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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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2
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Zhou L, Wu D, Zhou Y, Wang D, Fu H, Huang Q, Qin G, Chen J, Lv J, Lai S, Zhang H, Tang K, Ma J, Fiskesund R, Zhang Y, Zhang X, Huang B. Tumor cell-released kynurenine biases MEP differentiation into megakaryocytes in individuals with cancer by activating AhR-RUNX1. Nat Immunol 2023; 24:2042-2052. [PMID: 37919525 PMCID: PMC10681900 DOI: 10.1038/s41590-023-01662-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
Tumor-derived factors are thought to regulate thrombocytosis and erythrocytopenia in individuals with cancer; however, such factors have not yet been identified. Here we show that tumor cell-released kynurenine (Kyn) biases megakaryocytic-erythroid progenitor cell (MEP) differentiation into megakaryocytes in individuals with cancer by activating the aryl hydrocarbon receptor-Runt-related transcription factor 1 (AhR-RUNX1) axis. During tumor growth, large amounts of Kyn from tumor cells are released into the periphery, where they are taken up by MEPs via the transporter SLC7A8. In the cytosol, Kyn binds to and activates AhR, leading to its translocation into the nucleus where AhR transactivates RUNX1, thus regulating MEP differentiation into megakaryocytes. In addition, activated AhR upregulates SLC7A8 in MEPs to induce positive feedback. Importantly, Kyn-AhR-RUNX1-regulated MEP differentiation was demonstrated in both humanized mice and individuals with cancer, providing potential strategies for the prevention of thrombocytosis and erythrocytopenia.
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Affiliation(s)
- Li Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Dongxiao Wu
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Yabo Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Dianheng Wang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Haixia Fu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Qiusha Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Guohui Qin
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Chen
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Jiadi Lv
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Shaoyang Lai
- The Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Huafeng Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingwei Ma
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Roland Fiskesund
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China.
| | - Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China.
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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3
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Tao R, Wang K, Chen TL, Zhang XX, Cao JB, Zhao WQ, Du JL, Mu Y. A genetically encoded ratiometric indicator for tryptophan. Cell Discov 2023; 9:106. [PMID: 37907506 PMCID: PMC10618466 DOI: 10.1038/s41421-023-00608-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/24/2023] [Indexed: 11/02/2023] Open
Affiliation(s)
- Rongkun Tao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Kui Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Lun Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jian-Bin Cao
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wen-Quan Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yu Mu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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4
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Kim M, Panagiotakopoulou M, Chen C, Ruiz SB, Ganesh K, Tammela T, Heller DA. Micro-engineering and nano-engineering approaches to investigate tumour ecosystems. Nat Rev Cancer 2023; 23:581-599. [PMID: 37353679 PMCID: PMC10528361 DOI: 10.1038/s41568-023-00593-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/25/2023]
Abstract
The interactions among tumour cells, the tumour microenvironment (TME) and non-tumour tissues are of interest to many cancer researchers. Micro-engineering approaches and nanotechnologies are under extensive exploration for modelling these interactions and measuring them in situ and in vivo to investigate therapeutic vulnerabilities in cancer and extend a systemic view of tumour ecosystems. Here we highlight the greatest opportunities for improving the understanding of tumour ecosystems using microfluidic devices, bioprinting or organ-on-a-chip approaches. We also discuss the potential of nanosensors that can transmit information from within the TME or elsewhere in the body to address scientific and clinical questions about changes in chemical gradients, enzymatic activities, metabolic and immune profiles of the TME and circulating analytes. This Review aims to connect the cancer biology and engineering communities, presenting biomedical technologies that may expand the methodologies of the former, while inspiring the latter to develop approaches for interrogating cancer ecosystems.
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Affiliation(s)
- Mijin Kim
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Chen Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Stephen B Ruiz
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Tuomas Tammela
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY, USA
| | - Daniel A Heller
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
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5
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Jedličková V, Ebrahimi Naghani S, Robert HS. On the trail of auxin: Reporters and sensors. THE PLANT CELL 2022; 34:3200-3213. [PMID: 35708654 PMCID: PMC9421466 DOI: 10.1093/plcell/koac179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/07/2022] [Indexed: 05/22/2023]
Abstract
The phytohormone auxin is a master regulator of plant growth and development in response to many endogenous and environmental signals. The underlying coordination of growth is mediated by the formation of auxin maxima and concentration gradients. The visualization of auxin dynamics and distribution can therefore provide essential information to increase our understanding of the mechanisms by which auxin orchestrates these growth and developmental processes. Several auxin reporters have been developed to better perceive the auxin distribution and signaling machinery in vivo. This review focuses on different types of auxin reporters and biosensors used to monitor auxin distribution and its dynamics, as well as auxin signaling, at the cellular and tissue levels in different plant species. We provide a brief history of each reporter and biosensor group and explain their principles and utilities.
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Zhang J, Pan L, Wang Y, Yin L, Xu L, Tao J, Zhang L, Zhu Z, Cui D, Li F, Liu TF. DNA-templated silver nanoclusters light up tryptophan for combined detection of plasma tryptophan and albumin in sepsis. Anal Chim Acta 2022; 1213:339925. [DOI: 10.1016/j.aca.2022.339925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/23/2022] [Accepted: 05/09/2022] [Indexed: 11/01/2022]
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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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San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
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Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
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9
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Guarnieri T. Hypothesis: Emerging Roles for Aryl Hydrocarbon Receptor in Orchestrating CoV-2-Related Inflammation. Cells 2022; 11:cells11040648. [PMID: 35203299 PMCID: PMC8869960 DOI: 10.3390/cells11040648] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 02/05/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the pathogenic agent of Coronavirus-Induced Disease-2019 (COVID-19), a multi-organ syndrome which primarily targets the respiratory system. In this review, considering the large amount of data pointing out the role of the Aryl hydrocarbon Receptor (AhR) in the inflammatory response and in the modulation of innate and adaptive immunity, we describe some mechanisms that strongly suggest its involvement in the management of COVID-19′s inflammatory framework. It regulates both the expression of Angiotensin Converting Enzyme-2 (ACE-2) and its stabilizing partner, the Broad neutral Amino acid Transporter 1 (B0AT1). It induces Indolamine 2,3 dioxygenase (IDO-1), the enzyme which, starting from Tryptophan (Trp), produces Kynurenine (Kyn, Beta-Anthraniloyl-L-Alanine). The accumulation of Kyn and the depletion of Trp arrest T cell growth and induce apoptosis, setting up an immune-tolerant condition, whereas AhR and interferon type I (IFN-I) build a mutual inhibitory loop that also involves NF-kB and limits the innate response. AhR/Kyn binding boosts the production of Interleukin-6 (IL-6), thus reinforcing the inflammatory state and counteracting the IDO-dependent immune tolerance in the later stage of COVID-19. Taken together, these data depict a framework where sufficient clues suggest the possible participation of AhR in the management of COVID-19 inflammation, thus indicating an additional therapeutic target for this disease.
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Affiliation(s)
- Tiziana Guarnieri
- Cell Physiology Laboratory, Department of Biological, Geological and Environmental Sciences (BiGeA), Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy;
- Interuniversity Consortium “Istituto Nazionale Biostrutture e Biosistemi” (INBB–Biostructures and Biosystems National Institute), 00136 Rome, Italy
- Interdepartmental Center for Industrial Research in Life Sciences and Technologies, University of Bologna, 40126 Bologna, Italy
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10
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Cao T, Dai G, Chu H, Kong C, Duan H, Tian N, Sun Z. Single-nucleotide polymorphisms and activities of indoleamine 2,3-dioxygenase isoforms, IDO1 and IDO2, in tuberculosis patients. Hereditas 2022; 159:5. [PMID: 35045867 PMCID: PMC8767668 DOI: 10.1186/s41065-022-00219-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/29/2021] [Indexed: 11/21/2022] Open
Abstract
Purpose To explore the role and effects of the single-nucleotide polymorphisms (SNPs) of the two functionally related indoleamine 2,3-dioxygenase (IDO) isoforms on IDO activity in the Chinese Han ethnic population. Methods A total of 151 consecutive patients of Chinese Han ethnicity (99 men and 52 women; average age 51.92 ± 18.26 years) with pulmonary TB admitted to Beijing Chest Hospital between July 2016 and February 2017 were enrolled in the study. The serum levels of tryptophan (Trp) and its metabolites, IDO1 and IDO2 mRNA levels, and the relationship of IDO1 and IDO2 SNPs with the serum Kyn/Trp ratio in TB patients and healthy controls were examined by LC/ESI–MS/MS analysis. Genomic DNA was isolated from whole blood, and the PCR products were sequenced and analyzed. Results In Chinese Han participants, only IDO2 had SNPs R248W and Y359X that affected IDO activity, as determined by the serum Kyn/Trp ratio. IDO1 and IDO2 mRNA levels were inversely related in TB patients and healthy controls. Conclusions IDO2 SNPs and the opposite expression pattern of IDO1 and IDO2 affected IDO activity in Chinese Han TB patients.
