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Agnes RS, Traughber BJ, Muzic RF. Development of a selective novel fluorescent substrate for sodium-dependent transporters. Life Sci 2024; 351:122847. [PMID: 38880166 DOI: 10.1016/j.lfs.2024.122847] [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: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
AIM To synthesize, characterize, and validate 6FGA, a fluorescent glucose modified with a Cyanine5.5 at carbon-6 position, for probing the function of sodium-dependent glucose transporters, SGLT1 and SGLT2. MAIN METHODS The synthesis of fluorescent glucose analogue was achieved through "click chemistry" of Cyanine5.5-alkyne and 6-azido-6-deoxy-d-glucose. Cell system studies were conducted to characterize the in vivo transport properties. KEY FINDINGS Optical analyses revealed that 6FGA displayed similar spectral profiles to Cyanine5.5 in DMSO, allowing for concentration determination, thus supporting its utility in quantitative kinetic studies within biological assays. Uptake studies in cell system SGLT models, LLC-PK1 and HEK293 cells, exhibited concentration and time-dependent behavior, indicating saturation at specific concentrations and durations which are hallmarks of transported-mediated uptake. The results of cytotoxicity assays suggested cell viability at micromolar concentrations, enabling usage in assays for at least 1 h without significant toxicity. The dependence of 6FGA uptake on sodium, the co-transported cation, was demonstrated in LLC-PK1 and HEK293 cells. Fluorescence microscopy confirmed intracellular localization of 6FGA, particularly near the nucleus. Competition studies revealed that glucose tends to weakly reduce 6FGA uptake, although the effect did not achieve statistical significance. Assessments using standard SGLT and GLUT inhibitors highlighted 6FGA's sensitivity for probing SGLT-mediated transport. SIGNIFICANCE 6FGA is a new fluorescent glucose analog offering advantages over existing probes due to its improved photophysical properties, greater sensitivity, enabling subcellular resolution and efficient tissue penetration in near-infrared imaging. 6FGA presents practicality and cost-effectiveness, making it a promising tool for nonradioactive, microplate-based assays at investigating SGLT-mediated glucose transport mechanisms.
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Affiliation(s)
- Richard S Agnes
- Department of Radiology, University Hospitals of Cleveland and Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Bryan J Traughber
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Raymond F Muzic
- Department of Radiology, University Hospitals of Cleveland and Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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2
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Zhang B, Lingga C, De Groot H, Hackmann TJ. The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella. Sci Rep 2023; 13:16429. [PMID: 37777597 PMCID: PMC10542786 DOI: 10.1038/s41598-023-43282-9] [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: 06/28/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023] Open
Abstract
Propionate is a microbial metabolite formed in the gastrointestinal tract, and it affects host physiology as a source of energy and signaling molecule. Despite the importance of propionate, the biochemical pathways responsible for its formation are not clear in all microbes. For the succinate pathway used during fermentation, a key enzyme appears to be missing-one that oxidizes ferredoxin and reduces NAD. Here we show that Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)] is this key enzyme in two abundant bacteria of the rumen (Prevotella brevis and Prevotella ruminicola). We found these bacteria form propionate, succinate, and acetate with the classic succinate pathway. Without ferredoxin:NAD+ oxidoreductase, redox cofactors would be unbalanced; it would produce almost equal excess amounts of reduced ferredoxin and oxidized NAD. By combining growth experiments, genomics, proteomics, and enzyme assays, we point to the possibility that these bacteria solve this problem by oxidizing ferredoxin and reducing NAD with Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)]. Genomic and phenotypic data suggest many bacteria may use Rnf similarly. This work shows the ferredoxin:NAD+ oxidoreductase activity of Rnf is important to propionate formation in Prevotella species and other bacteria from the environment, and it provides fundamental knowledge for manipulating fermentative propionate production.
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Affiliation(s)
- Bo Zhang
- Department of Animal Science, University of California, Davis, CA, USA
| | | | - Hannah De Groot
- Department of Animal Science, University of California, Davis, CA, USA
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3
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Qi G, Zhang M, Tang J, Jin Y. Molecular/Nanomechanical Insights into Electrostimulation-Inhibited Energy Metabolism Mechanisms and Cytoskeleton Damage of Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207165. [PMID: 37029462 DOI: 10.1002/advs.202207165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/20/2023] [Indexed: 06/04/2023]
Abstract
Inhibiting energy metabolism of cancer cells is an effective way to treat cancer but remains a great challenge. Herein, electrostimulation (ES) is applied to effectively suppress energy metabolism of cancer cells to induce rapid cell death, and deeply reveal the underlying mechanisms at the molecular and nanomechanical levels by combined use of fluorescence imaging and atomic force microscopy. Cancer cells are found significantly less tolerant to ES than normal cells; and ES causes "domino effect" to induce mitochondrial dysfunction to impede electron transport chain (ETC) and tricarboxylic acid (TCA) cycle pathways, leading to fatal energy-supply crisis and death of cancer cells. From the perspective of cell mechanics, the Young's modulus decreases and cytoskeleton destruction of MCF-7 cell membranes caused by F-actin depolymerization occurs, along with down-regulation and sporadic distribution of glucose transporter 1 (GLUT1) after ES. Such a double whammy renders ES highly effective and promising for potential clinical cancer treatments.
