daria D Smolyarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Russia
| | - Oleg V Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, Moscow, Russia.,Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia.,Institute for Cardiovascular Physiology, Georg August University Göttingen, Germany
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15
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Rosini E, Volpi NA, Ziffels B, Grimaldi A, Sacchi S, Neri D, Pollegioni L. An antibody-based enzymatic therapy for cancer treatment: The selective localization of D-amino acid oxidase to EDA fibronectin. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 36:102424. [PMID: 34174417 DOI: 10.1016/j.nano.2021.102424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
In order to generate an antibody directed enzyme prodrug therapy, here we designed a chimeric protein by fusing the F8 antibody that recognizes the EDA of fibronectin (expressed on the tumor neovasculature) and an evolved variant of the ROS-generating enzyme D-amino acid oxidase (DAAO). The F8(scFv)-DAAO-Q144R recombinant protein is expressed by both CHO-S and E. coli cells. The F8(scFv)-DAAO-Q144R from E. coli cells is fully soluble, shows a high specific activity, is more thermostable in blood than the native DAAO, possesses a binding affinity for EDA well suited for efficient tumor accumulation, and localizes in tumor tissues. Notably, the F8(scFv)-DAAO-Q144R conjugate generates a stronger cytotoxicity to tumor cells than the native enzyme, especially when an inhibitor of heme oxygenase-1 (HO-1) is used, making it a promising candidate for a selective antitumor oxidative therapy controlled by the substrate addition, in the so called "activity on demand", thus sparing normal tissue from damage.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.
| | - Noemi Antonella Volpi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Barbara Ziffels
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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16
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Moussa S, Chhin D, Pollegioni L, Mauzeroll J. Quantitative measurements of free and immobilized RgDAAO Michaelis-Menten constant using an electrochemical assay reveal the impact of covalent cross-linking on substrate specificity. Anal Bioanal Chem 2021; 413:6793-6802. [PMID: 33791826 DOI: 10.1007/s00216-021-03273-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 11/29/2022]
Abstract
Challenges facing enzyme-based electrochemical sensors include substrate specificity, batch to batch reproducibility, and lack of quantitative metrics related to the effect of enzyme immobilization. We present a quick, simple, and general approach for measuring the effect of immobilization and cross-linking on enzyme activity and substrate specificity. The method can be generalized for electrochemical biosensors using an enzyme that releases hydrogen peroxide during its catalytic cycle. Using as proof of concept RgDAAO-based electrochemical biosensors, we found that the Michaelis-Menten constant (Km) decreases post immobilization, hinting at alterations in the enzyme kinetic properties and thus substrate specificity. We confirm the decrease in Km electrochemically by characterizing the substrate specificity of the immobilized RgDAAO using chronoamperometry. Our results demonstrate that enzyme immobilization affects enzyme substrate specificity and this must be carefully evaluated during biosensor development.
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Affiliation(s)
- Siba Moussa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Danny Chhin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, 21100, Varese, Italy
| | - Janine Mauzeroll
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
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17
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Using D- and L-Amino Acid Oxidases to Generate the Imino Acid Substrate to Measure the Activity of the Novel Rid (Enamine/Imine Deaminase) Class of Enzymes. Methods Mol Biol 2021. [PMID: 33751437 DOI: 10.1007/978-1-0716-1286-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
This chapter describes a method to assay the activity of reactive intermediate deaminases (Rid), a large family of conserved soluble enzymes, which have been proposed to prevent damages from metabolic intermediates such as the highly reactive and unstable compounds enamines/imines. In this method, the flavin adenine dinucleotide-dependent L- or D-amino acid oxidases generate an imino acid starting from a L- or D- amino acid, respectively. This reaction is coupled to the hydrolysis of the imino acid to the corresponding α-keto acid and ammonium ion catalyzed by a Rid enzyme. The spectrophotometric assay consists of measuring the decrease of the initial rate of formation of the semicarbazone, derived from the spontaneous reaction of the imino acid and semicarbazide, caused by the presence of the Rid enzyme. The set-up and testing of this method imply a preliminary characterization of the ability of the amino acid oxidase to release the imino acid required for the subsequent reactions. To this purpose, the activity of the L- or D-amino acid oxidases with different amino acids can be measured as production of hydrogen peroxide or formation of semicarbazone in parallel assays. The advantages and limitations of this assay of Rid activity are discussed.
