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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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2
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Ye ZT, Tseng SF, Tsou SX, Tsai CW. High-sensitivity flip chip blue Mini-LEDs miniaturized optical instrument for non-invasive glucose detection. DISCOVER NANO 2024; 19:6. [PMID: 38175421 PMCID: PMC10766880 DOI: 10.1186/s11671-023-03948-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
The colorimetric detection of glucose typically involves a peroxidase reaction producing a color, which is then recorded and analyzed. However, enzyme detection has difficulties with purification and storage. In addition, replacing enzyme detection with chemical methods involves time-consuming steps such as centrifugation and purification and the optical instruments used for colorimetric detection are often bulky and not portable. In this study, ammonium metavanadate and sulfuric acid were used to prepare the detection solution instead of peroxidase to produce color. We also analyzed the effect of different concentrations of detection solution on absorbance sensitivity. Finally, a flip chip blue Mini-LEDs miniaturized optical instrument (FC blue Mini-LEDs MOI) was designed for glucose detection using optics fiber, collimating lenses, a miniaturized spectrometer, and an FC Blue Mini-LEDs with a center wavelength of 459 nm. While detecting glucose solutions in the concentration range of 0.1-10 mM by the developed MOI, the regression equation of y = 0.0941x + 0.1341, R2 of 0.9744, the limit of detection was 2.15 mM, and the limit of quantification was 7.163 mM. Furthermore, the preparation of the detection solution only takes 10 min, and the absorbance sensitivity of the optimized detection solution could be increased by 2.3 times. The detection solution remained stable with only a 0.6% decrease in absorbance compared to the original after storing it in a refrigerated environment at 3 °C for 14 days. The method proposed in this study for detecting glucose using FC blue light Mini-LEDs MOI reduces the use of peroxidase. In addition, it has a wide detection range that includes blood as well as non-invasive saliva and tear fluids, providing patients with a miniaturized, highly sensitive, and quantifiable glucose detection system.
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Affiliation(s)
- Zhi Ting Ye
- Department of Mechanical Engineering, Advanced Institute of Manufacturing with High-Tech Innovations, National Chung Cheng University, 168, University Rd., Min-Hsiung, Chia-Yi, 62102, Taiwan, ROC.
| | - Shen Fu Tseng
- Department of Mechanical Engineering, Advanced Institute of Manufacturing with High-Tech Innovations, National Chung Cheng University, 168, University Rd., Min-Hsiung, Chia-Yi, 62102, Taiwan, ROC
| | - Shang Xuan Tsou
- Department of Mechanical Engineering, Advanced Institute of Manufacturing with High-Tech Innovations, National Chung Cheng University, 168, University Rd., Min-Hsiung, Chia-Yi, 62102, Taiwan, ROC
| | - Chun Wei Tsai
- Graduate Institute of Photonics and Optoelectronics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106319, Taiwan, ROC.
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Liu Y, Li T, Zhu H, Zhou Y, Shen Q, Liu D. Cysteine facilitates the lignocellulolytic response of Trichoderma guizhouense NJAU4742 by indirectly up-regulating membrane sugar transporters. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:159. [PMID: 37891614 PMCID: PMC10612256 DOI: 10.1186/s13068-023-02418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Filamentous fungi possess a rich CAZymes system, which is widely studied and applied in the bio-conversion of plant biomass to alcohol chemicals. Carbon source acquisition is the fundamental driver for CAZymes-producing sustainability and secondary metabolism, therefore, a deeper insight into the regulatory network of sugar transport in filamentous fungi has become urgent. RESULTS This study reports an important linkage of sulfur assimilation to lignocellulose response of filamentous fungus. Inorganic sulfur addition facilitated biodegradation of rice straw by Trichoderma guizhouense NJAU4742. Cysteine and glutathione were revealed as major intracellular metabolites responsive to sulfur addition by metabolomics, cysteine content was increased in this process and glutathione increased correspondingly. Two membrane sugar transporter genes, Tgmst1 and Tgmst2, were identified as the critical response genes significantly up-regulated when intracellular cysteine increased. Tgmst1 and Tgmst2 were both positively regulated by the glucose regulation-related protein (GRP), up-regulation of both Tgmst1 and Tggrp can cause a significant increase in intracellular glucose. The transcriptional regulatory function of GRP mainly relied on GSH-induced glutathionylation, and the transcription activating efficiency was positively related to the glutathionylation level, furthermore, DTT-induced deglutathionylation resulted in the down-regulation of downstream genes. CONCLUSIONS Inorganic sulfur addition induces a rise in intracellular Cys content, and the conversion of cysteine to glutathione caused the increase of glutathionylation level of GRP, which in turn up-regulated Tgmst1 and Tgmst2. Subsequently, the sugar transport efficiency of single cells was improved, which facilitated the maintenance of vigorous CAZymes metabolism and the straw-to-biomass conversion.
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Affiliation(s)
- Yang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Tuo Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yihao Zhou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China.
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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4
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Bi S, Kargeti M, Colin R, Farke N, Link H, Sourjik V. Dynamic fluctuations in a bacterial metabolic network. Nat Commun 2023; 14:2173. [PMID: 37061520 PMCID: PMC10105761 DOI: 10.1038/s41467-023-37957-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
The operation of the central metabolism is typically assumed to be deterministic, but dynamics and high connectivity of the metabolic network make it potentially prone to generating fluctuations. However, time-resolved measurements of metabolite levels in individual cells that are required to characterize such fluctuations remained a challenge, particularly in small bacterial cells. Here we use single-cell metabolite measurements based on Förster resonance energy transfer, combined with computer simulations, to explore the real-time dynamics of the metabolic network of Escherichia coli. We observe that steplike exposure of starved E. coli to glycolytic carbon sources elicits large periodic fluctuations in the intracellular concentration of pyruvate in individual cells. These fluctuations are consistent with predicted oscillatory dynamics of E. coli metabolic network, and they are primarily controlled by biochemical reactions around the pyruvate node. Our results further indicate that fluctuations in glycolysis propagate to other cellular processes, possibly leading to temporal heterogeneity of cellular states within a population.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Manika Kargeti
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Niklas Farke
- University of Tübingen, D-72076, Tübingen, Germany
| | - Hannes Link
- University of Tübingen, D-72076, Tübingen, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany.
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5
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Chen L, Lyu Y, Zhang X, Zheng L, Li Q, Ding D, Chen F, Liu Y, Li W, Zhang Y, Huang Q, Wang Z, Xie T, Zhang Q, Sima Y, Li K, Xu S, Ren T, Xiong M, Wu Y, Song J, Yuan L, Yang H, Zhang XB, Tan W. Molecular imaging: design mechanism and bioapplications. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1461-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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6
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Zhu H, Li T, Li C, Liu Y, Miao Y, Liu D, Shen Q. Intracellular kynurenine promotes acetaldehyde accumulation, further inducing the apoptosis in soil beneficial fungi Trichoderma guizhouense NJAU4742 under acid stress. Environ Microbiol 2023; 25:331-351. [PMID: 36367399 DOI: 10.1111/1462-2920.16286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022]
Abstract
In this study, the growth of fungi Trichoderma guizhouense NJAU4742 was significantly inhibited under acid stress, and the genes related to acid stress were identified based on transcriptome analysis. Four genes including tna1, adh2/4, and bna3 were significantly up-regulated. Meanwhile, intracellular hydrogen ions accumulated under acid stress, and ATP synthesis was induced to transport hydrogen ions to maintain hydrogen ion balance. The enhancement of glycolysis pathway was also detected, and a large amount of pyruvic acid from glycolysis was accumulated due to the activity limitation of PDH enzymes. Finally, acetaldehyde accumulated, resulting in the induction of adh2/4. In order to cope with stress caused by acetaldehyde, cells enhanced the synthesis of NAD+ by increasing the expression of tna1 and bna3 genes. NAD+ effectively improved the antioxidant capacity of cells, but the NAD+ supplement pathway mediated by bna3 could also cause the accumulation of kynurenine (KYN), which was an inducer of apoptosis. In addition, KYN had a specific promoting effect on acetaldehyde synthesis by improving the expression of eno2 gene, which led to the extremely high intracellular acetaldehyde in the cell under acidic stress. Our findings provided a route to better understand the response of filamentous fungi under acid stress.
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Affiliation(s)
- Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Tuo Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Chi Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Yang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
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7
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Kimura Y, Kashima D, Kawahara M. A growth-based platform for detecting domain-peptide interactions in the cytoplasm of mammalian cells. Sci Rep 2022; 12:18028. [PMID: 36302843 PMCID: PMC9607845 DOI: 10.1038/s41598-022-22770-4] [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: 07/11/2022] [Accepted: 10/19/2022] [Indexed: 01/20/2023] Open
Abstract
Development of a method for detecting protein-protein interactions (PPIs) in living cells is important for therapeutic drug screening against various diseases including infectious diseases. We have recently developed a method named SOS localization-based interaction screening (SOLIS), in which we designed membrane-anchored and SOS-fused chimeric proteins, whose PPI-dependent association triggers membrane localization of the SOS-fused chimeric protein, activates the Ras/MAPK pathway, and induces cell growth. While SOLIS was able to detect relatively strong PPIs, further sensitivity was required for detecting intracellular endogenous PPIs typically having a micromolar order of dissociation constant (Kd). Here we develop high-sensitive SOLIS (H-SOLIS) that could universally detect PPIs with lower affinities. In order to improve the sensitivity, H-SOLIS introduces a heterodimeric helper interaction, in which addition of a small-molecule helper ligand could accommodate association of the two chimeric proteins and regulate the sensitivity. Four types of domain-peptide interactions having known Kd values are employed to examine the versatility and detection limit of H-SOLIS. Consequently, the heterodimer-inducible helper ligand dramatically enhances detection sensitivity, lowering the detection limit to a ten-micromolar order of Kd. Thus, H-SOLIS could be a platform to detect disease-related domain-peptide interactions for drug discovery screening.