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Affiliation(s)
- Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
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4
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Morales A, Andrews MG. Approaches to investigating metabolism in human neurodevelopment using organoids: insights from intestinal and cancer studies. Development 2022; 149:dev200506. [PMID: 36255366 PMCID: PMC9720749 DOI: 10.1242/dev.200506] [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] [Indexed: 06/16/2023]
Abstract
Interrogating the impact of metabolism during development is important for understanding cellular and tissue formation, organ and systemic homeostasis, and dysregulation in disease states. To evaluate the vital functions metabolism coordinates during human brain development and disease, pluripotent stem cell-derived models, such as organoids, provide tractable access to neurodevelopmental processes. Despite many strengths of neural organoid models, the extent of their replication of endogenous metabolic programs is currently unclear and requires direct investigation. Studies in intestinal and cancer organoids that functionally evaluate dynamic bioenergetic changes provide a framework that can be adapted for the study of neural metabolism. Validation of in vitro models remains a significant challenge; investigation using in vivo models and primary tissue samples is required to improve our in vitro model systems and, concomitantly, improve our understanding of human development.
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Affiliation(s)
- Alexandria Morales
- Schoolof Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
- Biomedical Engineering Graduate Program, Arizona State University, Tempe, AZ 85281, USA
| | - Madeline G. Andrews
- Schoolof Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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D’Souza LJ, Wright SH, Bhattacharya D. Genetic evidence that uptake of the fluorescent analog 2NBDG occurs independently of known glucose transporters. PLoS One 2022; 17:e0261801. [PMID: 36001583 PMCID: PMC9401136 DOI: 10.1371/journal.pone.0261801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/11/2022] [Indexed: 12/26/2022] Open
Abstract
The fluorescent derivative of glucose, 2-Deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)-amino]-D-glucose (2NBDG), is a widely used surrogate reagent to visualize glucose uptake in live cells at single cell resolution. Using CRISPR-Cas9 gene editing in 5TGM1 myeloma cells, we demonstrate that ablation of the glucose transporter gene Slc2a1 abrogates radioactive glucose uptake but has no effect on the magnitude or kinetics of 2NBDG import. Extracellular 2NBDG, but not NBD-fructose was transported by primary plasma cells into the cytoplasm suggesting a specific mechanism that is unlinked from glucose import and that of chemically similar compounds. Neither excess glucose nor pharmacological inhibition of GLUT1 impacted 2NBDG uptake in myeloma cells or primary splenocytes. Genetic ablation of other expressed hexose transporters individually or in combination with one another also had no impact on 2NBDG uptake. Ablation of the genes in the Slc29 and Slc35 families of nucleoside and nucleoside sugar transporters also failed to impact 2NBDG import. Thus, cellular uptake of 2NBDG is not necessarily a faithful indicator of glucose transport and is promoted by an unknown mechanism.
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Affiliation(s)
- Lucas J. D’Souza
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Stephen H. Wright
- Department of Physiology, University of Arizona, Tucson, Arizona, United States of America
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
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6
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Pang X, Zhang H, Seck HL, Zhou W. Inactivation effect of low-energy X-ray irradiation against planktonic and biofilm Pseudomonas fluorescens and its antibacterial mechanism. Int J Food Microbiol 2022; 374:109716. [DOI: 10.1016/j.ijfoodmicro.2022.109716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 11/30/2022]
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Rudayni HA, Stephenson G, Posterino GS. Measurements of basal d-glucose transport through GLUT1 across the intact plasma membrane of isolated segments from single fast- and slow-twitch skeletal muscle fibres of rat. Acta Physiol (Oxf) 2022; 234:e13789. [PMID: 35038771 PMCID: PMC9541404 DOI: 10.1111/apha.13789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
Abstract
Aim To develop a method for direct measurement of the fluorescent d‐glucose analogue 2‐NBDG transport across the plasma membrane of single skeletal muscle fibres and derive the theoretical framework for determining the kinetic parameters for d‐glucose transport under basal conditions. Methods A novel method is described for measuring free 2‐NBDG transport across plasma membrane of single rat muscle fibres at rest. The 2‐NBDG uptake was >90% suppressed by 100 µM cytochalasin B in both fast‐twitch and slow‐twitch fibres, indicating that the 2‐NBDG transport is GLUT‐mediated. Fibres were identified as fast‐twitch or slow‐twitch based on the differential sensitivity of their contractile apparatus to Sr2+. Results The time course of 2‐NBDG uptake in the presence of 50 µM 2‐NBDG follows a one‐phase exponential plateau curve and is faster in fast‐twitch (rate constant 0.053 ± 0.0024 s‐1) than in slow‐twitch fibres (rate constant 0.031 ± 0.0021 s‐1). The rate constants were markedly reduced in the presence of 20 mM d‐glucose to 0.0082 ± 0.0004 s‐1 and 0.0056 ± 0.0002 s‐1 in fast‐twitch and slow‐twitch fibres respectively. 2‐NBDG transport was asymmetric, consistent with GLUT1 being the major functional GLUT isoform transporting 2‐NBDG in muscle fibres at rest. The parameters describing the transport kinetics for both 2‐NBDG and d‐glucose (dissociation constants, Michaelis–Menten constants, maximal rates of uptake and outflow) were calculated from the measurements made with 2‐NBDG. Conclusion Free 2‐NBDG and d‐glucose transport across the plasma membrane of single rat muscle fibres at rest is fast, conclusively showing that the rate‐limiting step in d‐glucose uptake in skeletal muscle is not necessarily the GLUT‐mediated transport of d‐glucose.