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Fernández-Gallego N, Sánchez-Madrid F, Cibrian D. Role of AHR Ligands in Skin Homeostasis and Cutaneous Inflammation. Cells 2021; 10:cells10113176. [PMID: 34831399 PMCID: PMC8622815 DOI: 10.3390/cells10113176] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 02/07/2023] Open
Abstract
Aryl hydrocarbon receptor (AHR) is an important regulator of skin barrier function. It also controls immune-mediated skin responses. The AHR modulates various physiological functions by acting as a sensor that mediates environment–cell interactions, particularly during immune and inflammatory responses. Diverse experimental systems have been used to assess the AHR’s role in skin inflammation, including in vitro assays of keratinocyte stimulation and murine models of psoriasis and atopic dermatitis. Similar approaches have addressed the role of AHR ligands, e.g., TCDD, FICZ, and microbiota-derived metabolites, in skin homeostasis and pathology. Tapinarof is a novel AHR-modulating agent that inhibits skin inflammation and enhances skin barrier function. The topical application of tapinarof is being evaluated in clinical trials to treat psoriasis and atopic dermatitis. In the present review, we summarize the effects of natural and synthetic AHR ligands in keratinocytes and inflammatory cells, and their relevance in normal skin homeostasis and cutaneous inflammatory diseases.
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Affiliation(s)
- Nieves Fernández-Gallego
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa (IIS-IP), 28006 Madrid, Spain;
- Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Francisco Sánchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa (IIS-IP), 28006 Madrid, Spain;
- Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (F.S.-M.); (D.C.)
| | - Danay Cibrian
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa (IIS-IP), 28006 Madrid, Spain;
- Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (F.S.-M.); (D.C.)
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12
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Balcerowicz M, Shetty KN, Jones AM. Fluorescent biosensors illuminating plant hormone research. PLANT PHYSIOLOGY 2021; 187:590-602. [PMID: 35237816 PMCID: PMC8491072 DOI: 10.1093/plphys/kiab278] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/22/2021] [Indexed: 05/20/2023]
Abstract
Phytohormones act as key regulators of plant growth that coordinate developmental and physiological processes across cells, tissues and organs. As such, their levels and distribution are highly dynamic owing to changes in their biosynthesis, transport, modification and degradation that occur over space and time. Fluorescent biosensors represent ideal tools to track these dynamics with high spatiotemporal resolution in a minimally invasive manner. Substantial progress has been made in generating a diverse set of hormone sensors with recent FRET biosensors for visualising hormone concentrations complementing information provided by transcriptional, translational and degron-based reporters. In this review, we provide an update on fluorescent biosensor designs, examine the key properties that constitute an ideal hormone biosensor, discuss the use of these sensors in conjunction with in vivo hormone perturbations and highlight the latest discoveries made using these tools.
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Affiliation(s)
| | | | - Alexander M. Jones
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, UK
- Author for communication:
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Sadoine M, Ishikawa Y, Kleist TJ, Wudick MM, Nakamura M, Grossmann G, Frommer WB, Ho CH. Designs, applications, and limitations of genetically encoded fluorescent sensors to explore plant biology. PLANT PHYSIOLOGY 2021; 187:485-503. [PMID: 35237822 PMCID: PMC8491070 DOI: 10.1093/plphys/kiab353] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/12/2021] [Indexed: 05/03/2023]
Abstract
The understanding of signaling and metabolic processes in multicellular organisms requires knowledge of the spatial dynamics of small molecules and the activities of enzymes, transporters, and other proteins in vivo, as well as biophysical parameters inside cells and across tissues. The cellular distribution of receptors, ligands, and activation state must be integrated with information about the cellular distribution of metabolites in relation to metabolic fluxes and signaling dynamics in order to achieve the promise of in vivo biochemistry. Genetically encoded sensors are engineered fluorescent proteins that have been developed for a wide range of small molecules, such as ions and metabolites, or to report biophysical processes, such as transmembrane voltage or tension. First steps have been taken to monitor the activity of transporters in vivo. Advancements in imaging technologies and specimen handling and stimulation have enabled researchers in plant sciences to implement sensor technologies in intact plants. Here, we provide a brief history of the development of genetically encoded sensors and an overview of the types of sensors available for quantifying and visualizing ion and metabolite distribution and dynamics. We further discuss the pros and cons of specific sensor designs, imaging systems, and sample manipulations, provide advice on the choice of technology, and give an outlook into future developments.
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Affiliation(s)
- Mayuri Sadoine
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Yuuma Ishikawa
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Thomas J. Kleist
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Michael M. Wudick
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Guido Grossmann
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute for Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B. Frommer
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Cheng-Hsun Ho
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Author for communication:
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Jennings MR, Munn D, Blazeck J. Immunosuppressive metabolites in tumoral immune evasion: redundancies, clinical efforts, and pathways forward. J Immunother Cancer 2021; 9:e003013. [PMID: 34667078 PMCID: PMC8527165 DOI: 10.1136/jitc-2021-003013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2021] [Indexed: 01/04/2023] Open
Abstract
Tumors accumulate metabolites that deactivate infiltrating immune cells and polarize them toward anti-inflammatory phenotypes. We provide a comprehensive review of the complex networks orchestrated by several of the most potent immunosuppressive metabolites, highlighting the impact of adenosine, kynurenines, prostaglandin E2, and norepinephrine and epinephrine, while discussing completed and ongoing clinical efforts to curtail their impact. Retrospective analyses of clinical data have elucidated that their activity is negatively associated with prognosis in diverse cancer indications, though there is a current paucity of approved therapies that disrupt their synthesis or downstream signaling axes. We hypothesize that prior lukewarm results may be attributed to redundancies in each metabolites' synthesis or signaling pathway and highlight routes for how therapeutic development and patient stratification might proceed in the future.
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Affiliation(s)
- Maria Rain Jennings
- Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - David Munn
- Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - John Blazeck
- Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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15
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Morita N, Hoshi M, Hara T, Ninomiya S, Enoki T, Yoneda M, Tsurumi H, Saito K. Viability of diffuse large B-cell lymphoma cells is regulated by kynurenine 3-monooxygenase activity. Oncol Lett 2021; 22:790. [PMID: 34584567 PMCID: PMC8461759 DOI: 10.3892/ol.2021.13051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a clinically heterogeneous lymphoid malignancy that is the most common type of lymphoma in Japan. Previous studies have demonstrated that patients with DLBCL have a poor prognosis due to increased levels of indoleamine 2,3-dioxygnase and kynurenine (KYN). However, the roles of metabolites acting downstream of KYN and associated enzymes are not fully understood. The present study investigated the role of kynurenine 3-monooxygenase (KMO), which catalyzes the conversion of KYN to 3-hydroxykynurenine (3-HK), using serum samples from patients with DLBCL and human DLBCL cell lines with different KMO expression [STR-428 cells with high levels of KMO expression (KMOhigh) and KML-1 cells with low levels of KMO expression (KMOlow)]. Serum samples from 28 patients with DLBCL and 34 healthy volunteers were used to investigate the association between prognosis and KMO activity or 3-HK levels. Furthermore, to investigate the roles of KMO and its related metabolites, STR-428 and KML-1 cell lines, and the lymph nodes of patients with DLBCL were analyzed by reverse transcription-quantitative PCR for KMO, KYNU, 3-hydroxyanthranilate-3,4-dioxygenase and quinolinate phosphoribosyltransferase, by western blotting, and immunohistochemical or immunofluorescence staining for KMO, and by cell viability and NAD+/NADH assays. KYN pathway metabolites in serum samples were measured by HPLC. Serum 3-HK levels were regulated independently of serum KYN levels, and increased serum 3-HK levels and KMO activity were found to be associated with worse disease progression. Notably, the addition of KMO inhibitors and 3-HK negatively and positively regulated the viability of DLBCL cells, respectively. Furthermore, NAD+ levels in KMOhigh STR-428 cells were significantly higher than those in KMOlow KML-1 cells. These results suggested that 3-HK generated by KMO activity may be involved in the regulation of DLBCL cell viability via NAD+ synthesis.