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Affiliation(s)
- Yosuke Kimura
- grid.26999.3d0000 0001 2151 536XDepartment of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656 Japan
| | - Daiki Kashima
- grid.26999.3d0000 0001 2151 536XDepartment of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656 Japan
| | - Masahiro Kawahara
- grid.26999.3d0000 0001 2151 536XDepartment of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656 Japan ,Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-Shi, Osaka, 567-0085 Japan
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8
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Jiang X. An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions. Proteins 2022; 90:1766-1778. [PMID: 35445447 PMCID: PMC9790349 DOI: 10.1002/prot.26351] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 12/30/2022]
Abstract
Despite intense elimination efforts, human malaria, caused by the infection of five Plasmodium species, remains the deadliest parasitic disease in the world. Even worse, with the emergence and spreading of the first-line drug-resistant Plasmodium parasites, therapeutic interventions based on novel plasmodial drug targets are more necessary than ever. Given that the blood-stage parasites primarily rely on glycolysis for their energy supply, blocking glucose uptake, the rate-limiting step of ATP generation, was considered a promising approach to kill these parasites. To achieve this goal, characterization of the plasmodial hexose transporter and development of selective inhibitors have been pursued for decades. Here, we review the identification and characterization of the Plasmodium falciparum hexose transporter (PfHT1) and summarize current advances in its inhibitor development.
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Affiliation(s)
- Xin Jiang
- School of Biotechnology and Biomolecular Sciencesthe University of New South WalesSydneyNew South Wales
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9
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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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10
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Wu LB, Eom JS, Isoda R, Li C, Char SN, Luo D, Schepler-Luu V, Nakamura M, Yang B, Frommer WB. OsSWEET11b, a potential sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility. THE NEW PHYTOLOGIST 2022; 234:975-989. [PMID: 35211968 DOI: 10.1111/nph.18054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by Transcription Activator-Like effectors (TALe) of Xanthomonas ssp. is key for virulence in rice, cassava and cotton. We identified OsSWEET11b with roles in male fertility and potential bacterial blight (BB) susceptibility in rice. While single ossweet11a or 11b mutants were fertile, double mutants were sterile. As clade III SWEETs can transport gibberellin (GA), a key hormone for spikelet fertility, sterility and BB susceptibility might be explained by GA transport deficiencies. However, in contrast with the Arabidopsis homologues, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility therefore are likely to depend on sucrose transport activity. Ectopic induction of OsSWEET11b by designer TALe enabled TALe-free Xanthomonas oryzae pv. oryzae (Xoo) to cause disease, identifying OsSWEET11b as a potential BB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence of Xoo. Notably, only three of six clade III SWEETs are targeted by known Xoo strains from Asia and Africa. The identification of OsSWEET11b is relevant for fertility and for protecting rice against emerging Xoo strains that target OsSWEET11b.
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Affiliation(s)
- Lin-Bo Wu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding I, Justus-Liebig University Giessen, Giessen, 35392, Germany
| | - Joon-Seob Eom
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Reika Isoda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Chenhao Li
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Si Nian Char
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dangping Luo
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Bing Yang
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
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11
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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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12
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Zhang C, Li Y, Wang J, Xue X, Beuchat G, Chen LQ. Two evolutionarily duplicated domains individually and post-transcriptionally control SWEET expression for phloem transport. THE NEW PHYTOLOGIST 2021; 232:1793-1807. [PMID: 34431115 DOI: 10.1111/nph.17688] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Cell type-specific gene expression is critical for the specialized functions within multicellular organisms. In Arabidopsis, SWEET11 and SWEET12 sugar transporters are specifically expressed in phloem parenchyma (PP) cells and are responsible for sucrose efflux from the PP, the first step of a two-step apoplasmic phloem-loading strategy that initiates the long-distance transport of sugar from leaves to nonphotosynthetic sink tissues. However, we know nothing about what determines the PP cell-specific expression of these SWEETs. Sequence deletions, histochemical β-glucuronidase (GUS) analysis, cross-sectioning, live-cell imaging, and evolutionary analysis were used to elucidate domains responsible for PP specificity, while a Förster resonance energy transfer (FRET) sensor-based transport assay was used to determine whether substrate specificity coevolved with PP specificity. We identified two domains in the Arabidopsis SWEET11 coding sequence that, along with its promoter (including 5' UTR), regulate PP-specific expression at the post-transcriptional level, probably involving RNA-binding proteins. This mechanism is conserved among vascular plants but independent of transport substrate specificity. We conclude that two evolutionarily duplicated coding sequence domains are essential and individually sufficient for PP-specific expression of SWEET11. We also provide a crucial experimental tool to study PP physiology and development.
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Affiliation(s)
- Chen Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ye Li
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Jiang Wang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xueyi Xue
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Gabriel Beuchat
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Li-Qing Chen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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13
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Horikawa M, Kakiuchi Y, Kashima D, Ogawa K, Kawahara M. Thrombopoietin receptor-based protein-protein interaction screening (THROPPIS). Biotechnol Bioeng 2021; 119:287-298. [PMID: 34708875 DOI: 10.1002/bit.27975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022]
Abstract
As protein-protein interactions (PPIs) are involved in many cellular events, development of mammalian cytosolic PPI detection systems is important for drug discovery as well as understanding biological phenomena. We have previously reported a c-kit-based PPI screening (KIPPIS) system, in which proteins of interest were fused with a receptor tyrosine kinase c-kit, leading to intracellular PPI-dependent cell growth. However, it has not been investigated whether PPI can be detected using other receptors. In this study, we employed a thrombopoietin receptor, which belongs to the Type I cytokine receptor family, to develop a thrombopoietin receptor-based PPI screening (THROPPIS) system. To improve the sensitivity of THROPPIS, we examined two strategies of (i) localization of the chimeric receptors on the cell membrane, and (ii) addition of a helper module to the chimeric receptors. Intriguingly, the nonlocalized chimeric receptor showed the best performance of THROPPIS. Furthermore, the addition of the helper module dramatically improved the detection sensitivity. In total, 5 peptide-domain interactions were detected successfully, demonstrating the versatility of THROPPIS. In addition, a peptide-domain interaction was detected even when insulin receptor or epidermal growth factor receptor was used as a signaling domain, demonstrating that this PPI detection system can be extended to other receptors.
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Affiliation(s)
- Makiko Horikawa
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yosuke Kakiuchi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Daiki Kashima
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenichiro Ogawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masahiro Kawahara
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-shi, Osaka, Japan
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14
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Koberstein JN, Stewart ML, Mighell TL, Smith CB, Cohen MS. A Sort-Seq Approach to the Development of Single Fluorescent Protein Biosensors. ACS Chem Biol 2021; 16:1709-1720. [PMID: 34431656 PMCID: PMC9807264 DOI: 10.1021/acschembio.1c00423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Motivated by the growing importance of single fluorescent protein biosensors (SFPBs) in biological research and the difficulty in rationally engineering these tools, we sought to increase the rate at which SFPB designs can be optimized. SFPBs generally consist of three components: a circularly permuted fluorescent protein, a ligand-binding domain, and linkers connecting the two domains. In the absence of predictive methods for biosensor engineering, most designs combining these three components will fail to produce allosteric coupling between ligand binding and fluorescence emission. While methods to construct diverse libraries with variation in the site of GFP insertion and linker sequences have been developed, the remaining bottleneck is the ability to test these libraries for functional biosensors. We address this challenge by applying a massively parallel assay termed "sort-seq," which combines binned fluorescence-activated cell sorting, next-generation sequencing, and maximum likelihood estimation to quantify the brightness and dynamic range for many biosensor variants in parallel. We applied this method to two common biosensor optimization tasks: the choice of insertion site and optimization of linker sequences. The sort-seq assay applied to a maltose-binding protein domain-insertion library not only identified previously described high-dynamic-range variants but also discovered new functional insertion sites with diverse properties. A sort-seq assay performed on a pyruvate biosensor linker library expressed in mammalian cell culture identified linker variants with substantially improved dynamic range. Machine learning models trained on the resulting data can predict dynamic range from linker sequences. This high-throughput approach will accelerate the design and optimization of SFPBs, expanding the biosensor toolbox.
