1
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Pedre B. A guide to genetically-encoded redox biosensors: State of the art and opportunities. Arch Biochem Biophys 2024; 758:110067. [PMID: 38908743 DOI: 10.1016/j.abb.2024.110067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Genetically-encoded redox biosensors have become invaluable tools for monitoring cellular redox processes with high spatiotemporal resolution, coupling the presence of the redox-active analyte with a change in fluorescence signal that can be easily recorded. This review summarizes the available fluorescence recording methods and presents an in-depth classification of the redox biosensors, organized by the analytes they respond to. In addition to the fluorescent protein-based architectures, this review also describes the recent advances on fluorescent, chemigenetic-based redox biosensors and other emerging chemigenetic strategies. This review examines how these biosensors are designed, the biosensors sensing mechanism, and their practical advantages and disadvantages.
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Affiliation(s)
- Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU Leuven, Belgium.
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2
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Ren C, Zhang S, Chen Y, Deng K, Kuang M, Gong Z, Zhang K, Wang P, Huang P, Zhou Z, Gong A. Exploring nicotinamide adenine dinucleotide precursors across biosynthesis pathways: Unraveling their role in the ovary. FASEB J 2024; 38:e23804. [PMID: 39037422 DOI: 10.1096/fj.202400453r] [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: 03/02/2024] [Revised: 05/31/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Natural Nicotinamide Adenine Dinucleotide (NAD+) precursors have attracted much attention due to their positive effects in promoting ovarian health. However, their target tissue, synthesis efficiency, advantages, and disadvantages are still unclear. This review summarizes the distribution of NAD+ at the tissue, cellular and subcellular levels, discusses its biosynthetic pathways and the latest findings in ovary, include: (1) NAD+ plays distinct roles both intracellularly and extracellularly, adapting its distribution in response to requirements. (2) Different precursors differs in target tissues, synthetic efficiency, biological utilization, and adverse effects. Importantly: tryptophan is primarily utilized in the liver and kidneys, posing metabolic risks in excess; nicotinamide (NAM) is indispensable for maintaining NAD+ levels; nicotinic acid (NA) constructs a crucial bridge between intestinal microbiota and the host with diverse functions; nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) increase NAD+ systemically and can be influenced by delivery route, tissue specificity, and transport efficiency. (3) The biosynthetic pathways of NAD+ are intricately intertwined. They provide multiple sources and techniques for NAD+ synthesis, thereby reducing the dependence on a single molecule to maintain cellular NAD+ levels. However, an excess of a specific precursor potentially influencing other pathways. In addition, Protein expression analysis suggest that ovarian tissues may preferentially utilize NAM and NMN. These findings summarize the specific roles and potential of NAD+ precursors in enhancing ovarian health. Future research should delve into the molecular mechanisms and intervention strategies of different precursors, aiming to achieve personalized prevention or treatment of ovarian diseases, and reveal their clinical application value.
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Affiliation(s)
- Caifang Ren
- School of Medicine, Jiangsu University, Zhenjiang, China
- Hematological Disease Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Shuang Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yanyan Chen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Kaiping Deng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Meiqian Kuang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zihao Gong
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ke Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Panqi Wang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Pan Huang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhengrong Zhou
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Aihua Gong
- School of Medicine, Jiangsu University, Zhenjiang, China
- Hematological Disease Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
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3
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Chang H, Clemens S, Gao P, Li Q, Zhao H, Wang L, Zhang J, Zhou P, Johnsson K, Wang L. Fluorogenic Rhodamine-Based Chemigenetic Biosensor for Monitoring Cellular NADPH Dynamics. J Am Chem Soc 2024. [PMID: 39037873 DOI: 10.1021/jacs.3c13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Ratiometric biosensors employing Förster Resonance Energy Transfer (FRET) enable the real-time tracking of metabolite dynamics. Here, we introduce an approach for generating a FRET-based biosensor in which changes in apparent FRET efficiency rely on the analyte-controlled fluorogenicity of a rhodamine rather than the commonly used distance change between donor-acceptor fluorophores. Our fluorogenic, rhodamine-based, chemigenetic biosensor (FOCS) relies on a synthetic, protein-tethered FRET probe, in which the rhodamine acting as the FRET acceptor switches in an analyte-dependent manner from a dark to a fluorescent state. This allows ratiometric sensing of the analyte concentration. We use this approach to generate a chemigenetic biosensor for nicotinamide adenine dinucleotide phosphate (NADPH). FOCS-NADPH exhibits a rapid and reversible response toward NAPDH with a good dynamic range, selectivity, and pH insensitivity. FOCS-NADPH allows real-time monitoring of cytosolic NADPH fluctuations in live cells during oxidative stress or after drug exposure. We furthermore used FOCS-NADPH to investigate NADPH homeostasis regulation through the pentose phosphate pathway of glucose metabolism. FOCS-NADPH is a powerful tool for studying NADPH metabolism and serves as a blueprint for the development of future fluorescent biosensors.
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Affiliation(s)
- Huimin Chang
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Simon Clemens
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg D-69120, Germany
| | - Pingting Gao
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Quanlin Li
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Hanqing Zhao
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Lehua Wang
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Jingye Zhang
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Pinghong Zhou
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg D-69120, Germany
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Lu Wang
- Key Laboratory of Smart Drug Delivery Ministry of Education, School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai 201203, China
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4
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Migaud ME, Ziegler M, Baur JA. Regulation of and challenges in targeting NAD + metabolism. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00752-w. [PMID: 39026037 DOI: 10.1038/s41580-024-00752-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Nicotinamide adenine dinucleotide, in its oxidized (NAD+) and reduced (NADH) forms, is a reduction-oxidation (redox) co-factor and substrate for signalling enzymes that have essential roles in metabolism. The recognition that NAD+ levels fall in response to stress and can be readily replenished through supplementation has fostered great interest in the potential benefits of increasing or restoring NAD+ levels in humans to prevent or delay diseases and degenerative processes. However, much about the biology of NAD+ and related molecules remains poorly understood. In this Review, we discuss the current knowledge of NAD+ metabolism, including limitations of, assumptions about and unappreciated factors that might influence the success or contribute to risks of NAD+ supplementation. We highlight several ongoing controversies in the field, and discuss the role of the microbiome in modulating the availability of NAD+ precursors such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), the presence of multiple cellular compartments that have distinct pools of NAD+ and NADH, and non-canonical NAD+ and NADH degradation pathways. We conclude that a substantial investment in understanding the fundamental biology of NAD+, its detection and its metabolites in specific cells and cellular compartments is needed to support current translational efforts to safely boost NAD+ levels in humans.
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Affiliation(s)
- Marie E Migaud
- Mitchell Cancer Institute, Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Joseph A Baur
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Lane AN, Higashi RM, Fan TWM. Challenges of Spatially Resolved Metabolism in Cancer Research. Metabolites 2024; 14:383. [PMID: 39057706 PMCID: PMC11278851 DOI: 10.3390/metabo14070383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Stable isotope-resolved metabolomics comprises a critical set of technologies that can be applied to a wide variety of systems, from isolated cells to whole organisms, to define metabolic pathway usage and responses to perturbations such as drugs or mutations, as well as providing the basis for flux analysis. As the diversity of stable isotope-enriched compounds is very high, and with newer approaches to multiplexing, the coverage of metabolism is now very extensive. However, as the complexity of the model increases, including more kinds of interacting cell types and interorgan communication, the analytical complexity also increases. Further, as studies move further into spatially resolved biology, new technical problems have to be overcome owing to the small number of analytes present in the confines of a single cell or cell compartment. Here, we review the overall goals and solutions made possible by stable isotope tracing and their applications to models of increasing complexity. Finally, we discuss progress and outstanding difficulties in high-resolution spatially resolved tracer-based metabolic studies.
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Affiliation(s)
- Andrew N. Lane
- Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, USA; (R.M.H.); (T.W.-M.F.)
