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Raveendran A, Gupta A, Lewis LE, Prabhu K, Moorkoth S. A comprehensive approach for detection of biotin deficiency from dried blood spot samples using liquid chromatography-mass spectrometry. Future Sci OA 2024; 10:2355038. [PMID: 38963009 PMCID: PMC11229587 DOI: 10.1080/20565623.2024.2355038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 07/05/2024] Open
Abstract
Aim: The aim of the present study is to develop a liquid chromatography-mass spectrometry method to measure two important biomarkers of biotin deficiency from dried blood spot samples for effective management of the disorder. Materials & methods: The method was developed on a liquid chromatography-mass spectrometry system using pentafluorophenyl column employing a mobile phase composition of methanol and water in the isocratic mode. A full validation of the method was performed as per relevant guidelines. Results & conclusion: Correlation between the results of dried blood spot and plasma method was evaluated to determine the interconvertibility of the method. The developed method was successfully applied for establishing the reference ranges for these biomarkers in the population of Udupi, a coastal district of South India.
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Affiliation(s)
- Arya Raveendran
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Ashutosh Gupta
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Leslie E Lewis
- Department of Pediatrics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Krishnananda Prabhu
- Department of Biochemistry, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Sudheer Moorkoth
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
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2
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Kim T, Hwang D, Kyun S, Jang I, Kim SW, Park HY, Hwang H, Lim K, Kim J. Exogenous Lactate Treatment Immediately after Exercise Promotes Glycogen Recovery in Type-II Muscle in Mice. Nutrients 2024; 16:2831. [PMID: 39275149 PMCID: PMC11397291 DOI: 10.3390/nu16172831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/16/2024] Open
Abstract
Recent studies suggest that lactate intake has a positive effect on glycogen recovery after exercise. However, it is important to verify the effect of lactate supplementation alone and the timing of glycogen recovery. Therefore, in this study, we aimed to examine the effect of lactate supplementation immediately after exercise on glycogen recovery in mice liver and skeletal muscle at 1, 3, and 5 h after exercise. Mice were randomly divided into the sedentary, exercise-only, lactate, and saline-treated groups. mRNA expression and activation of glycogen synthesis and lactate transport-related factors in the liver and skeletal muscle were assessed using real-time polymerase chain reaction. Skeletal muscle glycogen concentration showed an increasing trend in the lactate group compared with that in the control group at 3 and 5 h after post-supplementation. Additionally, exogenous lactate supplementation significantly increased the expression of core glycogen synthesis enzymes, lactate transporters, and pyruvate dehydrogenase E1 alpha 1 in the skeletal muscles. Conversely, glycogen synthesis, lactate transport, and glycogen oxidation to acetyl-CoA were not significantly affected in the liver by exogenous lactate supplementation. Overall, these results suggest that post-exercise lactate supplement enables glycogen synthesis and recovery in skeletal muscles.
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Affiliation(s)
- Taeho Kim
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Deunsol Hwang
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Sunghwan Kyun
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Inkwon Jang
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Sung-Woo Kim
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Hun-Young Park
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Hyejung Hwang
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
| | - Kiwon Lim
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
- Department of Physical Education, Konkuk University, Seoul 05029, Republic of Korea
| | - Jisu Kim
- Laboratory of Exercise and Nutrition, Department of Sports Medicine and Science in Graduate School, Konkuk University, Seoul 05029, Republic of Korea
- Physical Activity and Performance Institute (PAPI), Konkuk University, Seoul 05029, Republic of Korea
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3
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Holeček M. Origin and Roles of Alanine and Glutamine in Gluconeogenesis in the Liver, Kidneys, and Small Intestine under Physiological and Pathological Conditions. Int J Mol Sci 2024; 25:7037. [PMID: 39000145 PMCID: PMC11241752 DOI: 10.3390/ijms25137037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Alanine and glutamine are the principal glucogenic amino acids. Most originate from muscles, where branched-chain amino acids (valine, leucine, and isoleucine) are nitrogen donors and, under exceptional circumstances, a source of carbons for glutamate synthesis. Glutamate is a nitrogen source for alanine synthesis from pyruvate and a substrate for glutamine synthesis by glutamine synthetase. The following differences between alanine and glutamine, which can play a role in their use in gluconeogenesis, are shown: (i) glutamine appearance in circulation is higher than that of alanine; (ii) the conversion to oxaloacetate, the starting substance for glucose synthesis, is an ATP-consuming reaction for alanine, which is energetically beneficial for glutamine; (iii) most alanine carbons, but not glutamine carbons, originate from glucose; and (iv) glutamine acts a substrate for gluconeogenesis in the liver, kidneys, and intestine, whereas alanine does so only in the liver. Alanine plays a significant role during early starvation, exposure to high-fat and high-protein diets, and diabetes. Glutamine plays a dominant role in gluconeogenesis in prolonged starvation, acidosis, liver cirrhosis, and severe illnesses like sepsis and acts as a substrate for alanine synthesis in the small intestine. Interactions among muscles and the liver, kidneys, and intestine ensuring optimal alanine and glutamine supply for gluconeogenesis are suggested.