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Affiliation(s)
- John N. Koberstein
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa L. Stewart
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Taylor L. Mighell
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Chadwick B. Smith
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael S. Cohen
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, USA
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15
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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16
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Basu H, Pekkurnaz G, Falk J, Wei W, Chin M, Steen J, Schwarz TL. FHL2 anchors mitochondria to actin and adapts mitochondrial dynamics to glucose supply. J Cell Biol 2021; 220:212527. [PMID: 34342639 PMCID: PMC8340551 DOI: 10.1083/jcb.201912077] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/05/2021] [Accepted: 07/08/2021] [Indexed: 01/24/2023] Open
Abstract
Mitochondrial movement and distribution are fundamental to their function. Here we report a mechanism that regulates mitochondrial movement by anchoring mitochondria to the F-actin cytoskeleton. This mechanism is activated by an increase in glucose influx and the consequent O-GlcNAcylation of TRAK (Milton), a component of the mitochondrial motor-adaptor complex. The protein four and a half LIM domains protein 2 (FHL2) serves as the anchor. FHL2 associates with O-GlcNAcylated TRAK and is both necessary and sufficient to drive the accumulation of F-actin around mitochondria and to arrest mitochondrial movement by anchoring to F-actin. Disruption of F-actin restores mitochondrial movement that had been arrested by either TRAK O-GlcNAcylation or forced direction of FHL2 to mitochondria. This pathway for mitochondrial immobilization is present in both neurons and non-neuronal cells and can thereby adapt mitochondrial dynamics to changes in glucose availability.
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Affiliation(s)
- Himanish Basu
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA.,Division of Medical Sciences, Harvard Medical School, Boston, MA.,Department of Neurobiology, Harvard Medical School, Boston, MA
| | - Gulcin Pekkurnaz
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA.,Department of Neurobiology, Harvard Medical School, Boston, MA
| | - Jill Falk
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA.,Department of Neurobiology, Harvard Medical School, Boston, MA
| | - Wei Wei
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
| | - Morven Chin
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA.,Division of Medical Sciences, Harvard Medical School, Boston, MA.,Department of Neurobiology, Harvard Medical School, Boston, MA
| | - Judith Steen
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
| | - Thomas L Schwarz
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA.,Department of Neurobiology, Harvard Medical School, Boston, MA
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17
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Izadyar A, Van MN, Rodriguez KA, Seok I, Hood EE. A bienzymatic amperometric glucose biosensor based on using a novel recombinant Mn peroxidase from corn and glucose oxidase with a Nafion membrane. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Ciftci D, Huysmans GHM, Wang X, He C, Terry D, Zhou Z, Fitzgerald G, Blanchard SC, Boudker O. FRET-based Microscopy Assay to Measure Activity of Membrane Amino Acid Transporters with Single-transporter Resolution. Bio Protoc 2021; 11:e3970. [PMID: 33889664 DOI: 10.21769/bioprotoc.3970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 01/05/2023] Open
Abstract
Secondary active transporters reside in cell membranes transporting polar solutes like amino acids against steep concentration gradients, using electrochemical gradients of ions as energy sources. Commonly, ensemble-based measurements of radiolabeled substrate uptakes or transport currents inform on kinetic parameters of transporters. Here we describe a fluorescence-based functional assay for glutamate and aspartate transporters that provides single-transporter, single-transport cycle resolution using an archaeal elevator-type sodium and aspartate symporter GltPh as a model system. We prepare proteo-liposomes containing reconstituted purified GltPh transporters and an encapsulated periplasmic glutamate/aspartate-binding protein, PEB1a, labeled with donor and acceptor fluorophores. We then surface-immobilize the proteo-liposomes and measure transport-dependent Fluorescence Resonance Energy Transfer (FRET) efficiency changes over time using single-molecule Total Internal Reflection Fluorescence (TIRF) microscopy. The assay provides a 10-100 fold increase in temporal resolution compared to radioligand uptake assays. It also allows kinetic characterization of different transport cycle steps and discerns kinetic heterogeneities within the transporter population.
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Affiliation(s)
- Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA.,Tri-Institutional Training Program in Chemical Biology, New York, USA
| | - Gerard H M Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Xiaoyu Wang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Changhao He
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Daniel Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Gabriel Fitzgerald
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA.,Tri-Institutional Training Program in Chemical Biology, New York, USA
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA.,Tri-Institutional Training Program in Chemical Biology, New York, USA.,Howard Hughes Medical Institute, New York, USA
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19
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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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20
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McNally LA, Altamimi TR, Fulghum K, Hill BG. Considerations for using isolated cell systems to understand cardiac metabolism and biology. J Mol Cell Cardiol 2020; 153:26-41. [PMID: 33359038 DOI: 10.1016/j.yjmcc.2020.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Changes in myocardial metabolic activity are fundamentally linked to cardiac health and remodeling. Primary cardiomyocytes, induced pluripotent stem cell-derived cardiomyocytes, and transformed cardiomyocyte cell lines are common models used to understand how (patho)physiological conditions or stimuli contribute to changes in cardiac metabolism. These cell models are helpful also for defining metabolic mechanisms of cardiac dysfunction and remodeling. Although technical advances have improved our capacity to measure cardiomyocyte metabolism, there is often heterogeneity in metabolic assay protocols and cell models, which could hinder data interpretation and discernment of the mechanisms of cardiac (patho)physiology. In this review, we discuss considerations for integrating cardiomyocyte cell models with techniques that have become relatively common in the field, such as respirometry and extracellular flux analysis. Furthermore, we provide overviews of metabolic assays that complement XF analyses and that provide information on not only catabolic pathway activity, but biosynthetic pathway activity and redox status as well. Cultivating a more widespread understanding of the advantages and limitations of metabolic measurements in cardiomyocyte cell models will continue to be essential for the development of coherent metabolic mechanisms of cardiac health and pathophysiology.
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Affiliation(s)
- Lindsey A McNally
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, KY, USA
| | - Tariq R Altamimi
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, KY, USA
| | - Kyle Fulghum
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, KY, USA
| | - Bradford G Hill
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, KY, USA.
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21
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Fernández-Moncada I, Robles-Maldonado D, Castro P, Alegría K, Epp R, Ruminot I, Barros LF. Bidirectional astrocytic GLUT1 activation by elevated extracellular K . Glia 2020; 69:1012-1021. [PMID: 33277953 DOI: 10.1002/glia.23944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/07/2023]
Abstract
The acute rise in interstitial K+ that accompanies neural activity couples the energy demand of neurons to the metabolism of astrocytes. The effects of elevated K+ on astrocytes include activation of aerobic glycolysis, inhibition of mitochondrial respiration and the release of lactate. Using a genetically encoded FRET glucose sensor and a novel protocol based on 3-O-methylglucose trans-acceleration and numerical simulation of glucose dynamics, we report that extracellular K+ is also a potent and reversible modulator of the astrocytic glucose transporter GLUT1. In cultured mouse astrocytes, the stimulatory effect developed within seconds, engaged both the influx and efflux modes of the transporter, and was detected even at 1 mM incremental K+ . The modulation of GLUT1 explains how astrocytes are able to maintain their glucose pool in the face of strong glycolysis stimulation. We propose that the stimulation of GLUT1 by K+ supports the production of lactate by astrocytes and the timely delivery of glucose to active neurons.
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Affiliation(s)
- Ignacio Fernández-Moncada
- Centro de Estudios Científicos, Valdivia, Chile.,INSERM U1215 NeuroCentre Magendie, Bordeaux, France
| | - Daniel Robles-Maldonado
- Centro de Estudios Científicos, Valdivia, Chile.,Universidad Austral de Chile, Valdivia, Chile
| | | | | | - Robert Epp
- Institute of Fluid Dynamics, ETH Zurich, Zurich, Switzerland
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22
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Werley CA, Boccardo S, Rigamonti A, Hansson EM, Cohen AE. Multiplexed Optical Sensors in Arrayed Islands of Cells for multimodal recordings of cellular physiology. Nat Commun 2020; 11:3881. [PMID: 32753572 PMCID: PMC7403318 DOI: 10.1038/s41467-020-17607-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Cells typically respond to chemical or physical perturbations via complex signaling cascades which can simultaneously affect multiple physiological parameters, such as membrane voltage, calcium, pH, and redox potential. Protein-based fluorescent sensors can report many of these parameters, but spectral overlap prevents more than ~4 modalities from being recorded in parallel. Here we introduce the technique, MOSAIC, Multiplexed Optical Sensors in Arrayed Islands of Cells, where patterning of fluorescent sensor-encoding lentiviral vectors with a microarray printer enables parallel recording of multiple modalities. We demonstrate simultaneous recordings from 20 sensors in parallel in human embryonic kidney (HEK293) cells and in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and we describe responses to metabolic and pharmacological perturbations. Together, these results show that MOSAIC can provide rich multi-modal data on complex physiological responses in multiple cell types.
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Affiliation(s)
- Christopher A Werley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Q-State Biosciences, Cambridge, MA, 02139, USA
| | - Stefano Boccardo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Nobel Biocare AG, Kloten, Switzerland
| | - Alessandra Rigamonti
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
| | - Emil M Hansson
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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23
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Zhang Z, Cheng X, Zhao Y, Yang Y. Lighting Up Live-Cell and In Vivo Central Carbon Metabolism with Genetically Encoded Fluorescent Sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:293-314. [PMID: 32119572 DOI: 10.1146/annurev-anchem-091619-091306] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As the core component of cell metabolism, central carbon metabolism, consisting of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle converts nutrients into metabolic precursors for biomass and energy to sustain the life of virtually all extant species. The metabolite levels or distributions in central carbon metabolism often change dynamically with cell fates, development, and disease progression. However, traditional biochemical methods require cell lysis, making it challenging to obtain spatiotemporal information about metabolites in living cells and in vivo. Genetically encoded fluorescent sensors allow the rapid, sensitive, specific, and real-time readout of metabolite dynamics in living organisms, thereby offering the potential to fill the gap in current techniques. In this review, we introduce recent progress made in the development of genetically encoded fluorescent sensors for central carbon metabolism and discuss their advantages, disadvantages, and applications. Moreover, several future directions of metabolite sensors are also proposed.