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6
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Jamerson LE, Bradshaw PC. The Roles of White Adipose Tissue and Liver NADPH in Dietary Restriction-Induced Longevity. Antioxidants (Basel) 2024; 13:820. [PMID: 39061889 PMCID: PMC11273496 DOI: 10.3390/antiox13070820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Dietary restriction (DR) protocols frequently employ intermittent fasting. Following a period of fasting, meal consumption increases lipogenic gene expression, including that of NADPH-generating enzymes that fuel lipogenesis in white adipose tissue (WAT) through the induction of transcriptional regulators SREBP-1c and CHREBP. SREBP-1c knockout mice, unlike controls, did not show an extended lifespan on the DR diet. WAT cytoplasmic NADPH is generated by both malic enzyme 1 (ME1) and the pentose phosphate pathway (PPP), while liver cytoplasmic NADPH is primarily synthesized by folate cycle enzymes provided one-carbon units through serine catabolism. During the daily fasting period of the DR diet, fatty acids are released from WAT and are transported to peripheral tissues, where they are used for beta-oxidation and for phospholipid and lipid droplet synthesis, where monounsaturated fatty acids (MUFAs) may activate Nrf1 and inhibit ferroptosis to promote longevity. Decreased WAT NADPH from PPP gene knockout stimulated the browning of WAT and protected from a high-fat diet, while high levels of NADPH-generating enzymes in WAT and macrophages are linked to obesity. But oscillations in WAT [NADPH]/[NADP+] from feeding and fasting cycles may play an important role in maintaining metabolic plasticity to drive longevity. Studies measuring the WAT malate/pyruvate as a proxy for the cytoplasmic [NADPH]/[NADP+], as well as studies using fluorescent biosensors expressed in the WAT of animal models to monitor the changes in cytoplasmic [NADPH]/[NADP+], are needed during ad libitum and DR diets to determine the changes that are associated with longevity.
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Affiliation(s)
| | - Patrick C. Bradshaw
- Department of Biomedical Sciences, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
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7
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Noble M, Chatterjee A, Sekaran T, Schwarzl T, Hentze MW. Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase. RNA (NEW YORK, N.Y.) 2024; 30:839-853. [PMID: 38609156 PMCID: PMC11182015 DOI: 10.1261/rna.079925.123] [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: 12/11/2023] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Several enzymes of intermediary metabolism have been identified to bind RNA in cells, with potential consequences for the bound RNAs and/or the enzyme. In this study, we investigate the RNA-binding activity of the mitochondrial enzyme malate dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and the malate-aspartate shuttle. We confirmed in cellulo RNA binding of MDH2 using orthogonal biochemical assays and performed enhanced cross-linking and immunoprecipitation (eCLIP) to identify the cellular RNAs associated with endogenous MDH2. Surprisingly, MDH2 preferentially binds cytosolic over mitochondrial RNAs, although the latter are abundant in the milieu of the mature protein. Subcellular fractionation followed by RNA-binding assays revealed that MDH2-RNA interactions occur predominantly outside of mitochondria. We also found that a cytosolically retained N-terminal deletion mutant of MDH2 is competent to bind RNA, indicating that mitochondrial targeting is dispensable for MDH2-RNA interactions. MDH2 RNA binding increased when cellular NAD+ levels (MDH2's cofactor) were pharmacologically diminished, suggesting that the metabolic state of cells affects RNA binding. Taken together, our data implicate an as yet unidentified function of MDH2-binding RNA in the cytosol.
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Affiliation(s)
- Michelle Noble
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | | | - Thileepan Sekaran
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
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8
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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9
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Sauter R, Sharma S, Heiland I. Accounting for NAD Concentrations in Genome-Scale Metabolic Models Captures Important Metabolic Alterations in NAD-Depleted Systems. Biomolecules 2024; 14:602. [PMID: 38786009 PMCID: PMC11117748 DOI: 10.3390/biom14050602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) is a ubiquitous molecule found within all cells, acting as a crucial coenzyme in numerous metabolic reactions. It plays a vital role in energy metabolism, cellular signaling, and DNA repair. Notably, NAD levels decline naturally with age, and this decline is associated with the development of various age-related diseases. Despite this established link, current genome-scale metabolic models, which offer powerful tools for understanding cellular metabolism, do not account for the dynamic changes in NAD concentration. This impedes our understanding of a fluctuating NAD level's impact on cellular metabolism and its contribution to age-related pathologies. To bridge this gap in our knowledge, we have devised a novel method that integrates altered NAD concentration into genome-scale models of human metabolism. This approach allows us to accurately reflect the changes in fatty acid metabolism, glycolysis, and oxidative phosphorylation observed experimentally in an engineered human cell line with a compromised level of subcellular NAD.
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Affiliation(s)
- Roland Sauter
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Suraj Sharma
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway;
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9019 Tromsø, Norway;
- Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
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10
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Lu MJ, Busquets J, Impedovo V, Wilson CN, Chan HR, Chang YT, Matsui W, Tiziani S, Cambronne XA. SLC25A51 decouples the mitochondrial NAD +/NADH ratio to control proliferation of AML cells. Cell Metab 2024; 36:808-821.e6. [PMID: 38354740 PMCID: PMC10990793 DOI: 10.1016/j.cmet.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/30/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
SLC25A51 selectively imports oxidized NAD+ into the mitochondrial matrix and is required for sustaining cell respiration. We observed elevated expression of SLC25A51 that correlated with poorer outcomes in patients with acute myeloid leukemia (AML), and we sought to determine the role SLC25A51 may serve in this disease. We found that lowering SLC25A51 levels led to increased apoptosis and prolonged survival in orthotopic xenograft models. Metabolic flux analyses indicated that depletion of SLC25A51 shunted flux away from mitochondrial oxidative pathways, notably without increased glycolytic flux. Depletion of SLC25A51 combined with 5-azacytidine treatment limits expansion of AML cells in vivo. Together, the data indicate that AML cells upregulate SLC25A51 to decouple mitochondrial NAD+/NADH for a proliferative advantage by supporting oxidative reactions from a variety of fuels. Thus, SLC25A51 represents a critical regulator that can be exploited by cancer cells and may be a vulnerability for refractory AML.
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Affiliation(s)
- Mu-Jie Lu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jonathan Busquets
- Department of Nutritional Sciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Valeria Impedovo
- Department of Nutritional Sciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Crystal N Wilson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Ru Chan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Yu-Tai Chang
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA; LIVESTRONG Cancer Institutes, University of Texas at Austin, Austin, TX, USA
| | - William Matsui
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA; LIVESTRONG Cancer Institutes, University of Texas at Austin, Austin, TX, USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA; Department of Pediatrics, Dell Medical School, University of Texas at Austin, Austin, TX, USA; Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA; LIVESTRONG Cancer Institutes, University of Texas at Austin, Austin, TX, USA
| | - Xiaolu A Cambronne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA; LIVESTRONG Cancer Institutes, University of Texas at Austin, Austin, TX, USA.
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11
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Recent advancements of fluorescent biosensors using semisynthetic probes. Biosens Bioelectron 2024; 247:115862. [PMID: 38147718 DOI: 10.1016/j.bios.2023.115862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 12/28/2023]
Abstract
Fluorescent biosensors are crucial experimental tools for live-cell imaging and the quantification of different biological analytes. Fluorescent protein (FP)-based biosensors are widely used for imaging applications in living systems. However, the use of FP-based biosensors is hindered by their large size, poor photostability, and laborious genetic manipulations required to improve their properties. Recently, semisynthetic fluorescent biosensors have been developed to address the limitations of FP-based biosensors using chemically modified fluorescent probes and self-labeling protein tag/peptide tags or DNA/RNA-based hybrid systems. Semisynthetic biosensors have unique advantages, as they can be easily modified using different probes. Moreover, the self-labeling protein tag, which labels synthetically developed ligands via covalent bonds, has immense potential for biosensor development. This review discusses the recent progress in different types of fluorescent biosensors for metabolites, protein aggregation and degradation, DNA methylation, endocytosis and exocytosis, membrane tension, and cellular viscosity. Here, we explain in detail the design strategy and working principle of these biosensors. The information presented will help the reader to create new biosensors using self-labeling protein tags for various applications.
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Affiliation(s)
- Shahi Imam Reja
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Minoshima
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kazuya Kikuchi
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan; Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
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12
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Vogelsang L, Dietz KJ. Inactivation of Three Stacked Genes of Cytosolic Peroxiredoxins by Genome Editing. Methods Mol Biol 2024; 2798:235-263. [PMID: 38587748 DOI: 10.1007/978-1-0716-3826-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A set of peroxidases detoxifies H2O2 and mediates H2O2-dependent signal propagation. The peroxidases include peroxiredoxins, glutathione peroxidases, ascorbate peroxidases, and catalases. This at least partial redundancy impedes addressing individual proteins in living plant cells so that the protein functions are often studied by biochemical assays in vitro. In vivo analysis frequently relies on transgenic insertion lines resulting in the knockdown or knockout of the protein of interest. However, many proteins have multiple isoforms in close genomic arrangement so that even crossing of transgenic lines does not allow for a knockdown of all isoforms. The genes encoding for the three cytosolic peroxiredoxins PRXIIB, C, and D in Arabidopsis thaliana are located in close vicinity on chromosome 1 so that crossing over between the genes most rarely occurs and successful crossing of the plants appears impossible. Genome editing instead allows targeting of multiple isoforms and knocks out several genes at once. This chapter describes how to inactivate the three cytosolic peroxiredoxins by CRISPR/Cas9 in A. thaliana.
