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Chen H, Guo Z, Sun Y, Dai X. The immunometabolic reprogramming of microglia in Alzheimer's disease. Neurochem Int 2023; 171:105614. [PMID: 37748710 DOI: 10.1016/j.neuint.2023.105614] [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: 07/28/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative disorder (NDD). In the central nervous system (CNS), immune cells like microglia could reprogram intracellular metabolism to alter or exert cellular immune functions in response to environmental stimuli. In AD, microglia could be activated and differentiated into pro-inflammatory or anti-inflammatory phenotypes, and these differences in cellular phenotypes resulted in variance in cellular energy metabolism. Considering the enormous energy requirement of microglia for immune functions, the changes in mitochondria-centered energy metabolism and substrates of microglia are crucial for the cellular regulation of immune responses. Here we reviewed the mechanisms of microglial metabolic reprogramming by analyzing their flexible metabolic patterns and changes that occurred in their metabolism during the development of AD. Further, we summarized the role of drugs in modulating immunometabolic reprogramming to prevent neuroinflammation, which may shed light on a new research direction for AD treatment.
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Affiliation(s)
- Hongli Chen
- Beijing Key Laboratory of Bioactive Substances and Functional Food, College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China
| | - Zichen Guo
- Beijing Key Laboratory of Bioactive Substances and Functional Food, College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China
| | - Yaxuan Sun
- Beijing Key Laboratory of Bioactive Substances and Functional Food, College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China
| | - Xueling Dai
- Beijing Key Laboratory of Bioactive Substances and Functional Food, College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
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2
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Aptekmann AA, Buongiorno J, Giovannelli D, Glamoclija M, Ferreiro DU, Bromberg Y. mebipred: identifying metal binding potential in protein sequence. Bioinformatics 2022; 38:3532-3540. [PMID: 35639953 PMCID: PMC9272798 DOI: 10.1093/bioinformatics/btac358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/27/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022] Open
Abstract
Motivation metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. Results we developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred’s utility in analyzing microbiome metal requirements. Availability and implementation mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA.,Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | | | - D Giovannelli
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,Department of Biology, University of Naples Federico II, Naples, Italy.,Institute for Marine Biological Resources and Biotechnology-IRBIM, National Research Council of Italy, CNR, Ancona, Italy
| | - M Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, New Brunswick, NJ, 07102, USA
| | - D U Ferreiro
- Protein Physiology Lab, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, 1428, Argentina
| | - Y Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA
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3
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Szot JO, Slavotinek A, Chong K, Brandau O, Nezarati M, Cueto-González AM, Patel MS, Devine WP, Rego S, Acyinena AP, Shannon P, Myles-Reid D, Blaser S, Mieghem TV, Yavuz-Kienle H, Skladny H, Miller K, Riera MDT, Martínez SA, Tizzano EF, Dupuis L, James Stavropoulos D, McNiven V, Mendoza-Londono R, Elliott AM, Phillips RS, Chapman G, Dunwoodie SL. New cases that expand the genotypic and phenotypic spectrum of Congenital NAD Deficiency Disorder. Hum Mutat 2021; 42:862-876. [PMID: 33942433 DOI: 10.1002/humu.24211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential coenzyme involved in over 400 cellular reactions. During embryogenesis, mammals synthesize NAD de novo from dietary l -tryptophan via the kynurenine pathway. Biallelic, inactivating variants in three genes encoding enzymes of this biosynthesis pathway (KYNU, HAAO, and NADSYN1) disrupt NAD synthesis and have been identified in patients with multiple malformations of the heart, kidney, vertebrae, and limbs; these patients have Congenital NAD Deficiency Disorder HAAO and four families with biallelic variants in KYNU. These patients present similarly with multiple malformations of the heart, kidney, vertebrae, and limbs, of variable severity. We show that each variant identified in these patients results in loss-of-function, revealed by a significant reduction in NAD levels via yeast genetic complementation assays. For the first time, missense mutations are identified as a cause of malformation and shown to disrupt enzyme function. These missense and frameshift variants cause moderate to severe NAD deficiency in yeast, analogous to insufficient synthesized NAD in patients. We hereby expand the genotypic and corresponding phenotypic spectrum of Congenital NAD Deficiency Disorder.
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Affiliation(s)
- Justin O Szot
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Karen Chong
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Marjan Nezarati
- Genetics Program, North York General Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Anna M Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Millan S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Walter P Devine
- Department of Anatomic Pathology, University of California, San Francisco, California, USA
| | - Shannon Rego
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Alicia P Acyinena
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Patrick Shannon
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Diane Myles-Reid
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Susan Blaser
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tim V Mieghem
- Fetal Medicine Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Kristen Miller
- Genetics Program, North York General Hospital, Toronto, Ontario, Canada
| | - Miereia D T Riera
- Metabolic Unit and Pediatric Neurology Department, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Silvia A Martínez
- Fetal Medicine Unit and Obstetrics Department, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona, Barcelona, Spain
| | - Lucie Dupuis
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri James Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vanda McNiven
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Phillips
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A 2020; 117:19720-19730. [PMID: 32732435 PMCID: PMC7443976 DOI: 10.1073/pnas.2005327117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yu Yang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249;
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