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Affiliation(s)
- Zhuo Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiawei Cheng
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yuzheng Zhao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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24
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Mossoba ME, Vohra SN, Bigley E, Sprando J, Wiesenfeld PL. Genetically Engineered Human Kidney Cells for Real-Time Cytotoxicity Testing In Vitro. Mol Biotechnol 2020; 62:252-259. [PMID: 32146690 DOI: 10.1007/s12033-020-00245-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Classic toxicology studies often utilize in vivo animal models. Newer approaches employing in vitro organ-specific cellular models have been developed in recent years to help accelerate the speed and reduce the cost of traditional toxicology testing. Toward the goal of supporting in vitro cellular model research with a regulatory application in mind, we have developed a 'designer' human kidney cell line called HK2-Vi that can fluorescently measure the cytotoxicity of potential toxins on proximal tubule cell viability in a direct exposure in vitro model. HK2-Vi was designed to be a reagent-less kinetic assay that can yield data on short- or long-term cell viability after toxin exposure. To generate HK2-Vi, we used monocistronic lentiviral transduction methods to genetically engineer a human kidney cell line called HK-2 to stably co-express two transgenes. The first is Perceval HR, which encodes a fluorescent biosensor of both cytosolic ATP and ADP and the second is pHRed, which encodes a biosensor of cytosolic pH. Relative levels of cellular ATP and ADP effectively serve as a reliable and robust indicator of cell viability. Because the fluorescence Perceval HR is pH-dependent, we co-expressed the pHRed genetic biosensor to correct for variations in pH if necessary. Heterogenous populations of transduced renal cells were enriched by flow cytometry before monoclonal cellular populations were isolated by cell culture methods. A single clonal population of co-transduced cells expressing both Perceval HR and pHRed was selected to be HK2-Vi. This established cell line can now serve as a tool for in vitro toxicology testing and the methods described herein serve as a model for developing designer cell lines derived from other organs.
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Affiliation(s)
- Miriam E Mossoba
- Neurotoxicology and In Vitro Toxicology Branch (NIVTB), Division of Applied Regulatory Toxicology (DART), Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), Laurel, MD, USA.
| | - Sanah N Vohra
- Neurotoxicology and In Vitro Toxicology Branch (NIVTB), Division of Applied Regulatory Toxicology (DART), Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), Laurel, MD, USA
| | - Elmer Bigley
- Immunobiology Branch (IB), Division of Virulence Assessment (DVA), Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), Laurel, MD, USA
| | - Jessica Sprando
- Neurotoxicology and In Vitro Toxicology Branch (NIVTB), Division of Applied Regulatory Toxicology (DART), Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), Laurel, MD, USA
| | - Paddy L Wiesenfeld
- Neurotoxicology and In Vitro Toxicology Branch (NIVTB), Division of Applied Regulatory Toxicology (DART), Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), Laurel, MD, USA
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25
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Chowdhury HH. Differences in cytosolic glucose dynamics in astrocytes and adipocytes measured by FRET-based nanosensors. Biophys Chem 2020; 261:106377. [PMID: 32302866 DOI: 10.1016/j.bpc.2020.106377] [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: 02/08/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2022]
Abstract
The cellular response to fluctuations in blood glucose levels consists of integrative regulation of cell glucose uptake and glucose utilization in the cytosol, resulting in altered levels of glucose in the cytosol. Cytosolic glucose is difficult to be measured in the intact tissue, however recently methods have become available that allow measurements of glucose in single living cells with fluorescence resonance energy transfer (FRET) based protein sensors. By studying the dynamics of cytosolic glucose levels in different experimental settings, we can gain insights into the properties of plasma membrane permeability to glucose and glucose utilization in the cytosol, and how these processes are modulated by different environmental conditions, agents and enzymes. In this review, we compare the cytosolic regulation of glucose in adipocytes and astrocytes - two important regulators of energy balance and glucose homeostasis in whole body and brain, respectively, with particular emphasis on the data obtained with FRET based protein sensors as well as other biochemical and molecular approaches.
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Affiliation(s)
- Helena H Chowdhury
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, University of Ljubljana, Faculty of Medicine, 1000 Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, 1000 Ljubljana, Slovenia.
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26
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Kaschubowski KE, Kraft AE, Nikolaev VO, Haag F. Using FRET-Based Fluorescent Sensors to Monitor Cytosolic and Membrane-Proximal Extracellular ATP Levels. Methods Mol Biol 2020; 2041:223-231. [PMID: 31646492 DOI: 10.1007/978-1-4939-9717-6_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assessment of local concentrations of extracellular ATP (eATP) at the site of receptor binding remains a challenge in the field of purinergic signaling. In many cases, biosensors exploiting the principle of Förster resonance energy transfer (FRET) have provided useful tools to visualize local concentrations of metabolites. A series of FRET-based biosensors based on the epsilon subunits of bacterial ATP synthases have been described for the visualisation of ATP. These sensors carry ATP-sensing units with different affinities for ATP, permitting imaging of ATP under the widely different concentration conditions found in subcellular locations such as the cytoplasm and the membrane-proximal extracellular space.
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Affiliation(s)
- Klaus E Kaschubowski
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel E Kraft
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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27
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Wang HC, Chang FY, Tsai TM, Chen CH, Chen YY. Development and clinical trial of a smartphone-based colorimetric detection system for self-monitoring of blood glucose. BIOMEDICAL OPTICS EXPRESS 2020; 11:2166-2177. [PMID: 32341874 PMCID: PMC7173904 DOI: 10.1364/boe.389638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 05/28/2023]
Abstract
Blood glucose measurements help to guide insulin therapy, thus reducing disease severities, secondary complications, and related mortalities. Efforts are underway to allow diabetes patients to experience a more convenient way to measure blood glucose and consequently increase their adherence to regular self-monitoring of blood glucose (SMBG). This study demonstrated a new SMBG system that integrated all components of a glucometer via a smartphone's optical sensing module to detect the colorimetric blood strip and obtains the blood glucose concentration with calculations performed by an application install in the smartphone. To validate the accuracy and applicability of the new SMBG system regarding the ISO15197:2013 accuracy criteria and patient requirements, a clinical trial and usability survey involving participants from different age groups were conducted in collaboration with the China Medical University, where enrolled 120 diabetic patients were asked to operate the new SMBG system to measure their blood glucose concentration, and feedback was obtained from their user experience. The results showed that three different reagent system lots fulfilled the accuracy requirements with values of 97.4-97.5% , and all of the data were within zones A and B of the consensus error grid, which satisfies the ISO 15197:2013 requirement. The usability survey showed that 97.5% of the participants found the operations convenient, and 100% found the design easy for carrying. This new system could lead to improvements in blood glucose monitoring by people with diabetes, and thus, better management of the disease.
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Affiliation(s)
- Hung-Chih Wang
- Department of Mechanical Engineering, National Taiwan University of Science and Technology, Taiwan
| | - Fuh-Yu Chang
- Department of Mechanical Engineering, National Taiwan University of Science and Technology, Taiwan
| | | | - Chieh-Hsiao Chen
- iXensor Co., Ltd, Taiwan
- China Medical University and Beigang Hospital, Taiwan
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28
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Zhang Y, Shaikh N, Ferey JL, Wankhade UD, Chintapalli SV, Higgins CB, Crowley JR, Heitmeier MR, Stothard AI, Mihi B, Good M, Higashiyama T, Swarts BM, Hruz PW, Shankar K, Tarr PI, DeBosch BJ. Lactotrehalose, an Analog of Trehalose, Increases Energy Metabolism Without Promoting Clostridioides difficile Infection in Mice. Gastroenterology 2020; 158:1402-1416.e2. [PMID: 31838076 PMCID: PMC7103499 DOI: 10.1053/j.gastro.2019.11.295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 11/20/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Trehalose is a disaccharide that might be used in the treatment of cardiometabolic diseases. However, trehalose consumption promotes the expansion of Clostridioides difficile ribotypes that metabolize trehalose via trehalose-6-phosphate hydrolase. Furthermore, brush border and renal trehalases can reduce the efficacy of trehalose by cleaving it into monosaccharides. We investigated whether a trehalase-resistant analogue of trehalose (lactotrehalose) has the same metabolic effects of trehalose without expanding C difficile. METHODS We performed studies with HEK293 and Caco2 cells, primary hepatocytes from mice, and human intestinal organoids. Glucose transporters were overexpressed in HEK293 cells, and glucose tra2nsport was quantified. Primary hepatocytes were cultured with or without trehalose or lactotrehalose, and gene expression patterns were analyzed. C57B6/J mice were given oral antibiotics and trehalose or lactotrehalose in drinking water, or only water (control), followed by gavage with the virulent C difficile ribotype 027 (CD027); fecal samples were analyzed for toxins A (ToxA) or B (ToxB) by enzyme-linked immunosorbent assay. Other mice were given trehalose or lactotrehalose in drinking water for 2 days before placement on a chow or 60% fructose diet for 10 days. Liver tissues were collected and analyzed by histologic, serum biochemical, RNA sequencing, autophagic flux, and thermogenesis analyses. We quantified portal trehalose and lactotrehalose bioavailability by gas chromatography mass spectrometry. Fecal microbiomes were analyzed by 16S ribosomal RNA sequencing and principal component analyses. RESULTS Lactotrehalose and trehalose each blocked glucose transport in HEK293 cells and induced a gene expression pattern associated with fasting in primary hepatocytes. Compared with mice on the chow diet, mice on the high-fructose diet had increased circulating cholesterol, higher ratios of liver weight-to-body weight, hepatic lipid accumulation (steatosis), and liver gene expression patterns of carbohydrate-responsive de novo lipogenesis. Mice given lactotrehalose while on the high-fructose diet did not develop any of these features and had increased whole-body caloric expenditure compared with mice given trehalose or water and fed a high-fructose diet. Livers from mice given lactotrehalose had increased transcription of genes that regulate mitochondrial energy metabolism compared with liver from mice given trehalose or controls. Lactotrehalose was bioavailable in venous and portal circulation and fecal samples. Lactotrehalose reduced fecal markers of microbial branched-chain amino acid biosynthesis and increased expression of microbial genes that regulate insulin signaling. In mice given antibiotics followed by CD027, neither lactotrehalose nor trehalose increased levels of the bacteria or its toxin in stool-in fact, trehalose reduced the abundance of CD027 in stool. Lactotrehalose and trehalose reduced markers of inflammation in rectal tissue after CD027 infection. CONCLUSIONS Lactotrehalose is a trehalase-resistant analogue that increases metabolic parameters, compared with trehalose, without increasing the abundance or virulence of C difficile strain CD027. Trehalase-resistant trehalose analogues might be developed as next-generation fasting-mimetics for the treatment of diabetes and nonalcoholic fatty liver disease.