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Affiliation(s)
- Lara Vogelsang
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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13
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Dyachenko EI, Bel’skaya LV. The Role of Amino Acids in Non-Enzymatic Antioxidant Mechanisms in Cancer: A Review. Metabolites 2023; 14:28. [PMID: 38248831 PMCID: PMC10818545 DOI: 10.3390/metabo14010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Currently, the antioxidant properties of amino acids and their role in the physicochemical processes accompanying oxidative stress in cancer remain unclear. Cancer cells are known to extensively uptake amino acids, which are used as an energy source, antioxidant precursors that reduce oxidative stress in cancer, and as regulators of inhibiting or inducing tumor cell-associated gene expression. This review examines nine amino acids (Cys, His, Phe, Met, Trp, Tyr, Pro, Arg, Lys), which play a key role in the non-enzymatic oxidative process in various cancers. Conventionally, these amino acids can be divided into two groups, in one of which the activity increases (Cys, Phe, Met, Pro, Arg, Lys) in cancer, and in the other, it decreases (His, Trp, Tyr). The review examines changes in the metabolism of nine amino acids in eleven types of oncology. We have identified the main nonspecific mechanisms of changes in the metabolic activity of amino acids, and described direct and indirect effects on the redox homeostasis of cells. In the future, this will help to understand better the nature of life of a cancer cell and identify therapeutic targets more effectively.
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Affiliation(s)
| | - Lyudmila V. Bel’skaya
- Biochemistry Research Laboratory, Omsk State Pedagogical University, Omsk 644099, Russia;
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14
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Zhou HL, Grimmett ZW, Venetos NM, Stomberski CT, Qian Z, McLaughlin PJ, Bansal PK, Zhang R, Reynolds JD, Premont RT, Stamler JS. An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling. Cell 2023; 186:5812-5825.e21. [PMID: 38056462 PMCID: PMC10794992 DOI: 10.1016/j.cell.2023.11.009] [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: 03/28/2023] [Revised: 09/01/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
Acyl-coenzyme A (acyl-CoA) species are cofactors for numerous enzymes that acylate thousands of proteins. Here, we describe an enzyme that uses S-nitroso-CoA (SNO-CoA) as its cofactor to S-nitrosylate multiple proteins (SNO-CoA-assisted nitrosylase, SCAN). Separate domains in SCAN mediate SNO-CoA and substrate binding, allowing SCAN to selectively catalyze SNO transfer from SNO-CoA to SCAN to multiple protein targets, including the insulin receptor (INSR) and insulin receptor substrate 1 (IRS1). Insulin-stimulated S-nitrosylation of INSR/IRS1 by SCAN reduces insulin signaling physiologically, whereas increased SCAN activity in obesity causes INSR/IRS1 hypernitrosylation and insulin resistance. SCAN-deficient mice are thus protected from diabetes. In human skeletal muscle and adipose tissue, SCAN expression increases with body mass index and correlates with INSR S-nitrosylation. S-nitrosylation by SCAN/SNO-CoA thus defines a new enzyme class, a unique mode of receptor tyrosine kinase regulation, and a revised paradigm for NO function in physiology and disease.
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Affiliation(s)
- Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicholas M Venetos
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Colin T Stomberski
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhaoxia Qian
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Precious J McLaughlin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Puneet K Bansal
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rongli Zhang
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - James D Reynolds
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Anesthesiology and Perioperative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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15
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Goyal S, Cambronne XA. Layered mechanisms regulating the human mitochondrial NAD+ transporter SLC25A51. Biochem Soc Trans 2023; 51:1989-2004. [PMID: 38108469 PMCID: PMC10802112 DOI: 10.1042/bst20220318] [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: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
SLC25A51 is the primary mitochondrial NAD+ transporter in humans and controls many local reactions by mediating the influx of oxidized NAD+. Intriguingly, SLC25A51 lacks several key features compared with other members in the mitochondrial carrier family, thus its molecular mechanism has been unclear. A deeper understanding would shed light on the control of cellular respiration, the citric acid cycle, and free NAD+ concentrations in mammalian mitochondria. This review discusses recent insights into the transport mechanism of SLC25A51, and in the process highlights a multitiered regulation that governs NAD+ transport. The aspects regulating SLC25A51 import activity can be categorized as contributions from (1) structural characteristics of the transporter itself, (2) its microenvironment, and (3) distinctive properties of the transported ligand. These unique mechanisms further evoke compelling new ideas for modulating the activity of this transporter, as well as new mechanistic models for the mitochondrial carrier family.
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Affiliation(s)
- Shivansh Goyal
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Xiaolu A. Cambronne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
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16
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Stern A, Fokra M, Sarvin B, Alrahem AA, Lee WD, Aizenshtein E, Sarvin N, Shlomi T. Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution. Nat Commun 2023; 14:7525. [PMID: 37980339 PMCID: PMC10657349 DOI: 10.1038/s41467-023-42824-z] [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: 05/03/2021] [Accepted: 10/19/2023] [Indexed: 11/20/2023] Open
Abstract
The inability to inspect metabolic activities within distinct subcellular compartments has been a major barrier to our understanding of eukaryotic cell metabolism. Previous work addressed this challenge by analyzing metabolism in isolated organelles, which grossly bias metabolic activity. Here, we describe a method for inferring physiological metabolic fluxes and metabolite concentrations in mitochondria and cytosol based on isotope tracing experiments performed with intact cells. This is made possible by computational deconvolution of metabolite isotopic labeling patterns and concentrations into cytosolic and mitochondrial counterparts, coupled with metabolic and thermodynamic modelling. Our approach lowers the uncertainty regarding compartmentalized fluxes and concentrations by one and three orders of magnitude compared to existing modelling approaches, respectively. We derive a quantitative view of mitochondrial and cytosolic metabolic activities in central carbon metabolism across cultured cell lines without performing cell fractionation, finding major variability in compartmentalized malate-aspartate shuttle fluxes. We expect our approach for inferring metabolism at a subcellular resolution to be instrumental for a variety of studies of metabolic dysfunction in human disease and for bioengineering.
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Affiliation(s)
- Alon Stern
- Department of Computer Science, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Mariam Fokra
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Boris Sarvin
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Ahmad Abed Alrahem
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Won Dong Lee
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Elina Aizenshtein
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Nikita Sarvin
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Tomer Shlomi
- Department of Computer Science, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
- Lokey Center for Life Science and Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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17
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Tian J, Li B, Zhang F, Yao Z, Song W, Tang Y, Ping Y, Liu B. Activatable Type I Photosensitizer with Quenched Photosensitization Pre and Post Photodynamic Therapy. Angew Chem Int Ed Engl 2023; 62:e202307288. [PMID: 37681940 DOI: 10.1002/anie.202307288] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/09/2023]
Abstract
The phototoxicity of photosensitizers (PSs) pre and post photodynamic therapy (PDT), and the hypoxic tumor microenvironment are two major problems limiting the application of PDT. While activatable PSs can successfully address the PS phototoxicity pre PDT, and type I PS can generate reactive oxygen species (ROS) effectively in hypoxic environment, very limited approaches are available for addressing the phototoxicity post PDT. There is virtually no solution available to address all these issues using a single design. Herein, we propose a proof-of-concept on-demand switchable photosensitizer with quenched photosensitization pre and post PDT, which could be activated only in tumor hypoxic environment. Particularly, a hypoxia-normoxia cycling responsive type I PS TPFN-AzoCF3 was designed to demonstrate the concept, which was further formulated into TPFN-AzoCF3 nanoparticles (NPs) using DSPE-PEG-2000 as the encapsulation matrix. The NPs could be activated only in hypoxic tumors to generate type I ROS during PDT treatment, but remain non-toxic in normal tissues, pre or after PDT, thus minimizing side effects and improving the therapeutic effect. With promising results in in vitro and in vivo tumor treatment, this presented strategy will pave the way for the design of more on-demand switchable photosensitizers with minimized side effects in the future.