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Affiliation(s)
- Hassan A. Rudayni
- Department of Biology College of Science Imam Mohammad Ibn Saud Islamic University Riyadh Saudi Arabia
| | - George Stephenson
- Department of Physiology, Anatomy and Microbiology La Trobe University Melbourne Victoria Australia
| | - Giuseppe S. Posterino
- Department of Physiology, Anatomy and Microbiology La Trobe University Melbourne Victoria Australia
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8
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Ha B, Kim TJ, Moon E, Giaccia AJ, Pratx G. Flow radiocytometry using droplet optofluidics. Biosens Bioelectron 2021; 194:113565. [PMID: 34492500 PMCID: PMC8530933 DOI: 10.1016/j.bios.2021.113565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 11/29/2022]
Abstract
Flow-based cytometry methods are widely used to analyze heterogeneous cell populations. However, their use for small molecule studies remains limited due to bulky fluorescent labels that often interfere with biochemical activity in cells. In contrast, radiotracers require minimal modification of their target molecules and can track biochemical processes with negligible interference and high specificity. Here, we introduce flow radiocytometry (FRCM) that broadens the scope of current cytometry methods to include beta-emitting radiotracers as probes for single cell studies. FRCM uses droplet microfluidics and radiofluorogenesis to translate the radioactivity of single cells into a fluorescent signal that is then read out using a high-throughput optofluidic device. As a proof of concept, we quantitated [18F]fluorodeoxyglucose radiotracer uptake in single human breast cancer cells and successfully assessed the metabolic flux of glucose and its heterogeneity at the cellular level. We believe FRCM has potential applications ranging from analytical assays for cancer and other diseases to development of small-molecule drugs.
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Affiliation(s)
- Byunghang Ha
- Department of Radiation Oncology, Stanford University, Stanford, CA, 94305-5847, USA; Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305-3011, USA.
| | - Tae Jin Kim
- Department of Radiation Oncology, Stanford University, Stanford, CA, 94305-5847, USA
| | - Ejung Moon
- Department of Radiation Oncology, Stanford University, Stanford, CA, 94305-5847, USA
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford University, Stanford, CA, 94305-5847, USA
| | - Guillem Pratx
- Department of Radiation Oncology, Stanford University, Stanford, CA, 94305-5847, USA.
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9
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Khan S, Shin JH, Ferri V, Cheng N, Noel JE, Kuo C, Sunwoo JB, Pratx G. High-resolution positron emission microscopy of patient-derived tumor organoids. Nat Commun 2021; 12:5883. [PMID: 34620852 PMCID: PMC8497512 DOI: 10.1038/s41467-021-26081-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/03/2021] [Indexed: 01/15/2023] Open
Abstract
Tumor organoids offer new opportunities for translational cancer research, but unlike animal models, their broader use is hindered by the lack of clinically relevant imaging endpoints. Here, we present a positron-emission microscopy method for imaging clinical radiotracers in patient-derived tumor organoids with spatial resolution 100-fold better than clinical positron emission tomography (PET). Using this method, we quantify 18F-fluorodeoxyglucose influx to show that patient-derived tumor organoids recapitulate the glycolytic activity of the tumor of origin, and thus, could be used to predict therapeutic response in vitro. Similarly, we measure sodium-iodine symporter activity using 99mTc- pertechnetate and find that the iodine uptake pathway is functionally conserved in organoids derived from thyroid carcinomas. In conclusion, organoids can be imaged using clinical radiotracers, which opens new possibilities for identifying promising drug candidates and radiotracers, personalizing treatment regimens, and incorporating clinical imaging biomarkers in organoid-based co-clinical trials.
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Affiliation(s)
- Syamantak Khan
- Department of Radiation Oncology, Division of Medical Physics, Stanford University School of Medicine, Stanford, USA
| | - June Ho Shin
- Department of Otolaryngology, Division of Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Valentina Ferri
- Department of Radiology, Division of Nuclear Medicine and Molecular Imaging, Stanford University School of Medicine, Stanford, CA, USA
| | - Ning Cheng
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia E Noel
- Department of Otolaryngology, Division of Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Calvin Kuo
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - John B Sunwoo
- Department of Otolaryngology, Division of Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Guillem Pratx
- Department of Radiation Oncology, Division of Medical Physics, Stanford University School of Medicine, Stanford, USA.