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Affiliation(s)
- Milan Holeček
- Department of Physiology, Faculty of Medicine, Charles University, 500 03 Hradec Kralove, Czech Republic
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Su X, Zhang L, Meng H, Wang H, Zhao J, Sun X, Song X, Zhang X, Mao L. Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO 2 fixation pathways in coastal saline soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120743. [PMID: 38626484 DOI: 10.1016/j.jenvman.2024.120743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.
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Affiliation(s)
- Xunya Su
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Le Zhang
- China Agricultural University, Agronomy College, Beijing, 100193, China.
| | - Hao Meng
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Han Wang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Jiaxue Zhao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xuezhen Sun
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xianliang Song
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xiaopei Zhang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Lili Mao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
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5
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Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT. Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 2024; 9:e0094223. [PMID: 38323821 PMCID: PMC10949508 DOI: 10.1128/msystems.00942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024] Open
Abstract
There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules ("functional modules"), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.
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Affiliation(s)
- Andrew J. Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Keven D. Dooley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Zoe A. Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tracy L. Hodges
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
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6
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Hirano K, Sueda S. A fluorescence-based binding assay for proteins using the cell surface as a sensing platform. ANAL SCI 2024; 40:563-571. [PMID: 38091253 DOI: 10.1007/s44211-023-00476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/17/2023] [Indexed: 02/27/2024]
Abstract
Protein-protein interaction (PPI) analysis is very important for elucidating the functions of proteins because many proteins execute their functions in living cells by interacting with one another. In PPI analysis, methods using the sensor chips are widely employed to obtain quantitative data. However, these methods require that the target proteins be immobilized on the sensor chips, and the immobilization processes can affect the binding of the target proteins to their binding partners. In the present work, we propose a PPI analysis system in which the surface of the living cells is utilized as a sensing platform. In our approach, the target protein is displayed on the cell surface by expressing it as a fusion protein with a membrane protein, and the PPI analysis is then conducted by applying its binding partner labeled with a fluorescent dye to the cell surface. We have constructed a model of this binding analysis system using the interaction between biotin protein ligase (BPL) and biotin carboxyl carrier protein (BCCP), where BCCP was displayed on the cell surface and BPL labeled with fluorescein was applied to the cell surface. Here, a red fluorescent protein, mApple, was attached to the C-terminus of the fusion protein of BCCP with a membrane protein. We evaluated the binding level of the labeled BPL by using the intensity ratios of fluorescence from fluorescein to that from mApple. We found that the binding level of the labeled BPL was stably evaluated at least across 60 min observation period and estimated the binding dissociation constant between BPL and BCCP by equilibrium analysis to be 0.33 ± 0.05 μM.
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Affiliation(s)
- Kazuki Hirano
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, 820-8502, Japan
| | - Shinji Sueda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, 820-8502, Japan.
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Júnior MA, Silva LC, Rocha OB, Oliveira AA, Portis IG, Alonso A, Alonso L, Silva KS, Gomes MN, Andrade CH, Soares CM, Pereira M. Proteomic identification of metabolic changes in Paracoccidioides brasiliensis induced by a nitroheteroarylchalcone. Future Microbiol 2023; 18:1077-1093. [PMID: 37424510 DOI: 10.2217/fmb-2022-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023] Open
Abstract
Aim: To access the metabolic changes caused by a chalcone derivative (LabMol-75) through a proteomic approach. Methods: Proteomic analysis was performed after 9 h of Paracoccidioides brasiliensis yeast (Pb18) cell incubation with the LabMol-75 at MIC. The proteomic findings were validated through in vitro and in silico assays. Results: Exposure to the compound led to the downregulation of proteins associated with glycolysis and gluconeogenesis, β-oxidation, the citrate cycle and the electron transport chain. Conclusion: LabMol-75 caused an energetic imbalance in the fungus metabolism and deep oxidative stress. Additionally, the in silico molecular docking approach pointed to this molecule as a putative competitive inhibitor of DHPS.