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18
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Lee H, Kim D, Kim S, Lee HS. Conversion of Racemic Unnatural Amino Acids to Optically Pure Forms by a Coupled Enzymatic Reaction. Molecules 2021; 26:1274. [PMID: 33652889 PMCID: PMC7956486 DOI: 10.3390/molecules26051274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/30/2022] Open
Abstract
Genetic code expansion (GCE) technology is a useful tool for the site-specific modification of proteins. An unnatural amino acid (UAA) is one of the essential components of this technique, typically required at high concentration (1 mM or higher) in growth medium. The supply of UAAs is an important limitation to the application of GCE technology, as many UAAs are either expansive or commercially unavailable. In this study, two UAAs in a racemic mixture were converted into optically pure forms using two enzymes, the d-amino acid oxidase (RgDAAO) from Rhodotorula gracilis and the aminotransferase (TtAT) from Thermus thermophilus. In the coupled enzyme system, RgDAAO oxidizes the d-form of UAAs in a stereospecific manner and produces the corresponding α-keto acids, which are then converted into the l-form of UAAs by TtAT, resulting in the quantitative and stereospecific conversion of racemic UAAs to optically pure forms. The genetic incorporation of the optically pure UAAs into a target protein produced a better protein yield than the same experiments using the racemic mixtures of the UAAs. This method could not only be used for the preparation of optically pure UAAs from racemic mixtures, but also the broad substrate specificity of both enzymes would allow for its expansion to structurally diverse UAAs.
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Affiliation(s)
| | | | | | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Korea; (H.L.); (D.K.); (S.K.)
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19
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Maierhofer M, Rieger V, Mayr T. Optical ammonia sensors based on fluorescent aza-BODIPY dyes- a flexible toolbox. Anal Bioanal Chem 2020; 412:7559-7567. [PMID: 32839858 PMCID: PMC7533255 DOI: 10.1007/s00216-020-02891-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022]
Abstract
We present three types of optical ammonia sensors suitable for environmental, bioprocess, and reaction monitoring. A respective fluorescent BF2-chelated tetraarylazadipyrromethene dye (aza-BODIPYs) is physically entrapped in a polyurethane hydrogel (HydroMed D4) forming an emulsion system with vinyl-terminated polydimethylsiloxane (PDMS). The analyte-sensitive layer is covered by a hydrophobic membrane which excludes hydrophilic substances. Three different protection layers are tested, whereby the Teflon and the hydrophobic PES layers outperform a PDMS/TiO2 layer. Response times within their dynamic range of 15 s can be achieved, whereas the PDMS/TiO2-covered sensor requires at least 390 s. The three sensors entail the following concentration areas: first sensor 3 μg L-1-3 mg L-1 (LOD 0.23 μg L-1), second sensor 0.1-30 mg L-1 (LOD 28 μg L-1), and third sensor 3 mg L-1-1 g L-1 (LOD 0.51 mg L-1). Readout is performed with a commercially available phase fluorimeter combined with optical fibers. Dual-lifetime referencing (DLR) is used as referencing method and Egyptian blue acts as an inert reference material. No cross-sensitivity to pH changes can be detected.
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Affiliation(s)
- Maximilian Maierhofer
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/2, 8010, Graz, Austria
| | - Veronika Rieger
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/2, 8010, Graz, Austria
| | - Torsten Mayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/2, 8010, Graz, Austria.