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10
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Guo Z, DeLoid GM, Cao X, Bitounis D, Sampathkumar K, Woei Ng K, Joachim Loo SC, Philip D. Effects of ingested nanocellulose and nanochitosan materials on carbohydrate digestion and absorption in an in vitro small intestinal epithelium model. ENVIRONMENTAL SCIENCE. NANO 2021; 8:2554-2568. [PMID: 34840801 PMCID: PMC8622715 DOI: 10.1039/d1en00233c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nanoscale materials derived from natural biopolymers like cellulose and chitosan have many potentially useful agri-food and oral drug delivery applications. Because of their large and potentially bioactive surface areas and other unique physico-chemical properties, it is essential when evaluating their toxicological impact to assess potential effects on the digestion and absorption of co-ingested nutrients. Here, the effects of cellulose nanofibers (CNF), cellulose nanocrystals (CNC), and chitosan nanoparticles (Chnp) on the digestion and absorption of carbohydrates were studied. Starch digestion was assessed by measuring maltose released during simulated digestion of starch solutions. Glucose absorption was assessed by measuring translocation from the resulting digestas across an in vitro transwell tri-culture model of the small intestinal epithelium and calculating the area under the curve increase in absorbed glucose, analogous to the glycemic index. At 1% w/w, CNF and Chnp had small but significant effects (11% decrease and 14% increase, respectively) and CNC had no effect on starch hydrolysis during simulated digestion of a 1% w/w rice starch solution. In addition, at 2% w/w CNC had no effect on amylolysis in 1% solutions of either rice, corn, or wheat starch. Similarly, absorption of glucose from digestas of starch solutions (i.e., from maltose), was unaffected by 1% w/w CNF or CNC, but was slightly increased (10%, p<0.05) by 1% Chnp, possibly due to the slightly higher maltose concentration in the Chnp-containing digestas. In contrast, all of the test materials caused sharp increases (~1.2, 1.5, and 1.6 fold for CNC, CNF, and Chnp, respectively) in absorption of glucose from starch-free digestas spiked with free glucose at a concentration corresponding to complete hydrolysis of 1% w/w starch. The potential for ingested cellulose and chitosan nanomaterials to increase glucose absorption could have important health implications. Further studies are needed to elucidate the mechanisms underlying the observed increases and to evaluate the potential glycemic effects in an intact in vivo system.
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Affiliation(s)
- Zhongyuan Guo
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Glen M DeLoid
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Xiaoqiong Cao
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kaarunya Sampathkumar
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798, Singapore, Singapore
| | - Kee Woei Ng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798, Singapore, Singapore
- Skin Research Institute of Singapore, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment & Water Research Institute, 1 Cleantech Loop, CleanTech One, Singapore 637141
| | - Say Chye Joachim Loo
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798, Singapore, Singapore
| | - Demokritou Philip
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798, Singapore, Singapore
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11
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Wolf JR. Review: Self-radiolysis of compounds containing tritium and carbon-14. J Labelled Comp Radiopharm 2021; 64:286-335. [PMID: 33439502 DOI: 10.1002/jlcr.3903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 01/02/2023]
Abstract
Energy released from beta emission causes molecules that incorporate tritium (3 H) and carbon-14 (14 C) atoms to be less stable than their stable labeled counterparts, thus making radiolabeled compounds prone to self-radiolysis. This literature review examines the stability of organic compounds incorporating 3 H and 14 C atoms and discusses stability of the compound with respect to functional groups within the radiolabeled molecules. The goal of this paper is to serve as a reference for the stability of radiolabeled compounds.
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Affiliation(s)
- Jeremy R Wolf
- Synthesis Department, Eurofins BioPharma Testing, Columbia, Missouri, USA
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12
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Zhang B, Lingga C, Bowman C, Hackmann TJ. A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. Appl Environ Microbiol 2021; 87:e0295920. [PMID: 33931420 PMCID: PMC8231725 DOI: 10.1128/aem.02959-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are important for bacteria themselves because they often generate ATP. Here, we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found that the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl coenzyme A (succinyl-CoA):acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found that 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing that a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important for acetate formation in many branches of the tree of life. IMPORTANCE Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways in a range of organisms, from bacteria to animals, have been described. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here, we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating that it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance for foods, agriculture, and industry.
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Affiliation(s)
- Bo Zhang
- Department of Animal Science, University of California, Davis, California, USA
| | - Christopher Lingga
- Department of Animal Science, University of California, Davis, California, USA
| | - Courtney Bowman
- Department of Animal Sciences, University of Florida, Gainesville, Florida, USA
| | - Timothy J. Hackmann
- Department of Animal Science, University of California, Davis, California, USA
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 PMCID: PMC8369882 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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Hackmann TJ, Zhang B. Using neural networks to mine text and predict metabolic traits for thousands of microbes. PLoS Comput Biol 2021; 17:e1008757. [PMID: 33651810 PMCID: PMC7954334 DOI: 10.1371/journal.pcbi.1008757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/12/2021] [Accepted: 02/02/2021] [Indexed: 11/18/2022] Open
Abstract
Microbes can metabolize more chemical compounds than any other group of organisms. As a result, their metabolism is of interest to investigators across biology. Despite the interest, information on metabolism of specific microbes is hard to access. Information is buried in text of books and journals, and investigators have no easy way to extract it out. Here we investigate if neural networks can extract out this information and predict metabolic traits. For proof of concept, we predicted two traits: whether microbes carry one type of metabolism (fermentation) or produce one metabolite (acetate). We collected written descriptions of 7,021 species of bacteria and archaea from Bergey's Manual. We read the descriptions and manually identified (labeled) which species were fermentative or produced acetate. We then trained neural networks to predict these labels. In total, we identified 2,364 species as fermentative, and 1,009 species as also producing acetate. Neural networks could predict which species were fermentative with 97.3% accuracy. Accuracy was even higher (98.6%) when predicting species also producing acetate. Phylogenetic trees of species and their traits confirmed that predictions were accurate. Our approach with neural networks can extract information efficiently and accurately. It paves the way for putting more metabolic traits into databases, providing easy access of information to investigators.