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Affiliation(s)
- Jianwu Tian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 5 A Engineering Drive 1, Singapore, 117411, Singapore
| | - Bowen Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 5 A Engineering Drive 1, Singapore, 117411, Singapore
| | - Fu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhuo Yao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wentao Song
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 5 A Engineering Drive 1, Singapore, 117411, Singapore
| | - Yufu Tang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 5 A Engineering Drive 1, Singapore, 117411, Singapore
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 5 A Engineering Drive 1, Singapore, 117411, Singapore
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18
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Si D, Li Q, Bao Y, Zhang J, Wang L. Fluorogenic and Cell-Permeable Rhodamine Dyes for High-Contrast Live-Cell Protein Labeling in Bioimaging and Biosensing. Angew Chem Int Ed Engl 2023; 62:e202307641. [PMID: 37483077 DOI: 10.1002/anie.202307641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
The advancement of fluorescence microscopy techniques has opened up new opportunities for visualizing proteins and unraveling their functions in living biological systems. Small-molecule organic dyes, which possess exceptional photophysical properties, small size, and high photostability, serve as powerful fluorescent reporters in protein imaging. However, achieving high-contrast live-cell labeling of target proteins with conventional organic dyes remains a considerable challenge in bioimaging and biosensing due to their inadequate cell permeability and high background signal. Over the past decade, a novel generation of fluorogenic and cell-permeable dyes has been developed, which have substantially improved live-cell protein labeling by fine-tuning the reversible equilibrium between a cell-permeable, nonfluorescent spirocyclic state (unbound) and a fluorescent zwitterion (protein-bound) of rhodamines. In this review, we present the mechanism and design strategies of these fluorogenic and cell-permeable rhodamines, as well as their applications in bioimaging and biosensing.
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Affiliation(s)
- Dongjuan Si
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Quanlin Li
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Yifan Bao
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Jingye Zhang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Lu Wang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
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19
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Wang P, Chen M, Hou Y, Luan J, Liu R, Chen L, Hu M, Yu Q. Fingerstick blood assay maps real-world NAD + disparity across gender and age. Aging Cell 2023; 22:e13965. [PMID: 37641521 PMCID: PMC10577551 DOI: 10.1111/acel.13965] [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: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+ ) level has been associated with various age-related diseases and its pharmacological modulation emerges as a potential approach for aging intervention. But human NAD+ landscape exhibits large heterogeneity. The lack of rapid, low-cost assays limits the establishment of whole-blood NAD+ baseline and the development of personalized therapies, especially for those with poor responses towards conventional NAD+ supplementations. Here, we developed an automated NAD+ analyzer for the rapid measurement of NAD+ with 5 μL of capillary blood using recombinant bioluminescent sensor protein and automated optical reader. The minimal invasiveness of the assay allowed a frequent and decentralized mapping of real-world NAD+ dynamics. We showed that aerobic sport and NMN supplementation increased whole-blood NAD+ and that male on average has higher NAD+ than female before the age of 50. We further revealed the long-term stability of human NAD+ baseline over 100 days and identified major real-world NAD+ -modulating behaviors.
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Affiliation(s)
- Pei Wang
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
| | - Meiting Chen
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
| | - Yaying Hou
- Celfull (China) Operation and Research CenterShenzhenChina
| | - Jun Luan
- Department of Sports MedicineGuangzhou Sport UniversityGuangzhouChina
| | - Ruili Liu
- Celfull (China) Operation and Research CenterShenzhenChina
| | - Liuqing Chen
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
| | - Min Hu
- Department of Sports MedicineGuangzhou Sport UniversityGuangzhouChina
| | - Qiuliyang Yu
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
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20
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Güldenpfennig A, Hopp AK, Muskalla L, Manetsch P, Raith F, Hellweg L, Dördelmann C, Leslie Pedrioli D, Johnsson K, Superti-Furga G, Hottiger M. Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels. Nucleic Acids Res 2023; 51:9248-9265. [PMID: 37587695 PMCID: PMC10516648 DOI: 10.1093/nar/gkad659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Though the effect of the recently identified mitochondrial NAD+ transporter SLC25A51 on glucose metabolism has been described, its contribution to other NAD+-dependent processes throughout the cell such as ADP-ribosylation remains elusive. Here, we report that absence of SLC25A51 leads to increased NAD+ concentration not only in the cytoplasm and but also in the nucleus. The increase is not associated with upregulation of the salvage pathway, implying an accumulation of constitutively synthesized NAD+ in the cytoplasm and nucleus. This results in an increase of PARP1-mediated nuclear ADP-ribosylation, as well as faster repair of DNA lesions induced by different single-strand DNA damaging agents. Lastly, absence of SLC25A51 reduces both MMS/Olaparib induced PARP1 chromatin retention and the sensitivity of different breast cancer cells to PARP1 inhibition. Together these results provide evidence that SLC25A51 might be a novel target to improve PARP1 inhibitor based therapies by changing subcellular NAD+ redistribution.
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Affiliation(s)
- Anka Güldenpfennig
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Ann-Katrin Hopp
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Science, 1090 Vienna, Austria
| | - Lukas Muskalla
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, Cancer Biology Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Patrick Manetsch
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Fabio Raith
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Lars Hellweg
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Cyril Dördelmann
- Life Science Zurich Graduate School, Cancer Biology Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
- Institute of Molecular Cancer Research (IMCR), University of Zurich, 8057 Zurich, Switzerland
| | - Deena M Leslie Pedrioli
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL) Lausanne, 1015 Lausanne, Switzerland
| | - Giulio Superti-Furga
- Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Science, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
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21
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Hellweg L, Edenhofer A, Barck L, Huppertz MC, Frei MS, Tarnawski M, Bergner A, Koch B, Johnsson K, Hiblot J. A general method for the development of multicolor biosensors with large dynamic ranges. Nat Chem Biol 2023; 19:1147-1157. [PMID: 37291200 PMCID: PMC10449634 DOI: 10.1038/s41589-023-01350-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
Fluorescent biosensors enable the study of cell physiology with spatiotemporal resolution; yet, most biosensors suffer from relatively low dynamic ranges. Here, we introduce a family of designed Förster resonance energy transfer (FRET) pairs with near-quantitative FRET efficiencies based on the reversible interaction of fluorescent proteins with a fluorescently labeled HaloTag. These FRET pairs enabled the straightforward design of biosensors for calcium, ATP and NAD+ with unprecedented dynamic ranges. The color of each of these biosensors can be readily tuned by changing either the fluorescent protein or the synthetic fluorophore, which enables simultaneous monitoring of free NAD+ in different subcellular compartments following genotoxic stress. Minimal modifications of these biosensors furthermore allow their readout to be switched to fluorescence intensity, fluorescence lifetime or bioluminescence. These FRET pairs thus establish a new concept for the development of highly sensitive and tunable biosensors.
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Affiliation(s)
- Lars Hellweg
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anna Edenhofer
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Lucas Barck
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andrea Bergner
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
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22
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Tang HS, Gates CR, Schultz MC. Biochemical evidence that the whole compartment activity behavior of GAPDH differs between the cytoplasm and nucleus. PLoS One 2023; 18:e0290892. [PMID: 37651389 PMCID: PMC10470895 DOI: 10.1371/journal.pone.0290892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
Some metabolic enzymes normally occur in the nucleus and cytoplasm. These compartments differ in molecular composition. Since post-translational modification and interaction with allosteric effectors can tune enzyme activity, it follows that the behavior of an enzyme as a catalyst may differ between the cytoplasm and nucleus. We explored this possibility for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Homogenates of pristine nuclei and cytoplasms isolated from Xenopus laevis oocytes were used for whole compartment activity profiling in a near-physiological buffer. Titrations of NAD+ revealed similar whole compartment activity profiles for GAPDH in nuclear and cytoplasmic homogenates. Surprisingly however GAPDH in these compartments did not have the same behavior in assays of the dependence of initial velocity (v0) on G3P concentration. First, the peak v0 for nuclear GAPDH was up to 2.5-fold higher than the peak for cytoplasmic GAPDH. Second, while Michaelis Menten-like behavior was observed in all assays of cytoplasm, the v0 versus [G3P] plots for nuclear GAPDH typically exhibited a non-Michaelis Menten (sigmoidal) profile. Apparent Km and Vmax (G3P) values for nuclear GAPDH activity were highly variable, even between replicates of the same sample. Possible sources of this variability include in vitro processing of a metabolite that allosterically regulates GAPDH, turnover of a post-translational modification of the enzyme, and fluctuation of the state of interaction of GAPDH with other proteins. Collectively these findings are consistent with the hypothesis that the environment of the nucleus is distinct from the environment of the cytoplasm with regard to GAPDH activity and its modulation. This finding warrants further comparison of the regulation of nuclear and cytoplasmic GAPDH, as well as whole compartment activity profiling of other enzymes of metabolism with cytosolic and nuclear pools.