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Affiliation(s)
- Nanaka Morita
- Department of Disease Control and Prevention, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Masato Hoshi
- Department of Biochemical and Analytical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Takeshi Hara
- First Department of Internal Medicine, Gifu University Graduate School of Medicine, Yanagido, Gifu 501-1194, Japan.,Department of Hematology, Matsunami General Hospital, Kasamatsucho, Gifu 501-6062, Japan
| | - Soranobu Ninomiya
- Department of Hematology, Matsunami General Hospital, Kasamatsucho, Gifu 501-6062, Japan
| | - Taisuke Enoki
- Department of Educational Collaboration, Health and Safety Sciences, Osaka Kyoiku University, Kashiwara, Osaka 582-8285, Japan
| | - Misao Yoneda
- Department of Pathology, Suzuka University of Medical Sciences, Suzuka, Mie 510-0293, Japan
| | - Hisashi Tsurumi
- First Department of Internal Medicine, Gifu University Graduate School of Medicine, Yanagido, Gifu 501-1194, Japan.,Department of Hematology, Matsunami General Hospital, Kasamatsucho, Gifu 501-6062, Japan
| | - Kuniaki Saito
- Department of Disease Control and Prevention, Fujita Health University, Toyoake, Aichi 470-1192, Japan
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16
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Marszalek-Grabska M, Walczak K, Gawel K, Wicha-Komsta K, Wnorowska S, Wnorowski A, Turski WA. Kynurenine emerges from the shadows – Current knowledge on its fate and function. Pharmacol Ther 2021; 225:107845. [DOI: 10.1016/j.pharmthera.2021.107845] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022]
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17
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Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas. ACTA ACUST UNITED AC 2021; 2:723-740. [DOI: 10.1038/s43018-021-00201-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022]
Abstract
AbstractThe dynamics and phenotypes of intratumoral myeloid cells during tumor progression are poorly understood. Here we define myeloid cellular states in gliomas by longitudinal single-cell profiling and demonstrate their strict control by the tumor genotype: in isocitrate dehydrogenase (IDH)-mutant tumors, differentiation of infiltrating myeloid cells is blocked, resulting in an immature phenotype. In late-stage gliomas, monocyte-derived macrophages drive tolerogenic alignment of the microenvironment, thus preventing T cell response. We define the IDH-dependent tumor education of infiltrating macrophages to be causally related to a complex re-orchestration of tryptophan metabolism, resulting in activation of the aryl hydrocarbon receptor. We further show that the altered metabolism of IDH-mutant gliomas maintains this axis in bystander cells and that pharmacological inhibition of tryptophan metabolism can reverse immunosuppression. In conclusion, we provide evidence of a glioma genotype-dependent intratumoral network of resident and recruited myeloid cells and identify tryptophan metabolism as a target for immunotherapy of IDH-mutant tumors.
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18
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Balcerowicz M, Shetty KN, Jones AM. O auxin, where art thou? NATURE PLANTS 2021; 7:546-547. [PMID: 33958778 DOI: 10.1038/s41477-021-00921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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19
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Herud-Sikimić O, Stiel AC, Kolb M, Shanmugaratnam S, Berendzen KW, Feldhaus C, Höcker B, Jürgens G. A biosensor for the direct visualization of auxin. Nature 2021; 592:768-772. [PMID: 33828298 PMCID: PMC8081663 DOI: 10.1038/s41586-021-03425-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/05/2021] [Indexed: 01/03/2023]
Abstract
One of the most important regulatory small molecules in plants is indole-3-acetic acid, also known as auxin. Its dynamic redistribution has an essential role in almost every aspect of plant life, ranging from cell shape and division to organogenesis and responses to light and gravity1,2. So far, it has not been possible to directly determine the spatial and temporal distribution of auxin at a cellular resolution. Instead it is inferred from the visualization of irreversible processes that involve the endogenous auxin-response machinery3-7; however, such a system cannot detect transient changes. Here we report a genetically encoded biosensor for the quantitative in vivo visualization of auxin distribution. The sensor is based on the Escherichia coli tryptophan repressor8, the binding pocket of which is engineered to be specific to auxin. Coupling of the auxin-binding moiety with selected fluorescent proteins enables the use of a fluorescence resonance energy transfer signal as a readout. Unlike previous systems, this sensor enables direct monitoring of the rapid uptake and clearance of auxin by individual cells and within cell compartments in planta. By responding to the graded spatial distribution along the root axis and its perturbation by transport inhibitors-as well as the rapid and reversible redistribution of endogenous auxin in response to changes in gravity vectors-our sensor enables real-time monitoring of auxin concentrations at a (sub)cellular resolution and their spatial and temporal changes during the lifespan of a plant.
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Affiliation(s)
| | - Andre C Stiel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Institute for Biological and Medical Imaging, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Munich, Germany
| | - Martina Kolb
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sooruban Shanmugaratnam
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Kenneth W Berendzen
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | | | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany.
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Tübingen, Germany.
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20
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Leclerc D, Staats Pires AC, Guillemin GJ, Gilot D. Detrimental activation of AhR pathway in cancer: an overview of therapeutic strategies. Curr Opin Immunol 2021; 70:15-26. [PMID: 33429228 DOI: 10.1016/j.coi.2020.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022]
Abstract
Sustained transcriptional activation of the aryl hydrocarbon receptor (AhR) promotes tumour growth and impairs the immune defence, at least for cutaneous melanoma and glioma. AhR ligands are produced by the tumour microenvironment (TME) and by the tumour itself (intracrine). The recent identification of interleukin-4-induced-1 (IL4I1), a parallel pathway to indoleamine 2 3-dioxygenase 1 (IDO1)/ tryptophan 2,3-dioxygenase (TDO), and its ability to generate AhR ligands, confirms that a complete inhibition of AhR ligand production might be difficult to reach. Here, we have focused on recent discoveries explaining the large varieties of AhR ligands and the functional consequences in terms of cancer cell plasticity and consecutive therapy resistance. We also examined therapeutic strategies targeting the AhR signalling pathway and their possible adverse effects. Since the end of 2019, two phase I clinical trials have investigated the ability of the AhR antagonist to 'reset' the immune system and re-sensitize the cancer cells to therapies by preventing their dedifferentiation.
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Affiliation(s)
- Delphine Leclerc
- Inserm U1242, Université de Rennes, France, Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Ananda Christina Staats Pires
- Neuroinflammation Group, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia; Laboratório de Bioenergética e Estresse Oxidativo, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Gilles J Guillemin
- Neuroinflammation Group, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - David Gilot
- Inserm U1242, Université de Rennes, France, Centre de lutte contre le cancer Eugène Marquis, Rennes, France.