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20
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Lee CJ, Qiu TA, Sweedler JV. d-Alanine: Distribution, origin, physiological relevance, and implications in disease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140482. [DOI: 10.1016/j.bbapap.2020.140482] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023]
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21
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Rosini E, Pollegioni L. PEG-DAAO conjugate: A promising tool for cancer therapy optimized by protein engineering. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 24:102122. [DOI: 10.1016/j.nano.2019.102122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022]
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22
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Huang R, Chen H, Upp DM, Lewis JC, Zhang YHPJ. A High-Throughput Method for Directed Evolution of NAD(P) +-Dependent Dehydrogenases for the Reduction of Biomimetic Nicotinamide Analogues. ACS Catal 2019; 9:11709-11719. [PMID: 34765284 DOI: 10.1021/acscatal.9b03840] [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] [Indexed: 01/08/2023]
Abstract
Engineering flavin-free NAD(P)+-dependent dehydrogenases to reduce biomimetic nicotinamide analogues (mNAD+s) is of importance for eliminating the need for costly NAD(P)+ in coenzyme regeneration systems. Current redox dye-based screening methods for engineering the mNAD+ specificity of dehydrogenases are frequently encumbered by a background signal from endogenous NAD(P) and intracellular reducing compounds, making the detection of low mNAD+-based activities a limiting factor for directed evolution. Here, we develop a high-throughput screening method, NAD(P)-eliminated solid-phase assay (NESPA), which can reliably identify mNAD+-active mutants of dehydrogenases with a minimal background signal. This method involves (1) heat lysis of colonies to permeabilize the cell membrane, (2) colony transfer onto filter paper, (3) washing to remove endogenous NAD(P) and reducing compounds, (4) enzyme-coupled assay for mNADH-dependent color production, and (5) digital imaging of colonies to identify mNAD+-active mutants. This method was used to improve the activity of 6-phosphogluconate dehydrogenase on nicotinamide mononucleotide (NMN+). The best mutant obtained after six rounds of directed evolution exhibits a 50-fold enhancement in catalytic efficiency (k cat/K M) and a specific activity of 17.7 U/mg on NMN+, which is comparable to the wild-type enzyme on its natural coenzyme, NADP+. The engineered dehydrogenase was then used to construct an NMNH regeneration system to drive an ene-reductase catalysis. A comparable level of turnover frequency and product yield was observed using the engineered system relative to NADPH regeneration by using the wild-type dehydrogenase. NESPA provides a simple and accurate readout of mNAD+-based activities and the screening at high-throughput levels (approximately tens of thousands per round), thus opening up an avenue for the evolution of dehydrogenases with specific activities on mNAD+s similar to the levels of natural enzyme/coenzyme pairs.
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Affiliation(s)
- Rui Huang
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Hui Chen
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David M. Upp
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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23
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Sun Y, Zhan A, Zhou S, Kuang X, Shen H, Liu H, Xu Y. A novel mitochondria-targeting tetrapeptide for subcellular delivery of nanoparticles. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Nagatomo N, Yoshimoto M. High Permeability of Polyunsaturated Lipid Bilayers As Applied to Attoliter Enzyme Reactors. ACS APPLIED BIO MATERIALS 2019; 2:2453-2463. [DOI: 10.1021/acsabm.9b00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Naoyuki Nagatomo
- Department of Applied Chemistry, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Makoto Yoshimoto
- Department of Applied Chemistry, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
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25
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Kim SH, Shishido Y, Sogabe H, Rachadech W, Yorita K, Kato Y, Fukui K. Age- and gender-dependent D-amino acid oxidase activity in mouse brain and peripheral tissues: implication for aging and neurodegeneration. J Biochem 2019; 166:187-196. [DOI: 10.1093/jb/mvz025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/01/2019] [Indexed: 12/11/2022] Open
Abstract
Abstract
D-amino acid oxidase (DAO) is a flavoenzyme, catalysing oxidative deamination of D-amino acids to produce corresponding α-keto acids, ammonia and hydrogen peroxide. In our search for DAO activity among various tissues, we developed a sensitive assay based on hydrogen peroxide production involving enzyme-coupled colorimetric assay with peroxidase. We first optimized buffer components to extract DAO protein from mouse tissues. Here we show that DAO activity was detected in kidney, cerebellum, medulla oblongata, midbrain and spinal cord, but not in liver. In addition, we observed that DAO activity and expression were decreased in thoracic and lumbar regions of spinal cord in aged mice when compared with young mice, indicating that decreased DAO is involved in motoneuron degeneration during senescence. We also found gender difference in DAO activity in the kidney, suggesting that DAO activity is influenced by sexual dimorphism. We newly detected DAO activity in the epididymis, although undetected in testis. Furthermore, DAO activity was significantly higher in the caput region than corpus and cauda regions of epididymis, indicating that D-amino acids present in the testis are eliminated in epididymis. Taken together, age- and gender-dependent DAO activity in each organ may underlie the human pathophysiology regulated by D-amino acid metabolism.