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Affiliation(s)
- Helen S. Tang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Chelsea R. Gates
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael C. Schultz
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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23
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Wong HTC, Lukasz D, Drerup CM, Kindt KS. In vivo investigation of mitochondria in lateral line afferent neurons and hair cells. Hear Res 2023; 431:108740. [PMID: 36948126 PMCID: PMC10079644 DOI: 10.1016/j.heares.2023.108740] [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: 04/01/2022] [Revised: 02/17/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
To process sensory stimuli, intense energy demands are placed on hair cells and primary afferents. Hair cells must both mechanotransduce and maintain pools of synaptic vesicles for neurotransmission. Furthermore, both hair cells and afferent neurons must continually maintain a polarized membrane to propagate sensory information. These processes are energy demanding and therefore both cell types are critically reliant on mitochondrial health and function for their activity and maintenance. Based on these demands, it is not surprising that deficits in mitochondrial health can negatively impact the auditory and vestibular systems. In this review, we reflect on how mitochondrial function and dysfunction are implicated in hair cell-mediated sensory system biology. Specifically, we focus on live imaging approaches that have been applied to study mitochondria using the zebrafish lateral-line system. We highlight the fluorescent dyes and genetically encoded biosensors that have been used to study mitochondria in lateral-line hair cells and afferent neurons. We then describe the impact this in vivo work has had on the field of mitochondrial biology as well as the relationship between mitochondria and sensory system development, function, and survival. Finally, we delineate the areas in need of further exploration. This includes in vivo analyses of mitochondrial dynamics and biogenesis, which will round out our understanding of mitochondrial biology in this sensitive sensory system.
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Affiliation(s)
- Hiu-Tung C Wong
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daria Lukasz
- Section on Sensory Cell Development and Function, National Institute of Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine M Drerup
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Katie S Kindt
- Section on Sensory Cell Development and Function, National Institute of Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Poljšak B, Kovač V, Špalj S, Milisav I. The Central Role of the NAD+ Molecule in the Development of Aging and the Prevention of Chronic Age-Related Diseases: Strategies for NAD+ Modulation. Int J Mol Sci 2023; 24:ijms24032959. [PMID: 36769283 PMCID: PMC9917998 DOI: 10.3390/ijms24032959] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The molecule NAD+ is a coenzyme for enzymes catalyzing cellular redox reactions in several metabolic pathways, encompassing glycolysis, TCA cycle, and oxidative phosphorylation, and is a substrate for NAD+-dependent enzymes. In addition to a hydride and electron transfer in redox reactions, NAD+ is a substrate for sirtuins and poly(adenosine diphosphate-ribose) polymerases and even moderate decreases in its cellular concentrations modify signaling of NAD+-consuming enzymes. Age-related reduction in cellular NAD+ concentrations results in metabolic and aging-associated disorders, while the consequences of increased NAD+ production or decreased degradation seem beneficial. This article reviews the NAD+ molecule in the development of aging and the prevention of chronic age-related diseases and discusses the strategies of NAD+ modulation for healthy aging and longevity.
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Affiliation(s)
- Borut Poljšak
- Laboratory of Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Vito Kovač
- Laboratory of Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Stjepan Špalj
- Department of Orthodontics, Faculty of Dental Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Irina Milisav
- Laboratory of Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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25
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Li T, Zou Y, Liu S, Yang Y, Zhang Z, Zhao Y. Monitoring NAD(H) and NADP(H) dynamics during organismal development with genetically encoded fluorescent biosensors. CELL REGENERATION 2022; 11:5. [PMID: 35103852 PMCID: PMC8807777 DOI: 10.1186/s13619-021-00105-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022]
Abstract
Cell metabolism plays vital roles in organismal development, but it has been much less studied than transcriptional and epigenetic control of developmental programs. The difficulty might be largely attributed to the lack of in situ metabolite assays. Genetically encoded fluorescent sensors are powerful tools for noninvasive metabolic monitoring in living cells and in vivo by highly spatiotemporal visualization. Among all living organisms, the NAD(H) and NADP(H) pools are essential for maintaining redox homeostasis and for modulating cellular metabolism. Here, we introduce NAD(H) and NADP(H) biosensors, present example assays in developing organisms, and describe promising prospects for how sensors contribute to developmental biology research.
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26
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Chang H, Bennett AM, Cameron WD, Floro E, Au A, McFaul CM, Yip CM, Rocheleau JV. Targeting Apollo-NADP + to Image NADPH Generation in Pancreatic Beta-Cell Organelles. ACS Sens 2022; 7:3308-3317. [PMID: 36269889 PMCID: PMC9706804 DOI: 10.1021/acssensors.2c01174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NADPH/NADP+ redox state supports numerous reactions related to cell growth and survival; yet the full impact is difficult to appreciate due to organelle compartmentalization of NADPH and NADP+. To study glucose-stimulated NADPH production in pancreatic beta-cell organelles, we targeted the Apollo-NADP+ sensor by first selecting the most pH-stable version of the single-color sensor. We subsequently targeted mTurquoise2-Apollo-NADP+ to various organelles and confirmed activity in the cytoplasm, mitochondrial matrix, nucleus, and peroxisome. Finally, we measured the glucose- and glutamine-stimulated NADPH responses by single- and dual-color imaging of the targeted sensors. Overall, we developed multiple organelle-targeted Apollo-NADP+ sensors to reveal the prominent role of beta-cell mitochondria in determining NADPH production in the cytoplasm, nucleus, and peroxisome.
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Affiliation(s)
- Huntley
H. Chang
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Alex M. Bennett
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - William D. Cameron
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Eric Floro
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Aaron Au
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Christopher M. McFaul
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Christopher M. Yip
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Jonathan V. Rocheleau
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada,Department
of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada,Banting
and Best Diabetes Centre, University of
Toronto, Toronto, Ontario M5G 2C4, Canada,
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27
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Vecchia MD, Conte-Daban A, Cappe B, Vandenberg W, Vandenabeele P, Riquet FB, Dedecker P. Spectrally Tunable Förster Resonance Energy Transfer-Based Biosensors Using Organic Dye Grafting. ACS Sens 2022; 7:2920-2927. [PMID: 36162130 DOI: 10.1021/acssensors.2c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Biosensors based on Förster resonance energy transfer (FRET) have revolutionized cellular biology by allowing the direct measurement of biochemical processes in situ. Many genetically encoded sensors make use of fluorescent proteins that are limited in spectral versatility and that allow few ways to change the spectral properties once the construct has been created. In this work, we developed genetically encoded FRET biosensors based on the chemigenetic SNAP and HaloTag domains combined with matching organic fluorophores. We found that the resulting constructs can display comparable responses, kinetics, and reversibility compared to their fluorescent protein-based ancestors, but with the added advantage of spectral versatility, including the availability of red-shifted dye pairs. However, we also find that the introduction of these tags can alter the sensor readout, showing that careful validation is required before applying such constructs in practice. Overall, our approach delivers an innovative methodology that can readily expand the spectral variety and versatility of FRET-based biosensors.
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Affiliation(s)
- Marco Dalla Vecchia
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium.,Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | | | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Wim Vandenberg
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Peter Dedecker
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
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28
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Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
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Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
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29
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Zeng H, Pan T, Zhan M, Hailiwu R, Liu B, Yang H, Li P. Suppression of PFKFB3-driven glycolysis restrains endothelial-to-mesenchymal transition and fibrotic response. Signal Transduct Target Ther 2022; 7:303. [PMID: 36045132 PMCID: PMC9433407 DOI: 10.1038/s41392-022-01097-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/03/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Endothelial-to-mesenchymal transition (EndoMT), the process wherein endothelial cells lose endothelial identity and adopt mesenchymal-like phenotypes, constitutes a critical contributor to cardiac fibrosis. The phenotypic plasticity of endothelial cells can be intricately shaped by alteration of metabolic pathways, but how endothelial cells adjust cellular metabolism to drive EndoMT is incompletely understood. Here, we identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) as a critical driver of EndoMT via triggering abnormal glycolysis and compromising mitochondrial respiration. Pharmacological suppression of PFKFB3 with salvianolic acid C (SAC), a phenolic compound derived from Salvia miltiorrhiza, attenuates EndoMT and fibrotic response. PFKFB3-haplodeficiency recapitulates the anti-EndoMT effect of SAC while PFKFB3-overexpression augments the magnitude of EndoMT and exacerbates cardiac fibrosis. Mechanistically, PFKFB3-driven glycolysis compromises cytoplasmic nicotinamide adenine dinucleotide phosphate (reduced form, NADPH) production via hijacking glucose flux from pentose phosphate pathway. Efflux of mitochondrial NADPH through isocitrate/α-ketoglutarate shuttle replenishes cytoplasmic NADPH pool but meanwhile impairs mitochondrial respiration by hampering mitochondrial iron-sulfur cluster biosynthesis. SAC disrupts PFKFB3 stability by accelerating its degradation and thus maintains metabolic homeostasis in endothelial cells, underlying its anti-EndoMT effects. These findings for the first time identify the critical role of PFKFB3 in triggering EndoMT by driving abnormal glycolysis in endothelial cells, and also highlight the therapeutic potential for pharmacological intervention of PFKFB3 (with SAC or other PFKFB3 inhibitors) to combat EndoMT-associated fibrotic responses via metabolic regulation.