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Affiliation(s)
- Yiming Zhang
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Jeremie L. Ferey
- Department of Obstetrics & Gynecology, Washington University School of Medicine, St. Louis, MO 63110
| | - Umesh D. Wankhade
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Sree V. Chintapalli
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Cassandra B. Higgins
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Jan R. Crowley
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Monique R. Heitmeier
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Alicyn I. Stothard
- Department of Chemistry & Biochemistry, Central Michigan University, Mt. Pleasant, MI 48859
| | - Belgacem Mihi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | | | - Benjamin M. Swarts
- Department of Chemistry & Biochemistry, Central Michigan University, Mt. Pleasant, MI 48859
| | - Paul W. Hruz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Kartik Shankar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110,,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Brian J. DeBosch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110,,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO 63110,Correspondence: Brian DeBosch, Departments of Pediatrics and Cell Biology and Physiology, Washington University School of Medicine, 5107 McDonnell Pediatrics Research Building, 660 S. Euclid Ave, Box 8208, St. Louis, MO 63110. Telephone: 314-454-6173; FAX: 314-454-2412;
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29
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Lan R, Liu H, Zhu L, Lu F, Wu Q, Wu W. One-pot HTST synthesis of responsive fluorescent ZnO@apo-enzyme composite microgels for intracellular glucometry. RSC Adv 2020; 10:26566-26578. [PMID: 35519737 PMCID: PMC9055424 DOI: 10.1039/d0ra04339g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
One-pot high-temperature short-time heating synthesis allows harnessing of dynamic profile of apo-GOx on ZnO@apo-enzyme composite microgels for intracellular glucometry.
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Affiliation(s)
- Ruyue Lan
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Huijiao Liu
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Lin Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Fan Lu
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Qingshi Wu
- College of Chemical Engineering and Materials Science
- Quanzhou Normal University
- Quanzhou
- China
| | - Weitai Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- Department of Chemistry
- College of Chemistry and Chemical Engineering
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30
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Monteiro F, Hubmann G, Takhaveev V, Vedelaar SR, Norder J, Hekelaar J, Saldida J, Litsios A, Wijma HJ, Schmidt A, Heinemann M. Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor. Mol Syst Biol 2019; 15:e9071. [PMID: 31885198 PMCID: PMC6920703 DOI: 10.15252/msb.20199071] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
Metabolic heterogeneity between individual cells of a population harbors significant challenges for fundamental and applied research. Identifying metabolic heterogeneity and investigating its emergence require tools to zoom into metabolism of individual cells. While methods exist to measure metabolite levels in single cells, we lack capability to measure metabolic flux, i.e., the ultimate functional output of metabolic activity, on the single-cell level. Here, combining promoter engineering, computational protein design, biochemical methods, proteomics, and metabolomics, we developed a biosensor to measure glycolytic flux in single yeast cells. Therefore, drawing on the robust cell-intrinsic correlation between glycolytic flux and levels of fructose-1,6-bisphosphate (FBP), we transplanted the B. subtilis FBP-binding transcription factor CggR into yeast. With the developed biosensor, we robustly identified cell subpopulations with different FBP levels in mixed cultures, when subjected to flow cytometry and microscopy. Employing microfluidics, we were also able to assess the temporal FBP/glycolytic flux dynamics during the cell cycle. We anticipate that our biosensor will become a valuable tool to identify and study metabolic heterogeneity in cell populations.
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Affiliation(s)
- Francisca Monteiro
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
cE3c‐Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Georg Hubmann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
Laboratory of Molecular Cell BiologyDepartment of BiologyInstitute of Botany and MicrobiologyKU Leuven, & Center for Microbiology, VIBHeverlee, FlandersBelgium
| | - Vakil Takhaveev
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Silke R Vedelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Justin Norder
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Johan Hekelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Joana Saldida
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Athanasios Litsios
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Hein J Wijma
- Biotechnology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | | | - Matthias Heinemann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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31
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Ruminot I, Schmälzle J, Leyton B, Barros LF, Deitmer JW. Tight coupling of astrocyte energy metabolism to synaptic activity revealed by genetically encoded FRET nanosensors in hippocampal tissue. J Cereb Blood Flow Metab 2019; 39:513-523. [PMID: 29083247 PMCID: PMC6421254 DOI: 10.1177/0271678x17737012] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The potassium ion, K+, a neuronal signal that is released during excitatory synaptic activity, produces acute activation of glucose consumption in cultured astrocytes, a phenomenon mediated by the sodium bicarbonate cotransporter NBCe1 ( SLC4A4). We have explored here the relevance of this mechanism in brain tissue by imaging the effect of neuronal activity on pH, glucose, pyruvate and lactate dynamics in hippocampal astrocytes using BCECF and FRET nanosensors. Electrical stimulation of Schaffer collaterals produced fast activation of glucose consumption in astrocytes with a parallel increase in intracellular pyruvate and biphasic changes in lactate . These responses were blocked by TTX and were absent in tissue slices prepared from NBCe1-KO mice. Direct depolarization of astrocytes with elevated extracellular K+ or Ba2+ mimicked the metabolic effects of electrical stimulation. We conclude that the glycolytic pathway of astrocytes in situ is acutely sensitive to neuronal activity, and that extracellular K+ and the NBCe1 cotransporter are involved in metabolic crosstalk between neurons and astrocytes. Glycolytic activation of astrocytes in response to neuronal K+ helps to provide an adequate supply of lactate, a metabolite that is released by astrocytes and which acts as neuronal fuel and an intercellular signal.
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Affiliation(s)
- Iván Ruminot
- 1 Abteilung für Allgemeine Zoologie, FB Biologie, University of Kaiserslautern, Germany.,2 Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Jana Schmälzle
- 1 Abteilung für Allgemeine Zoologie, FB Biologie, University of Kaiserslautern, Germany
| | - Belén Leyton
- 2 Centro de Estudios Científicos (CECs), Valdivia, Chile.,3 Universidad Austral de Chile, Valdivia, Chile
| | | | - Joachim W Deitmer
- 1 Abteilung für Allgemeine Zoologie, FB Biologie, University of Kaiserslautern, Germany
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32
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Anand R, Agrawal M, Mattaparthi VS, Swaminathan R, Santra SB. Consequences of Heterogeneous Crowding on an Enzymatic Reaction: A Residence Time Monte Carlo Approach. ACS OMEGA 2019; 4:727-736. [PMID: 31459357 PMCID: PMC6649177 DOI: 10.1021/acsomega.8b02863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/26/2018] [Indexed: 05/06/2023]
Abstract
Translational diffusion of a free substrate in crowded metabolically active spaces such as cell cytoplasm or mitochondrial matrix is punctuated by collisions and nonspecific interactions with soluble/immobile macromolecules/macrostructures in a variety of shapes/sizes. It is not understood how such disruptions alter enzyme reaction kinetics in such spaces. A novel Monte Carlo (MC) technique, "residence time MC", has been developed to study the kinetics of a simple enzyme-substrate reaction in a crowded milieu using a single immobile enzyme in the midst of diffusing substrates and products. The reaction time lost while the substrate nonspecifically interacts or is transiently trapped with ambient macromolecules is quantified by introducing the residence time "tau". Tau scales with the size of crowding macromolecules but makes the knowledge of their shape redundant. The residence time thus presents a convenient parameter to realistically mimic the sticky surroundings encountered by a diffusing substrate in heterogeneously crowded physiological spaces. Results reveal that for identical substrate concentration and excluded volume, increase in tau significantly diminished enzymatic product yield and reaction rate, slowed down substrate/product diffusion, and prolonged their relaxation times. A smooth transition from the anomalous subdiffusive motion to normal diffusion at long time limits was observed irrespective of the value of tau. The predictions from the model are shown to be in qualitative agreement with in vitro experimental data revealing the rate of alkaline phosphatase-catalyzed hydrolysis of p-nitrophenyl phosphate in the midst of 40/500/2000 kDa dextrans. Our findings from the residence time MC model also attempt to rationalize previously unexplained experimental observations in crowded enzyme kinetics literature. Furthermore, major insights to emerge from this study are the reasons why free diffusion of the substrate in crowded physiological spaces is detrimental to enzyme function. It is argued that organized enzyme clusters such as "metabolon" may perhaps exist to regulate the substrate translocation in such sticky physiological spaces to maintain optimal enzyme function. In summary, this work provides key insights explaining why absence of substrate channeling can dramatically slow down enzyme reaction rate in crowded metabolically active spaces.