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21
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Isoda R, Yoshinari A, Ishikawa Y, Sadoine M, Simon R, Frommer WB, Nakamura M. Sensors for the quantification, localization and analysis of the dynamics of plant hormones. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:542-557. [PMID: 33231903 PMCID: PMC7898640 DOI: 10.1111/tpj.15096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/19/2020] [Indexed: 05/13/2023]
Abstract
Plant hormones play important roles in plant growth and development and physiology, and in acclimation to environmental changes. The hormone signaling networks are highly complex and interconnected. It is thus important to not only know where the hormones are produced, how they are transported and how and where they are perceived, but also to monitor their distribution quantitatively, ideally in a non-invasive manner. Here we summarize the diverse set of tools available for quantifying and visualizing hormone distribution and dynamics. We provide an overview over the tools that are currently available, including transcriptional reporters, degradation sensors, and luciferase and fluorescent sensors, and compare the tools and their suitability for different purposes.
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Affiliation(s)
- Reika Isoda
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Akira Yoshinari
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Yuuma Ishikawa
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Mayuri Sadoine
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Rüdiger Simon
- Developmental GeneticsHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Wolf B. Frommer
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Masayoshi Nakamura
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
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22
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Cerezo M, Rocchi S. Cancer cell metabolic reprogramming: a keystone for the response to immunotherapy. Cell Death Dis 2020; 11:964. [PMID: 33177494 PMCID: PMC7658964 DOI: 10.1038/s41419-020-03175-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/31/2022]
Abstract
By targeting the tumor microenvironment to stimulate antitumor immunity, immunotherapies have revolutionized cancer treatment. However, many patients do not respond initially or develop secondary resistance. Based on the limited resources in the tumor microenvironment and competition between tumor and immune cells, the field of immune metabolism has produced extensive knowledge showing that targeting metabolism could help to modulate antitumor immunity. However, among all the different potentially targetable metabolic pathways, it remains unclear which have more potential to overcome resistance to immune checkpoint inhibitors. Here, we explore metabolic reprogramming in cancer cells, which might inhibit antitumor immunity, and strategies that can be used to favor the antitumor response.
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Affiliation(s)
- Michaël Cerezo
- INSERM U981, Gustave Roussy, Villejuif, France.
- INSERM U1065, Team 12, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, Nice, France.
| | - Stéphane Rocchi
- INSERM U1065, Team 12, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, Nice, France.
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23
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Dalangin R, Kim A, Campbell RE. The Role of Amino Acids in Neurotransmission and Fluorescent Tools for Their Detection. Int J Mol Sci 2020; 21:E6197. [PMID: 32867295 PMCID: PMC7503967 DOI: 10.3390/ijms21176197] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Neurotransmission between neurons, which can occur over the span of a few milliseconds, relies on the controlled release of small molecule neurotransmitters, many of which are amino acids. Fluorescence imaging provides the necessary speed to follow these events and has emerged as a powerful technique for investigating neurotransmission. In this review, we highlight some of the roles of the 20 canonical amino acids, GABA and β-alanine in neurotransmission. We also discuss available fluorescence-based probes for amino acids that have been shown to be compatible for live cell imaging, namely those based on synthetic dyes, nanostructures (quantum dots and nanotubes), and genetically encoded components. We aim to provide tool developers with information that may guide future engineering efforts and tool users with information regarding existing indicators to facilitate studies of amino acid dynamics.
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Affiliation(s)
- Rochelin Dalangin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (R.D.); (A.K.)
| | - Anna Kim
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (R.D.); (A.K.)
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (R.D.); (A.K.)
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo City, Tokyo 113-0033, Japan
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24
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Linke H, Höcker B, Furuta K, Forde NR, Curmi PMG. Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers. Biophys Rev 2020; 12:1041-1054. [PMID: 32651904 PMCID: PMC7429643 DOI: 10.1007/s12551-020-00717-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. However, from the study of highly evolved, biological motors, it remains difficult to discern detailed mechanisms, for example, about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the "holy grail" of designing and building a functional synthetic protein motor has not been realized. Here, we review the progress made to date, and we put forward a roadmap for achieving the aim of constructing the first artificial, autonomously running protein motor. Specifically, we propose to break down the task into (i) enzymatic control of track binding, (ii) the engineering of asymmetry and (iii) the engineering of allosteric control for internal communication. We also propose specific approaches for solving each of these challenges.
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Affiliation(s)
- Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE 22100, Lund, Sweden
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia.
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25
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Galaz A, Cortés-Molina F, Arce-Molina R, Romero-Gómez I, Mardones GA, Felipe Barros L, San Martín A. Imaging of the Lactate/Pyruvate Ratio Using a Genetically Encoded Förster Resonance Energy Transfer Indicator. Anal Chem 2020; 92:10643-10650. [PMID: 32600029 DOI: 10.1021/acs.analchem.0c01741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ratio between the cytosolic concentrations of lactate and pyruvate is a direct readout of the balance between glycolysis and mitochondrial oxidative metabolism. Current approaches do not allow detection of the lactate/pyruvate ratio in a single readout with high spatial/temporal resolution in living systems. Using a Förster resonance energy transfer (FRET)-based screening strategy, we found that the orphan transcriptional factor LutR from Bacillus licheniformis is an endogenous sensor of the lactate/pyruvate ratio, suitable for use as a binding moiety to develop a lactate/pyruvate ratio FRET-based genetically encoded indicator, Lapronic. The sensitivity of the indicator to lactate and pyruvate was characterized through changes in the fluorescence FRET ratio and validated with isothermal titration calorimetry. Lapronic was insensitive to physiological pH and temperature and did not respond to structurally related molecules acetate and β-hydroxybutyrate or cofactors NAD+ and NADH. Lapronic was expressed in HEK 293 cells showing a homogeneous cytosolic localization and was also targeted to the mitochondrial matrix. A calibration protocol was designed to quantitatively assess the lactate/pyruvate ratio in intact mammalian cells. Purified protein from Escherichia coli showed robust stability over time and was found suitable for lactate/pyruvate ratio detection in biological samples. We envision that Lapronic will be of practical interest for basic and applied research.
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Affiliation(s)
- Alex Galaz
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | | | - Robinson Arce-Molina
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | - Ignacio Romero-Gómez
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | - Gonzalo Antonio Mardones
- Instituto de Fisiologı́a, Facultad de Medicina, Universidad Austral de Chile (UACh), Isla Teja s/n, Valdivia 5110566, Chile
| | - L Felipe Barros
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | - Alejandro San Martín
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
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26
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A Non-Invasive Tool for Real-Time Measurement of Sulfate in Living Cells. Int J Mol Sci 2020; 21:ijms21072572. [PMID: 32272790 PMCID: PMC7177696 DOI: 10.3390/ijms21072572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/19/2023] Open
Abstract
Sulfur (S) is an essential element for all forms of life. It is involved in numerous essential processes because S is considered as the primary source of one of the essential amino acids, methionine, which plays an important role in biological events. For the control and regulation of sulfate in a metabolic network through fluxomics, a non-invasive tool is highly desirable that opens the door to monitor the level of the sulfate in real time and space in living cells without fractionation of the cells or tissue. Here, we engineered a FRET (fluorescence resonance energy transfer) based sensor for sulfate, which is genetically-encoded and named as FLIP-SP (Fluorescent indicator protein for sulfate). The FLIP-SP can measure the level of the sulfate in live cells. This sensor was constructed by the fusion of fluorescent proteins at the N- and C-terminus of sulfate binding protein (sbp). The FLIP-SP is highly specific to sulfate, and showed pH stability. Real-time monitoring of the level of sulfate in prokaryotic and eukaryotic cells showed sensor bio-compatibility with living cells. We expect that this sulfate sensor offers a valuable strategy in the understanding of the regulation of the flux of sulfate in the metabolic network.