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Affiliation(s)
- Hao Zeng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ting Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Meiling Zhan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Renaguli Hailiwu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Baolin Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Hua Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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30
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Cercillieux A, Ciarlo E, Canto C. Balancing NAD + deficits with nicotinamide riboside: therapeutic possibilities and limitations. Cell Mol Life Sci 2022; 79:463. [PMID: 35918544 PMCID: PMC9345839 DOI: 10.1007/s00018-022-04499-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/20/2022] [Accepted: 07/20/2022] [Indexed: 12/21/2022]
Abstract
Alterations in cellular nicotinamide adenine dinucleotide (NAD+) levels have been observed in multiple lifestyle and age-related medical conditions. This has led to the hypothesis that dietary supplementation with NAD+ precursors, or vitamin B3s, could exert health benefits. Among the different molecules that can act as NAD+ precursors, Nicotinamide Riboside (NR) has gained most attention due to its success in alleviating and treating disease conditions at the pre-clinical level. However, the clinical outcomes for NR supplementation strategies have not yet met the expectations generated in mouse models. In this review we aim to provide a comprehensive view on NAD+ biology, what causes NAD+ deficits and the journey of NR from its discovery to its clinical development. We also discuss what are the current limitations in NR-based therapies and potential ways to overcome them. Overall, this review will not only provide tools to understand NAD+ biology and assess its changes in disease situations, but also to decide which NAD+ precursor could have the best therapeutic potential.
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Affiliation(s)
- Angelique Cercillieux
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., EPFL Campus, Innovation Park, Building G, 1015, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Eleonora Ciarlo
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., EPFL Campus, Innovation Park, Building G, 1015, Lausanne, Switzerland
| | - Carles Canto
- Nestlé Institute of Health Sciences, Nestlé Research Ltd., EPFL Campus, Innovation Park, Building G, 1015, Lausanne, Switzerland.
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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31
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Koju N, Qin ZH, Sheng R. Reduced nicotinamide adenine dinucleotide phosphate in redox balance and diseases: a friend or foe? Acta Pharmacol Sin 2022; 43:1889-1904. [PMID: 35017669 PMCID: PMC9343382 DOI: 10.1038/s41401-021-00838-7] [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: 07/05/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
The nicotinamide adenine dinucleotide (NAD+/NADH) and nicotinamide adenine dinucleotide phosphate (NADP+/NADPH) redox couples function as cofactors or/and substrates for numerous enzymes to retain cellular redox balance and energy metabolism. Thus, maintaining cellular NADH and NADPH balance is critical for sustaining cellular homeostasis. The sources of NADPH generation might determine its biological effects. Newly-recognized biosynthetic enzymes and genetically encoded biosensors help us better understand how cells maintain biosynthesis and distribution of compartmentalized NAD(H) and NADP(H) pools. It is essential but challenging to distinguish how cells sustain redox couple pools to perform their integral functions and escape redox stress. However, it is still obscure whether NADPH is detrimental or beneficial as either deficiency or excess in cellular NADPH levels disturbs cellular redox state and metabolic homeostasis leading to redox stress, energy stress, and eventually, to the disease state. Additional study of the pathways and regulatory mechanisms of NADPH generation in different compartments, and the means by which NADPH plays a role in various diseases, will provide innovative insights into its roles in human health and may find a value of NADPH for the treatment of certain diseases including aging, Alzheimer's disease, Parkinson's disease, cardiovascular diseases, ischemic stroke, diabetes, obesity, cancer, etc.
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Affiliation(s)
- Nirmala Koju
- grid.263761.70000 0001 0198 0694Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences of Soochow University, Suzhou, 215123 China
| | - Zheng-hong Qin
- grid.263761.70000 0001 0198 0694Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences of Soochow University, Suzhou, 215123 China
| | - Rui Sheng
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences of Soochow University, Suzhou, 215123, China.
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32
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More TH, Hiller K. Complexity of subcellular metabolism: strategies for compartment-specific profiling. Curr Opin Biotechnol 2022; 75:102711. [DOI: 10.1016/j.copbio.2022.102711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/03/2022]
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33
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Gansemer ER, Rutkowski DT. Pathways Linking Nicotinamide Adenine Dinucleotide Phosphate Production to Endoplasmic Reticulum Protein Oxidation and Stress. Front Mol Biosci 2022; 9:858142. [PMID: 35601828 PMCID: PMC9114485 DOI: 10.3389/fmolb.2022.858142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The endoplasmic reticulum (ER) lumen is highly oxidizing compared to other subcellular compartments, and maintaining the appropriate levels of oxidizing and reducing equivalents is essential to ER function. Both protein oxidation itself and other essential ER processes, such as the degradation of misfolded proteins and the sequestration of cellular calcium, are tuned to the ER redox state. Simultaneously, nutrients are oxidized in the cytosol and mitochondria to power ATP generation, reductive biosynthesis, and defense against reactive oxygen species. These parallel needs for protein oxidation in the ER and nutrient oxidation in the cytosol and mitochondria raise the possibility that the two processes compete for electron acceptors, even though they occur in separate cellular compartments. A key molecule central to both processes is NADPH, which is produced by reduction of NADP+ during nutrient catabolism and which in turn drives the reduction of components such as glutathione and thioredoxin that influence the redox potential in the ER lumen. For this reason, NADPH might serve as a mediator linking metabolic activity to ER homeostasis and stress, and represent a novel form of mitochondria-to-ER communication. In this review, we discuss oxidative protein folding in the ER, NADPH generation by the major pathways that mediate it, and ER-localized systems that can link the two processes to connect ER function to metabolic activity.
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Affiliation(s)
- Erica R. Gansemer
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - D. Thomas Rutkowski
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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34
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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: 10] [Impact Index Per Article: 5.0] [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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35
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Chen W, Liu S, Yang Y, Zhang Z, Zhao Y. Spatiotemporal Monitoring of NAD+ Metabolism with Fluorescent Biosensors. Mech Ageing Dev 2022; 204:111657. [DOI: 10.1016/j.mad.2022.111657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 01/07/2023]
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36
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Kumar P, Lavis LD. Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience. Annu Rev Neurosci 2022; 45:131-150. [PMID: 35226826 DOI: 10.1146/annurev-neuro-110520-030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced general strategies to combine the molecular specificity of small-molecule tools with the cellular specificity of genetically encoded reagents. Here, we survey the application, refinement, and extension of these hybrid small-molecule:protein methods to problems in neuroscience, which yields powerful reagents to precisely measure and manipulate neural systems. Expected final online publication date for the Annual Review of Neuroscience, Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pratik Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA;
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA;
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37
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Erlandsen H, Jecrois AM, Nichols JC, Cole JL, Royer WE. NADH/NAD + binding and linked tetrameric assembly of the oncogenic transcription factors CtBP1 and CtBP2. FEBS Lett 2022; 596:479-490. [PMID: 34997967 DOI: 10.1002/1873-3468.14276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022]
Abstract
The activation of oncogenic C-terminal binding Protein (CtBP) transcriptional activity is coupled with NAD(H) binding and homo-oligomeric assembly, although the level of CtBP assembly and nucleotide binding affinity continues to be debated. Here, we apply biophysical techniques to address these fundamental issues for CtBP1 and CtBP2. Our ultracentrifugation results unambiguously demonstrate that CtBP assembles into tetramers in the presence of saturating NAD+ or NADH with tetramer to dimer dissociation constants about 100 nm. Isothermal titration calorimetry measurements of NAD(H) binding to CtBP show dissociation constants between 30 and 500 nm, depending on the nucleotide and paralog. Given cellular levels of NAD+ , CtBP is likely to be fully saturated with NAD under physiological concentrations suggesting that CtBP is unable to act as a sensor for NADH levels.
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Affiliation(s)
- Heidi Erlandsen
- Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, USA
| | - Anne M Jecrois
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA
| | - Jeffry C Nichols
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA.,Chemistry Department, Worcester State University, MA, USA
| | - James L Cole
- Department of Molecular and Cell Biology, Department of Chemistry, University of Connecticut, CT, USA
| | - William E Royer
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA
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38
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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39
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Frei MS, Tarnawski M, Roberti MJ, Koch B, Hiblot J, Johnsson K. Engineered HaloTag variants for fluorescence lifetime multiplexing. Nat Methods 2022; 19:65-70. [PMID: 34916672 PMCID: PMC8748199 DOI: 10.1038/s41592-021-01341-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. Additionally, the brightest HaloTag variant showed up to 40% higher brightness in live-cell imaging applications.