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Affiliation(s)
- Rajat Anand
- Department of Biosciences and Bioengineering and Department of
Physics, Indian Institute of Technology
Guwahati, Guwahati 781039, Assam, India
| | - Manish Agrawal
- Department of Biosciences and Bioengineering and Department of
Physics, Indian Institute of Technology
Guwahati, Guwahati 781039, Assam, India
| | - Venkata Satish
Kumar Mattaparthi
- Department of Biosciences and Bioengineering and Department of
Physics, Indian Institute of Technology
Guwahati, Guwahati 781039, Assam, India
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering and Department of
Physics, Indian Institute of Technology
Guwahati, Guwahati 781039, Assam, India
- E-mail:
| | - Sitangshu Bikas Santra
- Department of Biosciences and Bioengineering and Department of
Physics, Indian Institute of Technology
Guwahati, Guwahati 781039, Assam, India
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33
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Looser ZJ, Barrett MJP, Hirrlinger J, Weber B, Saab AS. Intravitreal AAV-Delivery of Genetically Encoded Sensors Enabling Simultaneous Two-Photon Imaging and Electrophysiology of Optic Nerve Axons. Front Cell Neurosci 2018; 12:377. [PMID: 30405358 PMCID: PMC6205974 DOI: 10.3389/fncel.2018.00377] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/03/2018] [Indexed: 11/21/2022] Open
Abstract
Myelination of axons by oligodendrocytes is a key feature of the remarkably fast operating CNS. Oligodendrocytes not only tune axonal conduction speed but are also suggested to maintain long-term axonal integrity by providing metabolic support to the axons they ensheath. However, how myelinating oligodendrocytes impact axonal energy homeostasis remains poorly understood and difficult to investigate. Here, we provide a method of how to study electrically active myelinated axons expressing genetically encoded sensors by combining electrophysiology and two-photon imaging of acutely isolated optic nerves. We show that intravitreal adeno-associated viral (AAV) vector delivery is an efficient tool to achieve functional sensor expression in optic nerve axons, which is demonstrated by measuring axonal ATP dynamics following AAV-mediated sensor expression. This novel approach allows for fast expression of any optical sensor of interest to be studied in optic nerve axons without the need to go through the laborious process of producing new transgenic mouse lines. Viral-mediated biosensor expression in myelinated axons and the subsequent combination of nerve recordings and sensor imaging outlines a powerful method to investigate oligodendroglial support functions and to further interrogate cellular mechanisms governing axonal energy homeostasis under physiological and pathological conditions.
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Affiliation(s)
- Zoe J. Looser
- Institute of Pharmacology & Toxicology, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Matthew J. P. Barrett
- Institute of Pharmacology & Toxicology, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Johannes Hirrlinger
- Carl-Ludwig-Institute for Physiology, University of Leipzig, Leipzig, Germany
- Department of Neurogenetics, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Bruno Weber
- Institute of Pharmacology & Toxicology, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Aiman S. Saab
- Institute of Pharmacology & Toxicology, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
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34
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Zhang Z, Chen W, Zhao Y, Yang Y. Spatiotemporal Imaging of Cellular Energy Metabolism with Genetically-Encoded Fluorescent Sensors in Brain. Neurosci Bull 2018; 34:875-886. [PMID: 29679217 PMCID: PMC6129245 DOI: 10.1007/s12264-018-0229-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/24/2018] [Indexed: 12/21/2022] Open
Abstract
The brain has very high energy requirements and consumes 20% of the oxygen and 25% of the glucose in the human body. Therefore, the molecular mechanism underlying how the brain metabolizes substances to support neural activity is a fundamental issue for neuroscience studies. A well-known model in the brain, the astrocyte-neuron lactate shuttle, postulates that glucose uptake and glycolytic activity are enhanced in astrocytes upon neuronal activation and that astrocytes transport lactate into neurons to fulfill their energy requirements. Current evidence for this hypothesis has yet to reach a clear consensus, and new concepts beyond the shuttle hypothesis are emerging. The discrepancy is largely attributed to the lack of a critical method for real-time monitoring of metabolic dynamics at cellular resolution. Recent advances in fluorescent protein-based sensors allow the generation of a sensitive, specific, real-time readout of subcellular metabolites and fill the current technological gap. Here, we summarize the development of genetically encoded metabolite sensors and their applications in assessing cell metabolism in living cells and in vivo, and we believe that these tools will help to address the issue of elucidating neural energy metabolism.
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Affiliation(s)
- Zhuo Zhang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Weicai Chen
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuzheng Zhao
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, China.
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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35
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Piquet J, Toussay X, Hepp R, Lerchundi R, Le Douce J, Faivre É, Guiot E, Bonvento G, Cauli B. Supragranular Pyramidal Cells Exhibit Early Metabolic Alterations in the 3xTg-AD Mouse Model of Alzheimer's Disease. Front Cell Neurosci 2018; 12:216. [PMID: 30072874 PMCID: PMC6060432 DOI: 10.3389/fncel.2018.00216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/29/2018] [Indexed: 01/23/2023] Open
Abstract
The impairment of cerebral glucose utilization is an early and predictive biomarker of Alzheimer’s disease (AD) that is likely to contribute to memory and cognition disorders during the progression of the pathology. Yet, the cellular and molecular mechanisms underlying these metabolic alterations remain poorly understood. Here we studied the glucose metabolism of supragranular pyramidal cells at an early presymptomatic developmental stage in non-transgenic (non-Tg) and 3xTg-AD mice, a mouse model of AD replicating numerous hallmarks of the disease. We performed both intracellular glucose imaging with a genetically encoded fluorescence resonance energy transfer (FRET)-based glucose biosensor and transcriptomic profiling of key molecular elements of glucose metabolism with single-cell multiplex RT-PCR (scRT-mPCR). We found that juvenile pyramidal cells exhibit active glycolysis and pentose phosphate pathway at rest that are respectively enhanced and impaired in 3xTg-AD mice without alteration of neuronal glucose uptake or transcriptional modification. Given the importance of glucose metabolism for neuronal survival, these early alterations could initiate or at least contribute to the later neuronal dysfunction of pyramidal cells in AD.
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Affiliation(s)
- Juliette Piquet
- UPMC Univ Paris 06, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, Paris, France
| | - Xavier Toussay
- UPMC Univ Paris 06, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, Paris, France
| | - Régine Hepp
- UPMC Univ Paris 06, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, Paris, France
| | - Rodrigo Lerchundi
- CNRS UMR 9199, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut de Biologie François Jacob, Molecular Imaging Center (MIRCen), Université Paris-Sud, Université Paris-Saclay, Paris, France
| | - Juliette Le Douce
- CNRS UMR 9199, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut de Biologie François Jacob, Molecular Imaging Center (MIRCen), Université Paris-Sud, Université Paris-Saclay, Paris, France
| | - Émilie Faivre
- CNRS UMR 9199, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut de Biologie François Jacob, Molecular Imaging Center (MIRCen), Université Paris-Sud, Université Paris-Saclay, Paris, France
| | - Elvire Guiot
- UPMC Univ Paris 06, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, Paris, France
| | - Gilles Bonvento
- CNRS UMR 9199, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut de Biologie François Jacob, Molecular Imaging Center (MIRCen), Université Paris-Sud, Université Paris-Saclay, Paris, France
| | - Bruno Cauli
- UPMC Univ Paris 06, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, Paris, France
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36
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Lee H, Hong YJ, Baik S, Hyeon T, Kim D. Enzyme-Based Glucose Sensor: From Invasive to Wearable Device. Adv Healthc Mater 2018; 7:e1701150. [PMID: 29334198 DOI: 10.1002/adhm.201701150] [Citation(s) in RCA: 294] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/28/2017] [Indexed: 02/07/2023]
Abstract
Blood glucose concentration is a key indicator of patients' health, particularly for symptoms associated with diabetes mellitus. Because of the large number of diabetic patients, many approaches for glucose measurement have been studied to enable continuous and accurate glucose level monitoring. Among them, electrochemical analysis is prominent because it is simple and quantitative. This technology has been incorporated into commercialized and research-level devices from simple test strips to wearable devices and implantable systems. Although directly monitoring blood glucose assures accurate information, the invasive needle-pinching step to collect blood often results in patients (particularly young patients) being reluctant to adopt the process. An implantable glucose sensor may avoid the burden of repeated blood collections, but it is quite invasive and requires periodic replacement of the sensor owing to biofouling and its short lifetime. Therefore, noninvasive methods to estimate blood glucose levels from tears, saliva, interstitial fluid (ISF), and sweat are currently being studied. This review discusses the evolution of enzyme-based electrochemical glucose sensors, including materials, device structures, fabrication processes, and system engineering. Furthermore, invasive and noninvasive blood glucose monitoring methods using various biofluids or blood are described, highlighting the recent progress in the development of enzyme-based glucose sensors and their integrated systems.