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27
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Moffett JR, Arun P, Puthillathu N, Vengilote R, Ives JA, Badawy AAB, Namboodiri AM. Quinolinate as a Marker for Kynurenine Metabolite Formation and the Unresolved Question of NAD + Synthesis During Inflammation and Infection. Front Immunol 2020; 11:31. [PMID: 32153556 PMCID: PMC7047773 DOI: 10.3389/fimmu.2020.00031] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/08/2020] [Indexed: 12/26/2022] Open
Abstract
Quinolinate (Quin) is a classic example of a biochemical double-edged sword, acting as both essential metabolite and potent neurotoxin. Quin is an important metabolite in the kynurenine pathway of tryptophan catabolism leading to the de novo synthesis of nicotinamide adenine dinucleotide (NAD+). As a precursor for NAD+, Quin can direct a portion of tryptophan catabolism toward replenishing cellular NAD+ levels in response to inflammation and infection. Intracellular Quin levels increase dramatically in response to immune stimulation [e.g., lipopolysaccharide (LPS) or pokeweed mitogen (PWM)] in macrophages, microglia, dendritic cells, and other cells of the immune system. NAD+ serves numerous functions including energy production, the poly ADP ribose polymerization (PARP) reaction involved in DNA repair, and the activity of various enzymes such as the NAD+-dependent deacetylases known as sirtuins. We used highly specific antibodies to protein-coupled Quin to delineate cells that accumulate Quin as a key aspect of the response to immune stimulation and infection. Here, we describe Quin staining in the brain, spleen, and liver after LPS administration to the brain or systemic PWM administration. Quin expression was strong in immune cells in the periphery after both treatments, whereas very limited Quin expression was observed in the brain even after direct LPS injection. Immunoreactive cells exhibited diverse morphology ranging from foam cells to cells with membrane extensions related to cell motility. We also examined protein expression changes in the spleen after kynurenine administration. Acute (8 h) and prolonged (48 h) kynurenine administration led to significant changes in protein expression in the spleen, including multiple changes involved with cytoskeletal rearrangements associated with cell motility. Kynurenine administration resulted in several expression level changes in proteins associated with heat shock protein 90 (HSP90), a chaperone for the aryl-hydrocarbon receptor (AHR), which is the primary kynurenine metabolite receptor. We propose that cells with high levels of Quin are those that are currently releasing kynurenine pathway metabolites as well as accumulating Quin for sustained NAD+ synthesis from tryptophan. Further, we propose that the kynurenine pathway may be linked to the regulation of cell motility in immune and cancer cells.
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Affiliation(s)
- John R. Moffett
- Departments of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University Medical School, Bethesda, MD, United States
| | - Peethambaran Arun
- Departments of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University Medical School, Bethesda, MD, United States
| | - Narayanan Puthillathu
- Departments of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University Medical School, Bethesda, MD, United States
| | - Ranjini Vengilote
- Departments of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University Medical School, Bethesda, MD, United States
| | - John A. Ives
- The Center for Brain, Mind, and Healing, Samueli Institute, Alexandria, VA, United States
| | | | - Aryan M. Namboodiri
- Departments of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University Medical School, Bethesda, MD, United States
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Real-time monitoring of glutathione in living cells using genetically encoded FRET-based ratiometric nanosensor. Sci Rep 2020; 10:992. [PMID: 31969596 PMCID: PMC6976633 DOI: 10.1038/s41598-020-57654-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/02/2020] [Indexed: 01/11/2023] Open
Abstract
Reduced glutathione (GSH) level inside the cell is a critical determinant for cell viability. The level of GSH varies across the cells, tissues and environmental conditions. However, our current understanding of physiological and pathological GSH changes at high spatial and temporal resolution is limited due to non-availability of practicable GSH-detection methods. In order to measure GSH at real-time, a ratiometric genetically encoded nanosensor was developed using fluorescent proteins and fluorescence resonance energy transfer (FRET) approach. The construction of the sensor involved the introduction of GSH binding protein (YliB) as a sensory domain between cyan fluorescent protein (CFP; FRET donor) and yellow fluorescent protein (YFP; FRET acceptor). The developed sensor, named as FLIP-G (Fluorescence Indicator Protein for Glutathione) was able to measure the GSH level under in vitro and in vivo conditions. When the purified FLIP-G was titrated with different concentrations of GSH, the FRET ratio increased with increase in GSH-concentration. The sensor was found to be specific for GSH and also stable to changes in pH. Moreover, in live bacterial cells, the constructed sensor enabled the real-time quantification of cytosolic GSH that is controlled by the oxidative stress level. When expressed in yeast cells, FRET ratio increased with the external supply of GSH to living cells. Therefore, as a valuable tool, the developed FLIP-G can monitor GSH level in living cells and also help in gaining new insights into GSH metabolism.
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Yoshida T, Nakajima H, Takahashi S, Kakizuka A, Imamura H. OLIVe: A Genetically Encoded Fluorescent Biosensor for Quantitative Imaging of Branched-Chain Amino Acid Levels inside Single Living Cells. ACS Sens 2019; 4:3333-3342. [PMID: 31845569 DOI: 10.1021/acssensors.9b02067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Branched-chain amino acids (BCAAs) are essential amino acids, controlling cellular metabolic processes as signaling molecules; therefore, utilization of intracellular BCAAs may be regulated by the availability of nutrients in the environment. However, spatial and temporal regulation of intracellular BCAA concentration in response to environmental conditions has been unclear due to the lack of suitable methods for measuring BCAA concentrations inside single living cells. Here, we developed a Förster resonance energy transfer (FRET)-based genetically encoded biosensor for BCAAs, termed optical biosensor for leucine-isoleucine-valine (OLIVe). The biosensor showed approximately 2-fold changes in FRET values corresponding to BCAA concentrations. Importantly, FRET signals from HeLa cells expressing OLIVe in the cytoplasm and nucleus correlated with bulk intracellular BCAA concentrations determined from populations of cells by a biochemical method, and were decreased by knockdown of L-type amino acid transporter 1 (LAT1), a transporter for BCAAs, indicating that OLIVe can reliably report intracellular BCAA concentrations inside single living cells. We also succeeded in imaging BCAA concentrations in the mitochondria using mitochondria-targeted OLIVe. Using the BCAA imaging technique, we found apparently correlated concentrations between the cytoplasm and the mitochondria. We also found that extracellular non-BCAA amino acids affected intracellular BCAA concentrations. Of these amino acids, extracellular glutamine markedly increased intracellular BCAA concentrations in a LAT1-dependent manner. Unexpectedly, extracellular pyruvate was also found to have significant positive effects on maintaining intracellular BCAA concentrations, suggesting that the cells have pyruvate-dependent systems to import BCAAs and/or to regulate BCAA metabolism.
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Affiliation(s)
- Tomoki Yoshida
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitomi Nakajima
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Sena Takahashi
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Akira Kakizuka
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiromi Imamura
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
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Hoffmann D, Dvorakova T, Stroobant V, Bouzin C, Daumerie A, Solvay M, Klaessens S, Letellier MC, Renauld JC, van Baren N, Lelotte J, Marbaix E, Van den Eynde BJ. Tryptophan 2,3-Dioxygenase Expression Identified in Human Hepatocellular Carcinoma Cells and in Intratumoral Pericytes of Most Cancers. Cancer Immunol Res 2019; 8:19-31. [DOI: 10.1158/2326-6066.cir-19-0040] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/27/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022]
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Tryptophan metabolism as a common therapeutic target in cancer, neurodegeneration and beyond. Nat Rev Drug Discov 2019; 18:379-401. [PMID: 30760888 DOI: 10.1038/s41573-019-0016-5] [Citation(s) in RCA: 785] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
L-Tryptophan (Trp) metabolism through the kynurenine pathway (KP) is involved in the regulation of immunity, neuronal function and intestinal homeostasis. Imbalances in Trp metabolism in disorders ranging from cancer to neurodegenerative disease have stimulated interest in therapeutically targeting the KP, particularly the main rate-limiting enzymes indoleamine-2,3-dioxygenase 1 (IDO1), IDO2 and tryptophan-2,3-dioxygenase (TDO) as well as kynurenine monooxygenase (KMO). However, although small-molecule IDO1 inhibitors showed promise in early-stage cancer immunotherapy clinical trials, a phase III trial was negative. This Review summarizes the physiological and pathophysiological roles of Trp metabolism, highlighting the vast opportunities and challenges for drug development in multiple diseases.