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Affiliation(s)
- Soo Hyeon Kim
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Yuji Shishido
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Hirofumi Sogabe
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Wanitcha Rachadech
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Kazuko Yorita
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Yusuke Kato
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Kiyoshi Fukui
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
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Takahashi S, Osugi K, Shimekake Y, Shinbo A, Abe K, Kera Y. Characterization and improvement of substrate-binding affinity of D-aspartate oxidase of the thermophilic fungus Thermomyces dupontii. Appl Microbiol Biotechnol 2019; 103:4053-4064. [PMID: 30937498 DOI: 10.1007/s00253-019-09787-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/19/2019] [Indexed: 12/23/2022]
Abstract
D-Aspartate oxidase (DDO) is a valuable enzyme that can be utilized in the determination of acidic D-amino acids and the optical resolution of a racemic mixture of acidic amino acids, which require its higher stability, higher catalytic activity, and higher substrate-binding affinity. In the present study, we identified DDO gene (TdDDO) of a thermophilic fungus, Thermomyces dupontii, and characterized the recombinant enzyme expressed in Escherichia coli. In addition, we generated a variant that has a higher substrate-binding affinity. The recombinant TdDDO expressed in E. coli exhibited oxidase activity toward acidic D-amino acids and a neutral D-amino acid, D-Gln, with the highest activity toward D-Glu. The Km and kcat values for D-Glu were 2.16 mM and 217 s-1, respectively. The enzyme had an optimum pH and temperature 8.0 and 60 °C, respectively, and was stable between pH 5.0 and 10.0, with a T50 of ca. 51 °C, which was much higher than that in DDOs from other origins. Enzyme stability decreased following a decrease in protein concentration, and externally added FAD could not repress the destabilization. The mutation of Phe248, potentially located in the active site of TdDDO, to Tyr residue, conserved in DDOs and D-amino acid oxidases, markedly increased substrate-binding affinity. The results showed the great potential of TdDDO and the variant for practical applications.
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Affiliation(s)
- Shouji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.
| | - Kohei Osugi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yuya Shimekake
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akira Shinbo
- 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
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Bernardo-García N, Sánchez-Murcia PA, Espaillat A, Martínez-Caballero S, Cava F, Hermoso JA, Gago F. Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Org Biomol Chem 2019; 17:4350-4358. [DOI: 10.1039/c9ob00223e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The commonly used Tris buffer acts as a surrogate substrate and deformylates pyridoxal phosphate in a bacterial alanine racemase at subzero temperatures.
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Affiliation(s)
- Noelia Bernardo-García
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | | | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | - Federico Gago
- Department of Biomedical Sciences
- “Unidad Asociada IQM-CSIC”
- University of Alcalá
- Madrid
- Spain
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