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Affiliation(s)
- Timothy J. Hackmann
- Department of Animal Science, University of California, Davis, United States of America
| | - Bo Zhang
- Department of Animal Science, University of California, Davis, United States of America
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15
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Ripperger TJ, Bhattacharya D. Transcriptional and Metabolic Control of Memory B Cells and Plasma Cells. Annu Rev Immunol 2021; 39:345-368. [PMID: 33556247 DOI: 10.1146/annurev-immunol-093019-125603] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For many infections and almost all vaccines, neutralizing-antibody-mediated immunity is the primary basis and best functional correlate of immunological protection. Durable long-term humoral immunity is mediated by antibodies secreted by plasma cells that preexist subsequent exposures and by memory B cells that rapidly respond to infections once they have occurred. In the midst of the current pandemic of coronavirus disease 2019, it is important to define our current understanding of the unique roles of memory B cells and plasma cells in immunity and the factors that control the formation and persistence of these cell types. This fundamental knowledge is the basis to interpret findings from natural infections and vaccines. Here, we review transcriptional and metabolic programs that promote and support B cell fates and functions, suggesting points at which these pathways do and do not intersect.
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Affiliation(s)
- Tyler J Ripperger
- Department of Immunobiology, University of Arizona College of Medicine-Tucson, Tucson, Arizona 85724, USA; ,
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine-Tucson, Tucson, Arizona 85724, USA; ,
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16
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Jeckelmann JM, Erni B. The mannose phosphotransferase system (Man-PTS) - Mannose transporter and receptor for bacteriocins and bacteriophages. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183412. [PMID: 32710850 DOI: 10.1016/j.bbamem.2020.183412] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
Mannose transporters constitute a superfamily (Man-PTS) of the Phosphoenolpyruvate Carbohydrate Phosphotransferase System (PTS). The membrane complexes are homotrimers of protomers consisting of two subunits, IIC and IID. The two subunits without recognizable sequence similarity assume the same fold, and in the protomer are structurally related by a two fold pseudosymmetry axis parallel to membrane-plane (Liu et al. (2019) Cell Research 29 680). Two reentrant loops and two transmembrane helices of each subunit together form the N-terminal transport domain. Two three-helix bundles, one of each subunit, form the scaffold domain. The protomer is stabilized by a helix swap between these bundles. The two C-terminal helices of IIC mediate the interprotomer contacts. PTS occur in bacteria and archaea but not in eukaryotes. Man-PTS are abundant in Gram-positive bacteria living on carbohydrate rich mucosal surfaces. A subgroup of IICIID complexes serve as receptors for class IIa bacteriocins and as channel for the penetration of bacteriophage lambda DNA across the inner membrane. Some Man-PTS are associated with host-pathogen and -symbiont processes.
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Affiliation(s)
- Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
| | - Bernhard Erni
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
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17
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O'Brien EC, White CA, Wyse J, Leacy E, Porter RK, Little MA, Hickey FB. Pro-inflammatory Stimulation of Monocytes by ANCA Is Linked to Changes in Cellular Metabolism. Front Med (Lausanne) 2020; 7:553. [PMID: 33015103 PMCID: PMC7509421 DOI: 10.3389/fmed.2020.00553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/03/2020] [Indexed: 01/09/2023] Open
Abstract
Clinical and experimental data suggest that pathogenesis in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis is driven by ANCA-mediated activation of neutrophils and monocytes. While the role of neutrophils has been extensively investigated, the function of monocytes remains relatively understudied. We have previously demonstrated that stimulation of monocytes with anti-myeloperoxidase (MPO), but not anti-proteinase-3 (PR3), antibodies results in production of the pro-inflammatory cytokine IL-1β. Changes in cellular metabolism, particularly a switch to glycolysis, have recently been linked to activation of immune cells and production of IL-1β. Therefore, we investigated the metabolic profile of monocytes following ANCA stimulation. We found a significant increase in glucose uptake in anti-MPO stimulated monocytes. Interestingly, both anti-MPO and anti-PR3 stimulation resulted in an immediate increase in glycolysis, measured by Seahorse extracellular flux analysis. However, this increase in glycolysis was sustained (for up to 4 h) in anti-MPO- but not anti-PR3-treated cells. In addition, only anti-MPO-treated cells exhibited increased oxidative phosphorylation, a metabolic response that correlated with IL-1β production. These data indicate that monocyte metabolism is altered by ANCA, with divergent responses to anti-MPO and anti-PR3 antibodies. These metabolic changes may underlie pathologic immune activation in ANCA associated vasculitis, as well as potentially contributing to the differing clinical phenotype between PR3- and MPO-ANCA positive patients. These metabolic pathways may therefore be potential targets for therapeutic intervention.