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Soleja N, Manzoor O, Khan P, Mohsin M. Engineering genetically encoded FRET-based nanosensors for real time display of arsenic (As 3+) dynamics in living cells. Sci Rep 2019; 9:11240. [PMID: 31375744 PMCID: PMC6677752 DOI: 10.1038/s41598-019-47682-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Arsenic poisoning has been a major concern that causes severe toxicological damages. Therefore, intricate and inclusive understanding of arsenic flux rates is required to ascertain the cellular concentration and establish the carcinogenetic mechanism of this toxicant at real time. The lack of sufficiently sensitive sensing systems has hampered research in this area. In this study, we constructed a fluorescent resonance energy transfer (FRET)-based nanosensor, named SenALiB (Sensor for Arsenic Linked Blackfoot disease) which contains a metalloregulatory arsenic-binding protein (ArsR) as the As3+ sensing element inserted between the FRET pair enhanced cyan fluorescent protein (ECFP) and Venus. SenALiB takes advantage of the ratiometic FRET readout which measures arsenic with high specificity and selectivity. SenALiB offers rapid detection response, is stable to pH changes and provides highly accurate, real-time optical readout in cell-based assays. SenALiB-676n with a binding constant (Kd) of 0.676 × 10−6 M is the most efficient affinity mutant and can be a versatile tool for dynamic measurement of arsenic concentration in both prokaryotes and eukaryotes in vivo in a non-invasive manner.
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Affiliation(s)
- Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Ovais Manzoor
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India.
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Manzoor O, Soleja N, Khan P, Imtaiyaz Hassan M, Mohsin M. Visualization of thiamine in living cells using genetically encoded fluorescent nanosensor. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Köttgen A, Raffler J, Sekula P, Kastenmüller G. Genome-Wide Association Studies of Metabolite Concentrations (mGWAS): Relevance for Nephrology. Semin Nephrol 2019; 38:151-174. [PMID: 29602398 DOI: 10.1016/j.semnephrol.2018.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metabolites are small molecules that are intermediates or products of metabolism, many of which are freely filtered by the kidneys. In addition, the kidneys have a central role in metabolite anabolism and catabolism, as well as in active metabolite reabsorption and/or secretion during tubular passage. This review article illustrates how the coupling of genomics and metabolomics in genome-wide association analyses of metabolites can be used to illuminate mechanisms underlying human metabolism, with a special focus on insights relevant to nephrology. First, genetic susceptibility loci for reduced kidney function and chronic kidney disease (CKD) were reviewed systematically for their associations with metabolite concentrations in metabolomics studies of blood and urine. Second, kidney function and CKD-associated metabolites reported from observational studies were interrogated for metabolite-associated genetic variants to generate and discuss complementary insights. Finally, insights originating from the simultaneous study of both blood and urine or by modeling intermetabolite relationships are summarized. We also discuss methodologic questions related to the study of metabolite concentrations in urine as well as among CKD patients. In summary, genome-wide association analyses of metabolites using metabolite concentrations quantified from blood and/or urine are a promising avenue of research to illuminate physiological and pathophysiological functions of the kidney.
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Affiliation(s)
- Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
| | - Johannes Raffler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
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35
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Imaizumi A, Adachi Y, Kawaguchi T, Higasa K, Tabara Y, Sonomura K, Sato TA, Takahashi M, Mizukoshi T, Yoshida HO, Kageyama N, Okamoto C, Takasu M, Mori M, Noguchi Y, Shimba N, Miyano H, Yamada R, Matsuda F. Genetic basis for plasma amino acid concentrations based on absolute quantification: a genome-wide association study in the Japanese population. Eur J Hum Genet 2019; 27:621-630. [PMID: 30659259 PMCID: PMC6460579 DOI: 10.1038/s41431-018-0296-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 10/15/2018] [Accepted: 10/25/2018] [Indexed: 12/02/2022] Open
Abstract
To assess the use of plasma free amino acids (PFAAs) as biomarkers for metabolic disorders, it is essential to identify genetic factors that influence PFAA concentrations. PFAA concentrations were absolutely quantified by liquid chromatography–mass spectrometry using plasma samples from 1338 Japanese individuals, and genome-wide quantitative trait locus (QTL) analysis was performed for the concentrations of 21 PFAAs. We next conducted a conditional QTL analysis using the concentration of each PFAA adjusted by the other 20 PFAAs as covariates to elucidate genetic determinants that influence PFAA concentrations. We identified eight genes that showed a significant association with PFAA concentrations, of which two, SLC7A2 and PKD1L2, were identified. SLC7A2 was associated with the plasma levels of arginine and ornithine, and PKD1L2 with the level of glycine. The significant associations of these two genes were revealed in the conditional QTL analysis, but a significant association between serine and the CPS1 gene disappeared when glycine was used as a covariate. We demonstrated that conditional QTL analysis is useful for determining the metabolic pathways predominantly used for PFAA metabolism. Our findings will help elucidate the physiological roles of genetic components that control the metabolism of amino acids.
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Affiliation(s)
- Akira Imaizumi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan.
| | - Yusuke Adachi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan.,Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Kazuhiro Sonomura
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan.,Life Science Laboratories, Shimadzu Corporation, Seika, Kyoto, 619-0237, Japan
| | - Taka-Aki Sato
- Life Science Laboratories, Shimadzu Corporation, Seika, Kyoto, 619-0237, Japan
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Toshimi Mizukoshi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Hiro-O Yoshida
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Naoko Kageyama
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Chisato Okamoto
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Mariko Takasu
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Maiko Mori
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Yasushi Noguchi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Nobuhisa Shimba
- R&D Planning Dept., Ajinomoto Co., Inc, Tokyo, 104-8315, Japan
| | - Hiroshi Miyano
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Ryo Yamada
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan.
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36
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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37
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Kang YP, Ward NP, DeNicola GM. Recent advances in cancer metabolism: a technological perspective. Exp Mol Med 2018; 50:1-16. [PMID: 29657324 PMCID: PMC5938018 DOI: 10.1038/s12276-018-0027-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/12/2017] [Indexed: 01/28/2023] Open
Abstract
Cancer cells are highly dependent on metabolic pathways to sustain both their proliferation and adaption to harsh microenvironments. Thus, understanding the metabolic reprogramming that occurs in tumors can provide critical insights for the development of therapies targeting metabolism. In this review, we will discuss recent advancements in metabolomics and other multidisciplinary techniques that have led to the discovery of novel metabolic pathways and mechanisms in diverse cancer types. Researchers now have access to a rapidly growing number of tools for probing the metabolic abnormalities associated with tumor growth. Unrestrained growth puts special demands on cancer cells, and scientists have known for nearly a century that tumor metabolism differs considerably from healthy tissue metabolism. Gina DeNicola and colleagues at the Moffitt Cancer Center and Research Institute, Tampa, USA, have reviewed the technological tools available for monitoring the molecules that power cell growth and survival. These include mass spectrometry, which can generate an extremely detailed census of cellular metabolites in a single experiment. The authors also highlight techniques that can help ‘trap’ short-lived or unstable chemical intermediates for analysis. Other chemical labeling and tracing techniques can illuminate activity of selected metabolic processes in living tumor cells or even in patients, findings that could reveal therapeutic vulnerabilities.
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Affiliation(s)
- Yun Pyo Kang
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Nathan P Ward
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Gina M DeNicola
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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38
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Liu Y, Liang X, Dong W, Fang Y, Lv J, Zhang T, Fiskesund R, Xie J, Liu J, Yin X, Jin X, Chen D, Tang K, Ma J, Zhang H, Yu J, Yan J, Liang H, Mo S, Cheng F, Zhou Y, Zhang H, Wang J, Li J, Chen Y, Cui B, Hu ZW, Cao X, Xiao-Feng Qin F, Huang B. Tumor-Repopulating Cells Induce PD-1 Expression in CD8 + T Cells by Transferring Kynurenine and AhR Activation. Cancer Cell 2018. [PMID: 29533786 DOI: 10.1016/j.ccell.2018.02.005] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Despite the clinical successes fostered by immune checkpoint inhibitors, mechanisms underlying PD-1 upregulation in tumor-infiltrating T cells remain an enigma. Here, we show that tumor-repopulating cells (TRCs) drive PD-1 upregulation in CD8+ T cells through a transcellular kynurenine (Kyn)-aryl hydrocarbon receptor (AhR) pathway. Interferon-γ produced by CD8+ T cells stimulates release of high levels of Kyn produced by TRCs, which is transferred into adjacent CD8+ T cells via the transporters SLC7A8 and PAT4. Kyn induces and activates AhR and thereby upregulates PD-1 expression. This Kyn-AhR pathway is confirmed in both tumor-bearing mice and cancer patients and its blockade enhances antitumor adoptive T cell therapy efficacy. Thus, we uncovered a mechanism of PD-1 upregulation with potential tumor immunotherapeutic applications.