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Affiliation(s)
- Hyunjae Lee
- Center for Nanoparticle ResearchInstitute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University (SNU) Seoul 08826 Republic of Korea
| | - Yongseok Joseph Hong
- Center for Nanoparticle ResearchInstitute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University (SNU) Seoul 08826 Republic of Korea
| | - Seungmin Baik
- Center for Nanoparticle ResearchInstitute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University (SNU) Seoul 08826 Republic of Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle ResearchInstitute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University (SNU) Seoul 08826 Republic of Korea
| | - Dae‐Hyeong Kim
- Center for Nanoparticle ResearchInstitute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University (SNU) Seoul 08826 Republic of Korea
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37
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Hu H, Wei Y, Wang D, Su N, Chen X, Zhao Y, Liu G, Yang Y. Glucose monitoring in living cells with single fluorescent protein-based sensors. RSC Adv 2018; 8:2485-2489. [PMID: 35541484 PMCID: PMC9077360 DOI: 10.1039/c7ra11347a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 12/23/2017] [Indexed: 11/26/2022] Open
Abstract
Glucose is the main source of energy and carbon in organisms and plays a central role in metabolism and cellular homeostasis. However, the sensitive fluctuation of glucose in living cells is difficult to monitor. Thus, we developed a series of ratiometric, highly responsive, single fluorescent protein-based glucose sensors of wide dynamic range by combining a circularly permuted yellow fluorescent protein with a bacterial periplasmic glucose/galactose-binding protein. We used these sensors to monitor glucose transport in living Escherichia coli cells, and found that the cells take up glucose within 10 min to maintain physiological glucose levels, and observed the differences in glucose uptake and glucose metabolism between wild-type and Mlc knockout cells. These sensors can be specific and simple tools for glucose detection in vitro and non-invasive tools for real-time monitoring of glucose metabolism in vivo. Glucose is the main source of energy and carbon in organisms and plays a central role in metabolism and cellular homeostasis.![]()
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Affiliation(s)
- Hanyang Hu
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
| | - Yufeng Wei
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
| | - Daocheng Wang
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
| | - Ni Su
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
| | - Xianjun Chen
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
| | - Yuzheng Zhao
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- East China University of Science and Technology
- Shanghai 200237
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38
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Gagarinova A, Phanse S, Cygler M, Babu M. Insights from protein-protein interaction studies on bacterial pathogenesis. Expert Rev Proteomics 2017; 14:779-797. [DOI: 10.1080/14789450.2017.1365603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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39
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Molecular mechanism of substrate recognition and transport by the AtSWEET13 sugar transporter. Proc Natl Acad Sci U S A 2017; 114:10089-10094. [PMID: 28878024 DOI: 10.1073/pnas.1709241114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sugar Will Eventually be Exported Transporters (SWEETs) are recently identified sugar transporters that can discriminate and transport di- or monosaccharides across a membrane following the concentration gradient. SWEETs play key roles in plant biological processes, such as pollen nutrition, nectar secretion, seed filling, and phloem loading. SWEET13 from Arabidopsis thaliana (AtSWEET13) is an important sucrose transporter in pollen development. Here, we report the 2.8-Å resolution crystal structure of AtSWEET13 in the inward-facing conformation with a substrate analog, 2'-deoxycytidine 5'-monophosphate, bound in the central cavity. In addition, based on the results of an in-cell transport activity assay and single-molecule Förster resonance energy transfer analysis, we suggest a mechanism for substrate selectivity based on the size of the substrate-binding pocket. Furthermore, AtSWEET13 appears to form a higher order structure presumably related to its function.
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40
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Ratiometric Matryoshka biosensors from a nested cassette of green- and orange-emitting fluorescent proteins. Nat Commun 2017; 8:431. [PMID: 28874729 PMCID: PMC5585204 DOI: 10.1038/s41467-017-00400-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 06/24/2017] [Indexed: 01/25/2023] Open
Abstract
Sensitivity, dynamic and detection range as well as exclusion of expression and instrumental artifacts are critical for the quantitation of data obtained with fluorescent protein (FP)-based biosensors in vivo. Current biosensors designs are, in general, unable to simultaneously meet all these criteria. Here, we describe a generalizable platform to create dual-FP biosensors with large dynamic ranges by employing a single FP-cassette, named GO-(Green-Orange) Matryoshka. The cassette nests a stable reference FP (large Stokes shift LSSmOrange) within a reporter FP (circularly permuted green FP). GO- Matryoshka yields green and orange fluorescence upon blue excitation. As proof of concept, we converted existing, single-emission biosensors into a series of ratiometric calcium sensors (MatryoshCaMP6s) and ammonium transport activity sensors (AmTryoshka1;3). We additionally identified the internal acid-base equilibrium as a key determinant of the GCaMP dynamic range. Matryoshka technology promises flexibility in the design of a wide spectrum of ratiometric biosensors and expanded in vivo applications.Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range.
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41
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42
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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43
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Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem 2017; 86:277-304. [PMID: 28654323 DOI: 10.1146/annurev-biochem-061516-044952] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Matthias S Klein
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, California 95616.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
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44
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Chang M, Li L, Hu H, Hu Q, Wang A, Cao X, Yu X, Zhang S, Zhao Y, Chen J, Yang Y, Xu J. Using Fractional Intensities of Time-resolved Fluorescence to Sensitively Quantify NADH/NAD + with Genetically Encoded Fluorescent Biosensors. Sci Rep 2017. [PMID: 28646144 PMCID: PMC5482812 DOI: 10.1038/s41598-017-04051-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this paper, we propose a novel and sensitive ratiometric analysis method that uses the fractional intensities of time-resolved fluorescence of genetically encoded fluorescent NADH/NAD+ biosensors, Peredox, SoNar, and Frex. When the conformations of the biosensors change upon NADH/NAD+ binding, the fractional intensities (αiτi) have opposite changing trends. Their ratios could be exploited to quantify NADH/NAD+ levels with a larger dynamic range and higher resolution versus commonly used fluorescence intensity and lifetime methods. Moreover, only one excitation and one emission wavelength are required for this ratiometric measurement. This eliminates problems of traditional excitation-ratiometric and emission-ratiometric methods. This method could be used to simplify the design and achieve highly sensitive analyte quantification of genetically encoded fluorescent biosensors. Wide potential applications could be developed for imaging live cell metabolism based on this new method.
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Affiliation(s)
- Mengfang Chang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Lei Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Hanyang Hu
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Qingxun Hu
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Aoxue Wang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xiaodan Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xiantong Yu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Yuzheng Zhao
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China. .,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China. .,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
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45
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Bulusu V, Prior N, Snaebjornsson MT, Kuehne A, Sonnen KF, Kress J, Stein F, Schultz C, Sauer U, Aulehla A. Spatiotemporal Analysis of a Glycolytic Activity Gradient Linked to Mouse Embryo Mesoderm Development. Dev Cell 2017; 40:331-341.e4. [PMID: 28245920 PMCID: PMC5337618 DOI: 10.1016/j.devcel.2017.01.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 12/01/2016] [Accepted: 01/27/2017] [Indexed: 12/27/2022]
Abstract
How metabolism is rewired during embryonic development is still largely unknown, as it remains a major technical challenge to resolve metabolic activities or metabolite levels with spatiotemporal resolution. Here, we investigated metabolic changes during development of organogenesis-stage mouse embryos, focusing on the presomitic mesoderm (PSM). We measured glycolytic labeling kinetics from 13C-glucose tracing experiments and detected elevated glycolysis in the posterior, more undifferentiated PSM. We found evidence that the spatial metabolic differences are functionally relevant during PSM development. To enable real-time quantification of a glycolytic metabolite with spatiotemporal resolution, we generated a pyruvate FRET-sensor reporter mouse line. We revealed dynamic changes in cytosolic pyruvate levels as cells transit toward a more anterior PSM state. Combined, our approach identifies a gradient of glycolytic activity across the PSM, and we provide evidence that these spatiotemporal metabolic changes are intrinsically linked to PSM development and differentiation. Identification of glycolytic activity gradient in mouse presomitic mesoderm Development of a pyruvate FRET-reporter mouse model Real-time imaging reveals pyruvate gradient dynamics Metabolic state is linked to presomitic mesoderm cell differentiation
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Affiliation(s)
- Vinay Bulusu
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Nicole Prior
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marteinn T Snaebjornsson
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Katharina F Sonnen
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jana Kress
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Frank Stein
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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46
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San Martín A, Arce-Molina R, Galaz A, Pérez-Guerra G, Barros LF. Nanomolar nitric oxide concentrations quickly and reversibly modulate astrocytic energy metabolism. J Biol Chem 2017; 292:9432-9438. [PMID: 28341740 PMCID: PMC5454122 DOI: 10.1074/jbc.m117.777243] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/14/2017] [Indexed: 01/04/2023] Open
Abstract
Nitric oxide (NO) is an intercellular messenger involved in multiple bodily functions. Prolonged NO exposure irreversibly inhibits respiration by covalent modification of mitochondrial cytochrome oxidase, a phenomenon of pathological relevance. However, the speed and potency of NO's metabolic effects at physiological concentrations are incompletely characterized. To this end, we set out to investigate the metabolic effects of NO in cultured astrocytes from mice by taking advantage of the high spatiotemporal resolution afforded by genetically encoded Förster resonance energy transfer (FRET) nanosensors. NO exposure resulted in immediate and reversible intracellular glucose depletion and lactate accumulation. Consistent with cytochrome oxidase involvement, the glycolytic effect was enhanced at a low oxygen level and became irreversible at a high NO concentration or after prolonged exposure. Measurements of both glycolytic rate and mitochondrial pyruvate consumption revealed significant effects even at nanomolar NO concentrations. We conclude that NO can modulate astrocytic energy metabolism in the short term, reversibly, and at concentrations known to be released by endothelial cells under physiological conditions. These findings suggest that NO modulates the size of the astrocytic lactate reservoir involved in neuronal fueling and signaling.