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Affiliation(s)
- Eóin C O'Brien
- Department of Clinical Medicine, Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland
| | - Carla A White
- Department of Clinical Medicine, Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland
| | - Jason Wyse
- Discipline of Statistics and Information Systems, School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Emma Leacy
- Department of Clinical Medicine, Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland
| | - Richard K Porter
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, Ireland
| | - Mark A Little
- Department of Clinical Medicine, Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland
| | - Fionnuala B Hickey
- Department of Clinical Medicine, Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland
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Abstract
Assays to monitor the metabolic state or nutrient uptake capacity of immune cells at a single cell level are increasingly in demand. One assay, used by many immunologists, employs 2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose (2-NBDG), a fluorescent analogue of 2-deoxyglucose (2DG), as a substrate for glucose transporters. This molecule has been validated as a substrate for the glucose transporter Glut2 (Slc2a2) in mammalian cells but 2-NDBG selectivity for the glucose transporters expressed by T cells, Glut1 (Slc2a1) and Glut3 (Slc2a3), has never been explored. Nor has the possibility that 2-NBDG might bind to T cells that do not express glucose transporters been assessed. In this technical commentary we interrogate the specificity of 2-NBBG labelling as a readout for glucose transport in T lymphocytes. We compare flow cytometric 2-NBDG staining against well validated radiolabelled glucose transport assays in murine T cells. Our data show there can be a large discordance between glucose transport capacity and 2-NBDG labelling in T cells. We also find that 2-NBDG uptake into murine T cells is not inhibited by competitive substrates or facilitative glucose transporter inhibitors, nor can 2-NBDG competitively block glucose uptake in T cells. Collectively, these data argue that 2-NBDG uptake alone is not a reliable tool for the assessment of cellular glucose transport capacity.
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Lipopolysaccharide Stimulates the Growth of Bacteria That Contribute to Ruminal Acidosis. Appl Environ Microbiol 2020; 86:AEM.02193-19. [PMID: 31811042 DOI: 10.1128/aem.02193-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022] Open
Abstract
Lipopolysaccharide (LPS) has been reported to contribute to a ruminal acidosis of cattle by affecting ruminal bacteria. The goal of this study was to determine how LPS affects the growth of pure cultures of ruminal bacteria, including those that contribute to ruminal acidosis. We found that dosing LPS (200,000 EU) increased the maximum specific growth rates of four ruminal bacterial species (Streptococcus bovis JB1, Succinivibrio dextrinosolvens 24, Lactobacillus ruminis RF1, and Selenomonas ruminantium HD4). Interestingly, all the species ferment sugars and produce lactate, contributing to acidosis. Species that consume lactate or ferment fiber were not affected by LPS. We found that S. bovis JB1 failed to grow in LPS as the carbon source in the media; growth of S. bovis JB1 was increased by LPS when glucose was present. Growth of Megasphaera elsdenii T81, which consumes lactate, was not different between the detoxified (lipid A delipidated) and regular LPS. However, the maximum specific growth rate of S. bovis JB1 was greater in regular LPS than detoxified LPS. Mixed bacteria from a dual-flow continuous culture system were collected to determine changes of metabolic capabilities of bacteria by LPS, and genes associated with LPS biosynthesis were increased by LPS. In summary, LPS was not toxic to bacteria, and lipid A of LPS stimulated the growth of lactate-producing bacteria. Our results indicate that LPS not only is increased during acidosis but also may contribute to ruminal acidosis development by increasing the growth of lactic acid-producing bacteria.IMPORTANCE Gram-negative bacteria contain lipopolysaccharide (LPS) coating their thin peptidoglycan cell wall. The presence of LPS has been suggested to be associated with a metabolic disorder of cattle-ruminal acidosis-through affecting ruminal bacteria. Ruminal acidosis could reduce feed intake and milk production and increase the incidence of diarrhea, milk fat depression, liver abscesses, and laminitis. However, how LPS affects bacteria associated with ruminal acidosis has not been studied. In this study, we investigated how LPS affects the growth of ruminal bacteria by pure cultures, including those that contribute to acidosis, and the functional genes of ruminal bacteria. Thus, this work serves to further our understanding of the roles of LPS in the pathogenesis of ruminal acidosis, as well as providing information that may be useful for the prevention of ruminal acidosis and reducetion of economic losses for farmers.