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Affiliation(s)
- Yuying Liu
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China; Clinical Immunology Center, CAMS, Beijing 100005, China
| | - Xiaoyu Liang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Wenqian Dong
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Yi Fang
- National Cancer Center/Cancer Hospital, CAMS, Beijing 100005, China
| | - Jiadi Lv
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Tianzhen Zhang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Roland Fiskesund
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Jing Xie
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Jinyan Liu
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Xiaonan Yin
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Xun Jin
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Degao Chen
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Ke Tang
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Jingwei Ma
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Huafeng Zhang
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Jing Yu
- State Key Laboratory of Trauma, Burns and Combined Injury, Department 1, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Jun Yan
- State Key Laboratory of Trauma, Burns and Combined Injury, Department 1, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Huaping Liang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department 1, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Siqi Mo
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Feiran Cheng
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Yabo Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - Haizeng Zhang
- National Cancer Center/Cancer Hospital, CAMS, Beijing 100005, China
| | - Jing Wang
- National Cancer Center/Cancer Hospital, CAMS, Beijing 100005, China
| | - Jingnan Li
- Department of Gastroenterology, Peking Union Medical College Hospital, CAMS, Beijing 100005, China
| | - Yang Chen
- Department of Gastroenterology, Peking Union Medical College Hospital, CAMS, Beijing 100005, China
| | - Bing Cui
- Molecular Immunology and Pharmacology Group, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, CAMS, Beijing 100005, China
| | - Zhuo-Wei Hu
- Molecular Immunology and Pharmacology Group, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, CAMS, Beijing 100005, China
| | - Xuetao Cao
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China
| | - F Xiao-Feng Qin
- Center of Systems Medicine, Institute of Basic Medical Sciences, CAMS & Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100005, China; Clinical Immunology Center, CAMS, Beijing 100005, China; Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China.
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Liu Y, Liu Y, Wang M. Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering. Front Microbiol 2017; 8:2012. [PMID: 29089935 PMCID: PMC5651080 DOI: 10.3389/fmicb.2017.02012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/29/2017] [Indexed: 11/13/2022] Open
Abstract
The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors.
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Affiliation(s)
- Yang Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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40
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Okumoto S, Versaw W. Genetically encoded sensors for monitoring the transport and concentration of nitrogen-containing and phosphorus-containing molecules in plants. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:129-135. [PMID: 28750256 DOI: 10.1016/j.pbi.2017.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen and phosphorus are macronutrients indispensable for plant growth. The acquisition and reallocation of both elements require a multitude of dedicated transporters that specifically recognize inorganic and organic forms of nitrogen and phosphorous. Although many transporters have been discovered through elegant screening processes and sequence homology, many remain uncharacterized for their functions in planta. Genetically encoded sensors for nitrogen and phosphorous molecules offer a unique opportunity for studying transport mechanisms that were previously inaccessible. In the past few years, sensors for some of the key nitrogen molecules became available, and many improvements have been made for existing sensors for phosphorus molecules. Methodologies for detailed in vivo analysis also improved. We summarize the recent improvements in genetically encoded sensors for nitrogen and phosphorus molecules, and the discoveries made by using such sensors.
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Affiliation(s)
- Sakiko Okumoto
- Department of Soil and Crop Sciences, Texas A&M University, HEEP Center, College Station, TX 77843 USA.
| | - Wayne Versaw
- Department of Biology, Texas A&M University, Biological Sciences Building East, College Station, TX 77843 USA
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41
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Pelosse M, Cottet-Rousselle C, Grichine A, Berger I, Schlattner U. Genetically Encoded Fluorescent Biosensors to Explore AMPK Signaling and Energy Metabolism. ACTA ACUST UNITED AC 2017; 107:491-523. [PMID: 27812993 DOI: 10.1007/978-3-319-43589-3_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintenance of energy homeostasis is a basic requirement for cell survival. Different mechanisms have evolved to cope with spatial and temporal mismatch between energy-providing and -consuming processes. Among these, signaling by AMP-activated protein kinase (AMPK) is one of the key players, regulated by and itself regulating cellular adenylate levels. Further understanding its complex cellular function requires deeper insight into its activation patterns in space and time at a single cell level. This may become possible with an increasing number of genetically encoded fluorescent biosensors, mostly based on fluorescence resonance energy transfer, which have been engineered to monitor metabolic parameters and kinase activities. Here, we review basic principles of biosensor design and function and the advantages and limitations of their use and provide an overview on existing FRET biosensors to monitor AMPK activation, ATP concentration, and ATP/ADP ratios, together with other key metabolites and parameters of energy metabolism.
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Affiliation(s)
- Martin Pelosse
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Cécile Cottet-Rousselle
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Alexei Grichine
- Inserm, U1055 and U1209, Grenoble, France.,Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | | | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France. .,Inserm, U1055 and U1209, Grenoble, France.
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42
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Herbel C, Patsoukis N, Bardhan K, Seth P, Weaver JD, Boussiotis VA. Clinical significance of T cell metabolic reprogramming in cancer. Clin Transl Med 2016; 5:29. [PMID: 27510264 PMCID: PMC4980327 DOI: 10.1186/s40169-016-0110-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/15/2016] [Indexed: 02/06/2023] Open
Abstract
Conversion of normal cells to cancer is accompanied with changes in their metabolism. During this conversion, cell metabolism undergoes a shift from oxidative phosphorylation to aerobic glycolysis, also known as Warburg effect, which is a hallmark for cancer cell metabolism. In cancer cells, glycolysis functions in parallel with the TCA cycle and other metabolic pathways to enhance biosynthetic processes and thus support proliferation and growth. Similar metabolic features are observed in T cells during activation but, in contrast to cancer, metabolic transitions in T cells are part of a physiological process. Currently, there is intense interest in understanding the cause and effect relationship between metabolic reprogramming and T cell differentiation. After the recent success of cancer immunotherapy, the crosstalk between immune system and cancer has come to the forefront of clinical and basic research. One of the key goals is to delineate how metabolic alterations of cancer influence metabolism-regulated function and differentiation of tumor resident T cells and how such effects might be altered by immunotherapy. Here, we review the unique metabolic features of cancer, the implications of cancer metabolism on T cell metabolic reprogramming during antigen encounters, and the translational prospective of harnessing metabolism in cancer and T cells for cancer therapy.
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Affiliation(s)
- Christoph Herbel
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nikolaos Patsoukis
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Kankana Bardhan
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Pankaj Seth
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.,Beth Israel Deaconess Cancer Center, Harvard Medical School, 330 Brookline Avenue, Dana 513, Boston, MA, 02215, USA.,Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Boston, USA
| | - Jessica D Weaver
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Vassiliki A Boussiotis
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA. .,Beth Israel Deaconess Cancer Center, Harvard Medical School, 330 Brookline Avenue, Dana 513, Boston, MA, 02215, USA.