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Affiliation(s)
- Alejandro San Martín
- From the Centro de Estudios Científicos (CECs), 5110466 Valdivia and
- the Universidad Austral de Chile, 5110566 Valdivia, Chile
| | - Robinson Arce-Molina
- From the Centro de Estudios Científicos (CECs), 5110466 Valdivia and
- the Universidad Austral de Chile, 5110566 Valdivia, Chile
| | - Alex Galaz
- From the Centro de Estudios Científicos (CECs), 5110466 Valdivia and
| | - Gustavo Pérez-Guerra
- From the Centro de Estudios Científicos (CECs), 5110466 Valdivia and
- the Universidad Austral de Chile, 5110566 Valdivia, Chile
| | - L Felipe Barros
- From the Centro de Estudios Científicos (CECs), 5110466 Valdivia and
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47
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Cox KL, Meng F, Wilkins KE, Li F, Wang P, Booher NJ, Carpenter SCD, Chen LQ, Zheng H, Gao X, Zheng Y, Fei Z, Yu JZ, Isakeit T, Wheeler T, Frommer WB, He P, Bogdanove AJ, Shan L. TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton. Nat Commun 2017; 8:15588. [PMID: 28537271 PMCID: PMC5458083 DOI: 10.1038/ncomms15588] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/11/2017] [Indexed: 12/22/2022] Open
Abstract
Transcription activator-like (TAL) effectors from Xanthomonas citri subsp. malvacearum (Xcm) are essential for bacterial blight of cotton (BBC). Here, by combining transcriptome profiling with TAL effector-binding element (EBE) prediction, we show that GhSWEET10, encoding a functional sucrose transporter, is induced by Avrb6, a TAL effector determining Xcm pathogenicity. Activation of GhSWEET10 by designer TAL effectors (dTALEs) restores virulence of Xcm avrb6 deletion strains, whereas silencing of GhSWEET10 compromises cotton susceptibility to infections. A BBC-resistant line carrying an unknown recessive b6 gene bears the same EBE as the susceptible line, but Avrb6-mediated induction of GhSWEET10 is reduced, suggesting a unique mechanism underlying b6-mediated resistance. We show via an extensive survey of GhSWEET transcriptional responsiveness to different Xcm field isolates that additional GhSWEETs may also be involved in BBC. These findings advance our understanding of the disease and resistance in cotton and may facilitate the development cotton with improved resistance to BBC. Transcription activator-like effectors contribute to virulence of the Xanthomonas strain responsible for bacterial blight in cotton. Here Cox et al. show that the Xanthomonas Avrb6 effector induces expression of the cotton SWEET10 sugar transporter and that this induction promotes disease.
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Affiliation(s)
- Kevin L Cox
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Fanhong Meng
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Katherine E Wilkins
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Fangjun Li
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Ping Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Li-Qing Chen
- Department of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Hui Zheng
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Xiquan Gao
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - John Z Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Terry Wheeler
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Texas Agricultural Experiment Station, Lubbock, Texas 79403, USA
| | - Wolf B Frommer
- Carnegie Science, Department of Plant Biology, 260 Panama Street, Stanford, California 94305, USA
| | - Ping He
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Libo Shan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
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48
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Moroz P, Razgoniaeva N, He Y, Jensen G, Eckard H, Lu HP, Zamkov M. Tracking the Energy Flow on Nanoscale via Sample-Transmitted Excitation Photoluminescence Spectroscopy. ACS NANO 2017; 11:4191-4197. [PMID: 28324655 DOI: 10.1021/acsnano.7b01141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tracking the energy flow in nanoscale materials is an important yet challenging goal. Experimental methods for probing the intermolecular energy transfer (ET) are often burdened by the spectral crosstalk between donor and acceptor species, which complicates unraveling their individual contributions. This issue is particularly prominent in inorganic nanoparticles and biological macromolecules featuring broad absorbing profiles. Here, we demonstrate a general spectroscopic strategy for measuring the ET efficiency between nanostructured or molecular dyes exhibiting a significant donor-acceptor spectral overlap. The reported approach is enabled through spectral shaping of the broadband excitation light with solutions of donor molecules, which inhibits the excitation of respective donor species in the sample. The resulting changes in the acceptor emission induced by the spectral modulation of the excitation beam are then used to determine the quantum efficiency and the rate of ET processes between arbitrary fluorophores (molecules, nanoparticles, polymers) with high accuracy. The feasibility of the reported method was demonstrated using a control donor-acceptor system utilizing a protein-bridged Cy3-Cy5 dye pair and subsequently applied for studying the energy flow in a CdSe560-CdSe600 binary nanocrystal film.
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Affiliation(s)
- Pavel Moroz
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Natalia Razgoniaeva
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Yufan He
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Gregory Jensen
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Holly Eckard
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - H Peter Lu
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Mikhail Zamkov
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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49
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Cell competition with normal epithelial cells promotes apical extrusion of transformed cells through metabolic changes. Nat Cell Biol 2017; 19:530-541. [PMID: 28414314 DOI: 10.1038/ncb3509] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022]
Abstract
Recent studies have revealed that newly emerging transformed cells are often apically extruded from epithelial tissues. During this process, normal epithelial cells can recognize and actively eliminate transformed cells, a process called epithelial defence against cancer (EDAC). Here, we show that mitochondrial membrane potential is diminished in RasV12-transformed cells when they are surrounded by normal cells. In addition, glucose uptake is elevated, leading to higher lactate production. The mitochondrial dysfunction is driven by upregulation of pyruvate dehydrogenase kinase 4 (PDK4), which positively regulates elimination of RasV12-transformed cells. Furthermore, EDAC from the surrounding normal cells, involving filamin, drives the Warburg-effect-like metabolic alteration. Moreover, using a cell-competition mouse model, we demonstrate that PDK-mediated metabolic changes promote the elimination of RasV12-transformed cells from intestinal epithelia. These data indicate that non-cell-autonomous metabolic modulation is a crucial regulator for cell competition, shedding light on the unexplored events at the initial stage of carcinogenesis.
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50
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Sugiyama A, Saida Y, Yoshimizu M, Takanashi K, Sosso D, Frommer WB, Yazaki K. Molecular Characterization of LjSWEET3, a Sugar Transporter in Nodules of Lotus japonicus. PLANT & CELL PHYSIOLOGY 2017; 58:298-306. [PMID: 28007966 DOI: 10.1093/pcp/pcw190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
Symbiotic nitrogen fixation in legumes contributes greatly to the global nitrogen cycle on the earth. In nodules, resident rhizobia supply nitrogen nutrient fixed from atmospheric N2 to the host plant; in turn, the plant provides photosynthetic metabolites to bacteroids as a carbon source. In this process, various transporters are involved at different membrane systems; however, little is known at the molecular level about the flow of carbon from the host cells to the symbiotic bacteria. We have been studying transporters functioning in nodules of Lotus japonicus, and found that out of 13 SWEET genes in the L. japonicus genome LjSWEET3, a member of the SWEET transporter family, is highly expressed in nodules. The SWEET family was first identified in Arabidopsis, where members of the family are involved in phloem loading, nectar secretion, pollen nutrition and seed filling. The expression of LjSWEET3 strongly increased during nodule development and reached the highest level in mature nodules. Histochemical analysis using L. japonicus plants transformed with LjSWEET3 promoter:GUS (β-glucuronidase) showed strong expression in the vascular systems of nodules. Analysis of an LjSWEET3-green fluorescent protein (GFP) fusion expressed in Nicotiana banthamiana and Coptis japonica indicates that LjSWEET3 localizes to the plasma membrane. Together these data are consistent with a role for LjSWEET3 in sugar translocation towards nodules and also suggest the possible existence of multiple routes of carbon supply into nodules.
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Affiliation(s)
- Akifumi Sugiyama
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Yuka Saida
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Mayuko Yoshimizu
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Kojiro Takanashi
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
- Institute of Mountain Science, Shinshu University, Matsumoto, Japan
| | - Davide Sosso
- Department of Plant Biology, Carnegie Institution of Science, Stanford, CA , USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution of Science, Stanford, CA , USA
| | - Kazufumi Yazaki
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
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