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Affiliation(s)
- Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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40
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Alterations in Kynurenine and NAD + Salvage Pathways during the Successful Treatment of Inflammatory Bowel Disease Suggest HCAR3 and NNMT as Potential Drug Targets. Int J Mol Sci 2021; 22:ijms222413497. [PMID: 34948292 PMCID: PMC8705244 DOI: 10.3390/ijms222413497] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023] Open
Abstract
A meta-analysis of publicly available transcriptomic datasets was performed to identify metabolic pathways profoundly implicated in the progression and treatment of inflammatory bowel disease (IBD). The analysis revealed that genes involved in tryptophan (Trp) metabolism are upregulated in Crohn’s disease (CD) and ulcerative colitis (UC) and return to baseline after successful treatment with infliximab. Microarray and mRNAseq profiles from multiple experiments confirmed that enzymes responsible for Trp degradation via the kynurenine pathway (IDO1, KYNU, IL4I1, KMO, and TDO2), receptor of Trp metabolites (HCAR3), and enzymes catalyzing NAD+ turnover (NAMPT, NNMT, PARP9, CD38) were synchronously coregulated in IBD, but not in intestinal malignancies. The modeling of Trp metabolite fluxes in IBD indicated that changes in gene expression shifted intestinal Trp metabolism from the synthesis of 5-hydroxytryptamine (5HT, serotonin) towards the kynurenine pathway. Based on pathway modeling, this manifested in a decline in mucosal Trp and elevated kynurenine (Kyn) levels, and fueled the production of downstream metabolites, including quinolinate, a substrate for de novo NAD+ synthesis. Interestingly, IBD-dependent alterations in Trp metabolites were normalized in infliximab responders, but not in non-responders. Transcriptomic reconstruction of the NAD+ pathway revealed an increased salvage biosynthesis and utilization of NAD+ in IBD, which normalized in patients successfully treated with infliximab. Treatment-related changes in NAD+ levels correlated with shifts in nicotinamide N-methyltransferase (NNMT) expression. This enzyme helps to maintain a high level of NAD+-dependent proinflammatory signaling by removing excess inhibitory nicotinamide (Nam) from the system. Our analysis highlights the prevalent deregulation of kynurenine and NAD+ biosynthetic pathways in IBD and gives new impetus for conducting an in-depth examination of uncovered phenomena in clinical studies.
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41
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Nomiyama T, Setoyama D, Yasukawa T, Kang D. Mitochondria Metabolomics Reveals a Role of β-Nicotinamide Mononucleotide Metabolism in Mitochondrial DNA Replication. J Biochem 2021; 171:325-338. [PMID: 34865026 DOI: 10.1093/jb/mvab136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/30/2021] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) replication is tightly regulated and necessary for cellular homeostasis; however, its relationship with mitochondrial metabolism remains unclear. Advances in metabolomics integrated with the rapid isolation of mitochondria will allow for remarkable progress in analyzing mitochondrial metabolism. Here, we propose a novel methodology for mitochondria-targeted metabolomics, which employs a quick isolation procedure using a hemolytic toxin from Streptococcus pyogenes streptolysin O (SLO). SLO-isolation of mitochondria from cultured HEK293 cells is time- and labor-saving for simultaneous multi-sample processing and has been applied to various other cell lines in this study. Furthermore, our method can detect the time-dependent reduction in mitochondrial ATP in response to a glycolytic inhibitor 2-deoxyglucose, indicating the suitability to prepare metabolite analysis-competent mitochondria. Using this methodology, we searched for specific mitochondrial metabolites associated with mtDNA replication activation, and nucleotides and NAD+ were identified to be prominently altered. Most notably, treatment of β-Nicotinamide Mononucleotide (β-NMN), a precursor of NAD+, to HEK293 cells activated and improved the rate of mtDNA replication by increasing nucleotides in mitochondria and decreasing their degradation products: nucleosides. Our results suggest that β-NMN metabolism play a role in supporting mtDNA replication by maintaining the nucleotide pool balance in the mitochondria.
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Affiliation(s)
- Tomoko Nomiyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
| | - Takehiro Yasukawa
- Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Tokyo, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
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42
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Chellappa K, Baur JA. Reducing NAD(H) to amplify rhythms. Nat Metab 2021; 3:1589-1590. [PMID: 34903882 DOI: 10.1038/s42255-021-00494-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Karthikeyani Chellappa
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Baur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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43
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Erdogan YC, Altun HY, Secilmis M, Ata BN, Sevimli G, Cokluk Z, Zaki AG, Sezen S, Akgul Caglar T, Sevgen İ, Steinhorn B, Ai H, Öztürk G, Belousov VV, Michel T, Eroglu E. Complexities of the chemogenetic toolkit: Differential mDAAO activation by d-amino substrates and subcellular targeting. Free Radic Biol Med 2021; 177:132-142. [PMID: 34687864 PMCID: PMC8639799 DOI: 10.1016/j.freeradbiomed.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023]
Abstract
A common approach to investigate oxidant-regulated intracellular pathways is to add exogenous H2O2 to living cells or tissues. However, the addition of H2O2 to the culture medium of cells or tissues approach does not accurately replicate intracellular redox-mediated cell responses. d-amino acid oxidase (DAAO)-based chemogenetic tools represent informative methodological advances that permit the generation of H2O2 on demand with a high spatiotemporal resolution by providing or withdrawing the DAAO substrate d-amino acids. Much has been learned about the intracellular transport of H2O2 through studies using DAAO, yet these valuable tools remain incompletely characterized in many cultured cells. In this study, we describe and characterize in detail the features of a new modified variant of DAAO (termed mDAAO) with improved catalytic activities. We tested mDAAO functionality in several cultured cell lines employing live-cell imaging techniques. Our imaging experiments show that mDAAO is suitable for the generation of H2O2 under hypoxic conditions imaged with the novel ultrasensitive H2O2 sensor (HyPer7). Moreover, this approach was suitable for generating H2O2 in a reversible and concentration-dependent manner in subcellular locales. Furthermore, we show that the choice of d-amino acids differentially affects mDAAO-dependent intracellular H2O2 generation. When paired with the hydrogen sulfide (H2S) sensor hsGFP, administration of the sulfur-containing amino acid d-cysteine to cells expressing mDAAO generates robust H2S signals. We also show that chemogenetic H2O2 generation in different cell types yields distinct HyPer7 profiles. These studies fully characterize the new mDAAO as a novel chemogenetic tool and provide multiparametric approaches for cell manipulation that may open new lines of investigations for redox biochemists to dissect the role of ROS signaling pathways with high spatial and temporal precision.
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Affiliation(s)
- Yusuf C Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hamza Y Altun
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Busra N Ata
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Serap Sezen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Tuba Akgul Caglar
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - İlker Sevgen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Benjamin Steinhorn
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Huiwang Ai
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Physiology Department, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Vsevelod V Belousov
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Institute of Cardiovascular Physiology, Universitätsmedizin Göttingen, 37073, Göttingen, Germany
| | - Thomas Michel
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey; Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Austria; Nanotechnology Research and Application Center, Sabanci University, Istanbul, Turkey.
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44
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Boon R. Metabolic Fuel for Epigenetic: Nuclear Production Meets Local Consumption. Front Genet 2021; 12:768996. [PMID: 34804127 PMCID: PMC8595138 DOI: 10.3389/fgene.2021.768996] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/20/2021] [Indexed: 12/28/2022] Open
Abstract
Epigenetic modifications are responsible for finetuning gene expression profiles to the needs of cells, tissues, and organisms. To rapidly respond to environmental changes, the activity of chromatin modifiers critically depends on the concentration of a handful of metabolites that act as substrates and co-factors. In this way, these enzymes act as metabolic sensors that directly link gene expression to metabolic states. Although metabolites can easily diffuse through the nuclear pore, molecular mechanisms must be in place to regulate epigenetic marker deposition in specific nuclear subdomains or even on single loci. In this review, I explore the possible subcellular sites of metabolite production that influence the epigenome. From the relationship between cytoplasmic metabolism and nuclear metabolite deposition, I converse to the description of a compartmentalized nuclear metabolism. Last, I elaborate on the possibility of metabolic enzymes to operate in phase-separated nuclear microdomains formed by multienzyme and chromatin-bound protein complexes.
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Affiliation(s)
- Ruben Boon
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, United States.,The Broad Institute of Harvard and MIT, Cambridge, MA, United States.,Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
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45
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Boehi F, Manetsch P, Hottiger MO. Interplay between ADP-ribosyltransferases and essential cell signaling pathways controls cellular responses. Cell Discov 2021; 7:104. [PMID: 34725336 PMCID: PMC8560908 DOI: 10.1038/s41421-021-00323-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Signaling cascades provide integrative and interactive frameworks that allow the cell to respond to signals from its environment and/or from within the cell itself. The dynamic regulation of mammalian cell signaling pathways is often modulated by cascades of protein post-translational modifications (PTMs). ADP-ribosylation is a PTM that is catalyzed by ADP-ribosyltransferases and manifests as mono- (MARylation) or poly- (PARylation) ADP-ribosylation depending on the addition of one or multiple ADP-ribose units to protein substrates. ADP-ribosylation has recently emerged as an important cell regulator that impacts a plethora of cellular processes, including many intracellular signaling events. Here, we provide an overview of the interplay between the intracellular diphtheria toxin-like ADP-ribosyltransferase (ARTD) family members and five selected signaling pathways (including NF-κB, JAK/STAT, Wnt-β-catenin, MAPK, PI3K/AKT), which are frequently described to control or to be controlled by ADP-ribosyltransferases and how these interactions impact the cellular responses.