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43
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Ameen S, Ahmad M, Mohsin M, Qureshi MI, Ibrahim MM, Abdin MZ, Ahmad A. Designing, construction and characterization of genetically encoded FRET-based nanosensor for real time monitoring of lysine flux in living cells. J Nanobiotechnology 2016; 14:49. [PMID: 27334743 PMCID: PMC4917951 DOI: 10.1186/s12951-016-0204-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Engineering microorganisms in order to improve the metabolite flux needs a detailed knowledge of the concentrations and flux rates of metabolites and metabolic intermediates in vivo. Fluorescence resonance energy transfer (FRET) based genetically encoded nanosensors represent a promising tool for measuring the metabolite levels and corresponding rate changes in live cells. Here, we report the development of a series of FRET based genetically encoded nanosensor for real time measurement of lysine at cellular level, as the improvement of microbial strains for the production of L-lysine is of major interest in industrial biotechnology. RESULTS The lysine binding periplasmic protein (LAO) from Salmonella enterica serovar typhimurium LT2 strain was used as the reporter element for the sensor. The LAO was sandwiched between GFP variants i.e. cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Affinity, pH stability, specificity and metal ions effects was scrutinized for the in vitro characterization of this nanosensor, named as FLIPK. The FLIPK is specific to lysine and found to be stable with the pH within the physiological range. The calculated affinity (K d ) of FLIPK was 97 µM. For physiological applications, mutants with different binding affinities were also generated and investigated in vitro. The developed nanosensor efficiently monitored the intracellular level of lysine in bacterial as well as yeast cell. CONCLUSION The developed novel lysine fluorescence resonance energy transfer sensors can be used for in vivo monitoring of lysine levels in prokaryotes as well as eukaryotes. The potential of these sensors is that they can be used as reporter tools in the development of metabolically engineered microbial strains or for real-time monitoring of intracellular lysine during fermentation.
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Affiliation(s)
- Seema Ameen
- Department of Botany, Faculty of Science, Hamdard University, New Delhi, India
| | - Mohammad Ahmad
- Department of Botany, Faculty of Science, Hamdard University, New Delhi, India
| | - Mohd Mohsin
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - M Irfan Qureshi
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed M Ibrahim
- Department of Botany & Microbiology, Science College, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, Alexandria University, P.O. Box 21511, Alexandria, Egypt
| | - Malik Z Abdin
- Department of Biotechnology, Faculty of Science, Hamdard University, New Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Science, Hamdard University, New Delhi, India. .,Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
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Ahmad M, Ameen S, Siddiqi TO, Khan P, Ahmad A. Live cell monitoring of glycine betaine by FRET-based genetically encoded nanosensor. Biosens Bioelectron 2016; 86:169-175. [PMID: 27371825 DOI: 10.1016/j.bios.2016.06.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/25/2022]
Abstract
Glycine betaine (GB) is one of the key compatible solutes that accumulate in the cell at exceedingly high level under the conditions of high salinity. It plays a crucial role in the maintenance of osmolarity of the cell without affecting the physiological processes. Analysis of stress-induced physiological conditions in living cells, therefore, requires real-time monitoring of cellular GB level. Glycine Betaine Optical Sensor (GBOS), a genetically-encoded FRET-based nanosensor developed in this study, allows the real-time monitoring of GB levels inside living cells. This nanosensor has been developed by sandwiching GB binding protein (ProX) between the Förster resonance energy transfer (FRET) pair, the cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Conformational change in ProX, which was used as sensory domain, reported the change in the level of this compatible solute in in vitro and in vivo conditions. Binding of the GB to the sensory domain fetches close to both the fluorescent moieties that result in the form of increased FRET ratio. So, any change in the concentration of GB is correlated with change in FRET ratio. This sensor also reported the GB cellular dynamics in real-time in Escherichia coli cells after the addition of its precursor, choline. The GBOS was also expressed in yeast and mammalian cells to monitor the intracellular GB. Therefore, the GBOS represents a unique FRET-based nanosensor which allows the non-invasive ratiometric analysis of the GB in living cells.
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Affiliation(s)
- Mohammad Ahmad
- Department of Botany, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Seema Ameen
- Department of Botany, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Tariq Omar Siddiqi
- Department of Botany, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Parvez Khan
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
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Real-time functional characterization of cationic amino acid transporters using a new FRET sensor. Pflugers Arch 2015; 468:563-72. [PMID: 26555760 DOI: 10.1007/s00424-015-1754-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Abstract
L-arginine is a semi-essential amino acid that serves as precursor for the production of urea, nitric oxide (NO), polyamines, and other biologically important metabolites. Hence, a fast and reliable assessment of its intracellular concentration changes is highly desirable. Here, we report on a genetically encoded Förster resonance energy transfer (FRET)-based arginine nanosensor that employs the arginine repressor/activator ahrC gene from Bacillus subtilis. This new nanosensor was expressed in HEK293T cells, and experiments with cell lysate showed that it binds L-arginine with high specificity and with a K d of ∼177 μM. Live imaging experiments showed that the nanosensor was expressed throughout the cytoplasm and displayed a half maximal FRET increase at an extracellular L-arginine concentration of ∼22 μM. By expressing the nanosensor together with SLC7A1, SLC7A2B, or SLC7A3 cationic amino acid transporters (CAT1-3), it was shown that L-arginine was imported at a similar rate via SLC7A1 and SLC7A2B and slower via SLC7A3. In contrast, upon withdrawal of extracellular L-arginine, intracellular levels decreased as fast in SLC7A3-expressing cells compared with SLC7A1, but the efflux was slower via SLC7A2B. SLC7A4 (CAT4) could not be convincingly shown to transport L-arginine. We also demonstrated the impact of membrane potential on L-arginine transport and showed that physiological concentrations of symmetrical and asymmetrical dimethylarginine do not significantly interfere with L-arginine transport through SLC7A1. Our results demonstrate that the FRET nanosensor can be used to assess L-arginine transport through plasma membrane in real time.
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46
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Development of biosensors and their application in metabolic engineering. Curr Opin Chem Biol 2015; 28:1-8. [DOI: 10.1016/j.cbpa.2015.05.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 05/04/2015] [Accepted: 05/14/2015] [Indexed: 01/30/2023]
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47
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Mohsin M, Diwan H, Khan I, Ahmad A. Genetically encoded FRET-based nanosensor for in vivo monitoring of zinc concentration in physiological environment of living cell. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Gam J, Ha JS, Kim H, Lee DH, Lee J, Lee SG. Ratiometric analyses at critical temperatures can magnify the signal intensity of FRET-based sugar sensors with periplasmic binding proteins. Biosens Bioelectron 2015; 72:37-43. [DOI: 10.1016/j.bios.2015.04.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/24/2015] [Accepted: 04/25/2015] [Indexed: 11/29/2022]
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49
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FRET-based genetically-encoded sensors for quantitative monitoring of metabolites. Biotechnol Lett 2015; 37:1919-28. [DOI: 10.1007/s10529-015-1873-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/26/2015] [Indexed: 10/23/2022]
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50
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Abstract
IDO1 (indoleamine 2,3-dioxygenase 1) is a member of a unique class of mammalian haem dioxygenases that catalyse the oxidative catabolism of the least-abundant essential amino acid, L-Trp (L-tryptophan), along the kynurenine pathway. Significant increases in knowledge have been recently gained with respect to understanding the fundamental biochemistry of IDO1 including its catalytic reaction mechanism, the scope of enzyme reactions it catalyses, the biochemical mechanisms controlling IDO1 expression and enzyme activity, and the discovery of enzyme inhibitors. Major advances in understanding the roles of IDO1 in physiology and disease have also been realised. IDO1 is recognised as a prominent immune regulatory enzyme capable of modulating immune cell activation status and phenotype via several molecular mechanisms including enzyme-dependent deprivation of L-Trp and its conversion into the aryl hydrocarbon receptor ligand kynurenine and other bioactive kynurenine pathway metabolites, or non-enzymatic cell signalling actions involving tyrosine phosphorylation of IDO1. Through these different modes of biochemical signalling, IDO1 regulates certain physiological functions (e.g. pregnancy) and modulates the pathogenesis and severity of diverse conditions including chronic inflammation, infectious disease, allergic and autoimmune disorders, transplantation, neuropathology and cancer. In the present review, we detail the current understanding of IDO1’s catalytic actions and the biochemical mechanisms regulating IDO1 expression and activity. We also discuss the biological functions of IDO1 with a focus on the enzyme's immune-modulatory function, its medical implications in diverse pathological settings and its utility as a therapeutic target.
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