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20
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D'Souza L, Bhattacharya D. Plasma cells: You are what you eat. Immunol Rev 2019; 288:161-177. [PMID: 30874356 DOI: 10.1111/imr.12732] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022]
Abstract
Plasma cells are terminally differentiated B lymphocytes that constitutively secrete antibodies. These antibodies can provide protection against pathogens, and their quantity and quality are the best clinical correlates of vaccine efficacy. As such, plasma cell lifespan is the primary determinant of the duration of humoral immunity. Yet dysregulation of plasma cell function can cause autoimmunity or multiple myeloma. The longevity of plasma cells is primarily dictated by nutrient uptake and non-transcriptionally regulated metabolic pathways. We have previously shown a positive effect of glucose uptake and catabolism on plasma cell longevity and function. In this review, we discuss these findings with an emphasis on nutrient uptake and its effects on respiratory capacity, lifespan, endoplasmic reticulum stress, and antibody secretion in plasma cells. We further discuss how some of these pathways may be dysregulated in multiple myeloma, potentially providing new therapeutic targets. Finally, we speculate on the connection between plasma cell intrinsic metabolism and systemic changes in nutrient availability and metabolic diseases.
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Affiliation(s)
- Lucas D'Souza
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Arizona
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Arizona
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Abstract
Cellular imaging is an active area of research that enables researchers to monitor cellular dynamics, as well as responses to various external stimuli (physiological stress, exogenous compounds, etc.). Stimulated Raman scattering (SRS) microscopy is one popular experimental tool used to image cells, largely because of its chemical specificity, high spatial resolution, and high image acquisition speed. In this Perspective, the theoretical background and experimental implementation of SRS microscopy are discussed and recent developments in the field of cellular imaging with SRS are highlighted and summarized.
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Affiliation(s)
- Andrew H Hill
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Dan Fu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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22
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Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose. Appl Environ Microbiol 2019; 85:AEM.03018-18. [PMID: 30709823 DOI: 10.1128/aem.03018-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/30/2019] [Indexed: 12/13/2022] Open
Abstract
Few characteristics are more important to a bacterium than the substrates it consumes. It is hard to identify what substrates are consumed by bacteria in natural communities, however, because most bacteria have not been cultured. In this study, we developed a method that uses fluorescent substrate analogs, cell sorting, and DNA sequencing to identify substrates taken up by bacteria. We deployed this method using 2[N-(7-nitrobenz-2-oxa-1,2-diaxol-4-yl)amino]-2-deoxyglucose (2-NBDG), a fluorescent glucose analog, and bacteria of the bovine rumen. This method revealed over 40 different bacteria (amplicon sequence variants [ASVs]) from the rumen that take up glucose. Nearly half of these ASVs represent previously uncultured bacteria. We attempted to grow these ASVs on agar media, and we confirmed that nearly two-thirds resisted culture. In coculture experiments, the fluorescent label of 2-NBDG was not transferred to nontarget bacteria by cross-feeding. Because it is not affected by cross-feeding, our method has an advantage over stable isotope probing. Though we focus on glucose, many substrates can be labeled with the fluorophore NBD. Our method represents a new paradigm for identifying substrates used by uncultured bacteria. It will help delineate the niche of bacteria in their environment.IMPORTANCE We introduce a method for identifying what substrates are consumed by bacteria in natural communities. Our method offers significant improvement over existing methods for studying this characteristic. Our method uses a fluorescently labeled substrate which clearly labels target bacteria (glucose consumers in our case). Previous methods use isotope-labeled substrates, which are notorious for off-target labeling (due to cross-feeding of labeled metabolites). Our method can be deployed with a variety of substrates and microbial communities. It represents a major advance in connecting bacteria to the substrates they take up.
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Affiliation(s)
- Clair M. Gardiner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin Dublin 2 Ireland
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24
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The emergence of metabolic heterogeneity and diverse growth responses in isogenic bacterial cells. ISME JOURNAL 2018; 12:1199-1209. [PMID: 29335635 DOI: 10.1038/s41396-017-0036-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 11/08/2022]
Abstract
Microorganisms adapt to frequent environmental changes through population diversification. Previous studies demonstrated phenotypic diversity in a clonal population and its important effects on microbial ecology. However, the dynamic changes of phenotypic composition have rarely been characterized. Also, cellular variations and environmental factors responsible for phenotypic diversity remain poorly understood. Here, we studied phenotypic diversity driven by metabolic heterogeneity. We characterized metabolic activities and growth kinetics of starved Escherichia coli cells subject to nutrient upshift at single-cell resolution. We observed three subpopulations with distinct metabolic activities and growth phenotypes. One subpopulation was metabolically active and immediately grew upon nutrient upshift. One subpopulation was metabolically inactive and non-viable. The other subpopulation was metabolically partially active, and did not grow upon nutrient upshift. The ratio of these subpopulations changed dynamically during starvation. A long-term observation of cells with partial metabolic activities indicated that their metabolism was later spontaneously restored, leading to growth recovery. Further investigations showed that oxidative stress can induce the emergence of a subpopulation with partial metabolic activities. Our findings reveal the emergence of metabolic heterogeneity and associated dynamic changes in phenotypic composition. In addition, the results shed new light on microbial dormancy, which has important implications in microbial ecology and biomedicine.