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Affiliation(s)
- Flurina Boehi
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Cancer Biology PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Patrick Manetsch
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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46
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Groslambert J, Prokhorova E, Ahel I. ADP-ribosylation of DNA and RNA. DNA Repair (Amst) 2021; 105:103144. [PMID: 34116477 PMCID: PMC8385414 DOI: 10.1016/j.dnarep.2021.103144] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022]
Abstract
ADP-ribosylation is a chemical modification of macromolecules found across all domains of life and known to regulate a variety of cellular processes. Notably, it has a well-established role in the DNA damage response. While it was historically known as a post-translational modification of proteins, recent studies have shown that nucleic acids can also serve as substrates of reversible ADP-ribosylation. More precisely, ADP-ribosylation of DNA bases, phosphorylated DNA ends and phosphorylated RNA ends have been reported. We will discuss these three types of modification in details. In a variety of bacterial species, including Mycobacterium tuberculosis, ADP-ribosylation of thymidine has emerged as the mode of action of a toxin-antitoxin system named DarTG, with the resultant products perceived as DNA damage by the cell. On the other hand, mammalian DNA damage sensors PARP1, PARP2 and PARP3 were shown to ADP-ribosylate phosphorylated ends of double-stranded DNA in vitro. Additionally, TRPT1 and several PARP enzymes, including PARP10, can add ADP-ribose to the 5'-phosphorylated end of single-stranded RNA in vitro, representing a novel RNA capping mechanism. Together, these discoveries have led to the emergence of a new and exciting research area, namely DNA and RNA ADP-ribosylation, that is likely to have far-reaching implications for the fields of DNA repair, replication and epigenetics.
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Affiliation(s)
- Joséphine Groslambert
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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47
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Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 2021; 60:2560-2575. [PMID: 34339177 PMCID: PMC8388125 DOI: 10.1021/acs.biochem.1c00258] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Indexed: 01/16/2023]
Abstract
The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
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Affiliation(s)
- Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Guillaume Gotthard
- Structural
Biology Group, European Synchrotron Radiation
Facility (ESRF), 38043 Grenoble, France
| | - Jana Tünnermann
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Timo Tänzer
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julie Karpenko
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nicole Mertes
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Lin Xue
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical
Biology Core Facility, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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48
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Abstract
Fluorescent biochemical sensors allow probing metabolic states in a living cell with high spatiotemporal dynamics. This chapter describes a method for the in situ detection of changes in NAD+ level in living cells using fluorescence lifetime imaging (FLIM).
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Affiliation(s)
- Heejun Choi
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
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49
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Felber JG, Zeisel L, Poczka L, Scholzen K, Busker S, Maier MS, Theisen U, Brandstädter C, Becker K, Arnér ESJ, Thorn-Seshold J, Thorn-Seshold O. Selective, Modular Probes for Thioredoxins Enabled by Rational Tuning of a Unique Disulfide Structure Motif. J Am Chem Soc 2021; 143:8791-8803. [PMID: 34061528 DOI: 10.1021/jacs.1c03234] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Specialized cellular networks of oxidoreductases coordinate the dithiol/disulfide-exchange reactions that control metabolism, protein regulation, and redox homeostasis. For probes to be selective for redox enzymes and effector proteins (nM to μM concentrations), they must also be able to resist non-specific triggering by the ca. 50 mM background of non-catalytic cellular monothiols. However, no such selective reduction-sensing systems have yet been established. Here, we used rational structural design to independently vary thermodynamic and kinetic aspects of disulfide stability, creating a series of unusual disulfide reduction trigger units designed for stability to monothiols. We integrated the motifs into modular series of fluorogenic probes that release and activate an arbitrary chemical cargo upon reduction, and compared their performance to that of the literature-known disulfides. The probes were comprehensively screened for biological stability and selectivity against a range of redox effector proteins and enzymes. This design process delivered the first disulfide probes with excellent stability to monothiols yet high selectivity for the key redox-active protein effector, thioredoxin. We anticipate that further applications of these novel disulfide triggers will deliver unique probes targeting cellular thioredoxins. We also anticipate that further tuning following this design paradigm will enable redox probes for other important dithiol-manifold redox proteins, that will be useful in revealing the hitherto hidden dynamics of endogenous cellular redox systems.
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Affiliation(s)
- Jan G Felber
- Department of Pharmacy, Ludwig Maximilians University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lukas Zeisel
- Department of Pharmacy, Ludwig Maximilians University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lena Poczka
- Department of Pharmacy, Ludwig Maximilians University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Karoline Scholzen
- Department of Medical Biochemistry, Karolinska Institutet, Solnavägen 9, 17177 Stockholm, Sweden
| | - Sander Busker
- Department of Medical Biochemistry, Karolinska Institutet, Solnavägen 9, 17177 Stockholm, Sweden
| | - Martin S Maier
- Department of Pharmacy, Ludwig Maximilians University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Ulrike Theisen
- Institute of Pharmacology and Toxicology, Medical Center, University of Rostock, Schillingallee 70, 18057 Rostock, Germany
| | - Christina Brandstädter
- Interdisciplinary Research Centre (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Katja Becker
- Interdisciplinary Research Centre (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Elias S J Arnér
- Department of Medical Biochemistry, Karolinska Institutet, Solnavägen 9, 17177 Stockholm, Sweden.,Department of Selenoprotein Research, National Institute of Oncology, 1122 Budapest, Hungary
| | - Julia Thorn-Seshold
- Department of Pharmacy, Ludwig Maximilians University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig Maximilians University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
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50
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Camarca A, Minazzato G, Pennacchio A, Capo A, Amici A, D’Auria S, Raffaelli N. Characterization of Two NMN Deamidase Mutants as Possible Probes for an NMN Biosensor. Int J Mol Sci 2021; 22:ijms22126334. [PMID: 34199271 PMCID: PMC8231969 DOI: 10.3390/ijms22126334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 12/02/2022] Open
Abstract
Nicotinamide mononucleotide (NMN) is a key intermediate in the nicotinamide adenine dinucleotide (NAD+) biosynthesis. Its supplementation has demonstrated beneficial effects on several diseases. The aim of this study was to characterize NMN deamidase (PncC) inactive mutants to use as possible molecular recognition elements (MREs) for an NMN-specific biosensor. Thermal stability assays and steady-state fluorescence spectroscopy measurements were used to study the binding of NMN and related metabolites (NaMN, Na, Nam, NR, NAD, NADP, and NaAD) to the PncC mutated variants. In particular, the S29A PncC and K61Q PncC variant forms were selected since they still preserve the ability to bind NMN in the micromolar range, but they are not able to catalyze the enzymatic reaction. While S29A PncC shows a similar affinity also for NaMN (the product of the PncC catalyzed reaction), K61Q PncC does not interact significantly with it. Thus, PncC K61Q mutant seems to be a promising candidate to use as specific probe for an NMN biosensor.
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Affiliation(s)
- Alessandra Camarca
- Institute of Food Sciences, National Research Council, Via Roma 64, 83100 Avellino, Italy; (A.C.); (A.P.); (A.C.)
| | - Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Angela Pennacchio
- Institute of Food Sciences, National Research Council, Via Roma 64, 83100 Avellino, Italy; (A.C.); (A.P.); (A.C.)
| | - Alessandro Capo
- Institute of Food Sciences, National Research Council, Via Roma 64, 83100 Avellino, Italy; (A.C.); (A.P.); (A.C.)
| | - Adolfo Amici
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Sabato D’Auria
- Institute of Food Sciences, National Research Council, Via Roma 64, 83100 Avellino, Italy; (A.C.); (A.P.); (A.C.)
- Department of Biology, Agriculture and Food Science, CNR, Piazzale Aldo Moro 7, 00125 Rome, Italy
- Correspondence: (S.D.); (N.R.); Tel.: +39-3683422770 (S.D.); +39-71-2204-682 (N.R.); Fax: +39-71-2204-677 (N.R.)
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
- Correspondence: (S.D.); (N.R.); Tel.: +39-3683422770 (S.D.); +39-71-2204-682 (N.R.); Fax: +39-71-2204-677 (N.R.)
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