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25
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Hackmann TJ, Ngugi DK, Firkins JL, Tao J. Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids. Environ Microbiol 2017; 19:4670-4683. [PMID: 28892251 DOI: 10.1111/1462-2920.13929] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/17/2017] [Accepted: 09/06/2017] [Indexed: 11/27/2022]
Abstract
Bacteria have been thought to follow only a few well-recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well-recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden-Meyerhof-Parnas pathway. This study shows that reconstruction of metabolic pathways - a common goal of omics studies - could be incorrect if well-recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Science, University of Florida, P.O. Box 110910, Gainesville, FL 32611, USA
| | - David Kamanda Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jeffrey L Firkins
- Department of Animal Science, The Ohio State University, 2029 Fyffe Rd, Columbus, OH 43210, USA
| | - Junyi Tao
- Department of Animal Science, University of Florida, P.O. Box 110910, Gainesville, FL 32611, USA
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26
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Adamczyk M, Szatkowska R. Low RNA Polymerase III activity results in up regulation of HXT2 glucose transporter independently of glucose signaling and despite changing environment. PLoS One 2017; 12:e0185516. [PMID: 28961268 PMCID: PMC5621690 DOI: 10.1371/journal.pone.0185516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/14/2017] [Indexed: 01/13/2023] Open
Abstract
Background Saccharomyces cerevisiae responds to glucose availability in the environment, inducing the expression of the low-affinity transporters and high-affinity transporters in a concentration dependent manner. This cellular decision making is controlled through finely tuned communication between multiple glucose sensing pathways including the Snf1-Mig1, Snf3/Rgt2-Rgt1 (SRR) and cAMP-PKA pathways. Results We demonstrate the first evidence that RNA Polymerase III (RNAP III) activity affects the expression of the glucose transporter HXT2 (RNA Polymerase II dependent—RNAP II) at the level of transcription. Down-regulation of RNAP III activity in an rpc128-1007 mutant results in a significant increase in HXT2 mRNA, which is considered to respond only to low extracellular glucose concentrations. HXT2 expression is induced in the mutant regardless of the growth conditions either at high glucose concentration or in the presence of a non-fermentable carbon source such as glycerol. Using chromatin immunoprecipitation (ChIP), we found an increased association of Rgt1 and Tup1 transcription factors with the highly activated HXT2 promoter in the rpc128-1007 strain. Furthermore, by measuring cellular abundance of Mth1 corepressor, we found that in rpc128-1007, HXT2 gene expression was independent from Snf3/Rgt2-Rgt1 (SRR) signaling. The Snf1 protein kinase complex, which needs to be active for the release from glucose repression, also did not appear perturbed in the mutated strain. Conclusions/Significance These findings suggest that the general activity of RNAP III can indirectly affect the RNAP II transcriptional machinery on the HXT2 promoter when cellular perception transduced via the major signaling pathways, broadly recognized as on/off switch essential to either positive or negative HXT gene regulation, remain entirely intact. Further, Rgt1/Ssn6-Tup1 complex, which has a dual function in gene transcription as a repressor-activator complex, contributes to HXT2 transcriptional activation.
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Affiliation(s)
- Malgorzata Adamczyk
- Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
- * E-mail:
| | - Roza Szatkowska
- Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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27
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Quantitative chemical imaging with stimulated Raman scattering microscopy. Curr Opin Chem Biol 2017; 39:24-31. [DOI: 10.1016/j.cbpa.2017.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/02/2017] [Accepted: 05/04/2017] [Indexed: 12/14/2022]
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28
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Teixeira CRV, Lana RDP, Tao J, Hackmann TJ. Comparing the responses of rumen ciliate protozoa and bacteria to excess carbohydrate. FEMS Microbiol Ecol 2017; 93:3806671. [PMID: 28486619 DOI: 10.1093/femsec/fix060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/08/2017] [Indexed: 11/12/2022] Open
Abstract
When given excess carbohydrate, certain microbial species respond by storing energy (synthesizing reserve carbohydrate), but other species respond by dissipating the energy as heat (spilling energy). To determine the importance of these responses in the rumen microbial community, this study quantified the responses of mixed ciliate protozoa vs bacteria to glucose. We hypothesized that ciliates would direct more glucose to synthesis of reserve carbohydrate (and less to energy spilling) than would bacteria. Ciliates and bacteria were isolated from rumen fluid using filtration and centrifugation, resuspended in nitrogen-free buffer to limit growth, and dosed with 5 mM glucose. Compared with bacteria, ciliates consumed glucose >3-fold faster and synthesized reserve carbohydrate 4-fold faster. They incorporated 53% of glucose carbon into reserve carbohydrate-nearly double the value (27%) for bacteria. Energy spilling was not detected for ciliates, as all heat production (104%) was accounted by synthesis of reserve carbohydrate and endogenous metabolism. For bacteria, reserve carbohydrate and endogenous metabolism accounted for only 68% of heat production, and spilling was detected within 11 min of dosing glucose. These results suggest that ciliates alter the course of ruminal carbohydrate metabolism by outcompeting bacteria for excess carbohydrate, maximizing reserve carbohydrate synthesis, and minimizing energy spilling.
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Affiliation(s)
- César R V Teixeira
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil 36570-000
| | - Rogério de Paula Lana
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil 36570-000
| | - Junyi Tao
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Timothy J Hackmann
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
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