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Affiliation(s)
- Marcos Abc Júnior
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lívia C Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Olivia B Rocha
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Amanda A Oliveira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Igor G Portis
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Antonio Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lais Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kleber Sf Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Marcelo N Gomes
- InsiChem, Goiás State University, Anápolis, Goiás, Brazil
- Faculdade Metropolitana de Anápolis, Anápolis, Goiás, Brazil
| | - Carolina H Andrade
- Laboratory for Molecular Modeling & Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Célia Ma Soares
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Maristela Pereira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
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8
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Muroya S, Otomaru K, Oshima K, Oshima I, Ojima K, Gotoh T. DNA Methylation of Genes Participating in Hepatic Metabolisms and Function in Fetal Calf Liver Is Altered by Maternal Undernutrition during Gestation. Int J Mol Sci 2023; 24:10682. [PMID: 37445858 DOI: 10.3390/ijms241310682] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
This study aimed to elucidate the effects of maternal undernutrition (MUN) on epigenetic modification of hepatic genes in Japanese Black fetal calves during gestation. Using a previously established experimental design feeding the dams with 60% (LN) or 120% (HN) of their global nutritional requirements during the 8.5-month gestational period, DNA methylation in the fetal liver was analyzed with reduced representation bisulfite sequencing (RRBS). The promoters and gene bodies in the LN fetuses were hypomethylated compared to HN fetuses. Pathway analysis showed that the genes with DMR in the exon/intron in the LN group were associated with pathways involved in Cushing syndrome, gastric acid secretion, and aldosterone synthesis and secretion. Promoter hypomethylation in the LN group was frequently observed in genes participating in various signaling pathways (thyroid hormone, Ras/Rap1, PIK3-Akt, cAMP), fatty acid metabolism, and cholesterol metabolism. The promoter hypomethylated genes ALPL and GNAS were upregulated in the LN group, whereas the promoter hypermethylated genes GRB10 and POR were downregulated. The intron/exon hypomethylated genes IGF2, IGF2R, ACAD8, TAT, RARB, PINK1, and SOAT2 were downregulated, whereas the hypermethylated genes IGF2BP2, NOS3, and NR2F1 were upregulated. Collectively, MUN alters the promoter and gene body methylation of genes associated with hepatic metabolisms (energy, cholesterol, mitochondria) and function, suggesting an impact of altered gene methylation on the dysregulation of gene expression in the fetal liver.
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Affiliation(s)
- Susumu Muroya
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Tsukuba 305-0901, Ibaraki, Japan
| | - Konosuke Otomaru
- Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Kagoshima, Japan
| | - Kazunaga Oshima
- Division of Year-Round Grazing Research, NARO Western Region Agricultural Research Center, 60 Yoshinaga, Ohda 694-0013, Shimane, Japan
| | - Ichiro Oshima
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Kagoshima, Japan
| | - Koichi Ojima
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Tsukuba 305-0901, Ibaraki, Japan
| | - Takafumi Gotoh
- Field Science Center for Northern Biosphere, Hokkaido University, N11W10, Kita, Sapporo 060-0811, Hokkaido, Japan
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9
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Yang S, Li J, Meng R, Yu T, Wang Z, Xiong P, Gao Z. Screening and identification of genes involved in β-alanine biosynthesis in Bacillus subtilis. Arch Biochem Biophys 2023:109664. [PMID: 37301357 DOI: 10.1016/j.abb.2023.109664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
β-alanine is the only naturally occurring β-amino acid, which is widely used in medicine, food, and feed fields, and generally produced through synthetic biological methods based on engineered strains of Escherichia coli or Corynebacterium glutamicum. However, the β-alanine biosynthesis in Bacillus subtilis, a traditional industrial model microorganism of food safety grade, has not been thoroughly explored. In this study, the native l-aspartate-α-decarboxylase was overexpressed in B. subtilis 168 to obtain an increase of 842% in β-alanine production. A total of 16 single-gene knockout strains were constructed to block the competitive consumption pathways to identify a total of 6 genes (i.e., ptsG, fbp, ydaP, yhfS, mmgA, and pckA) involved in β-alanine synthesis, while the multigene knockout of these 6 genes obtained an increased β-alanine production by 40.1%. Ten single-gene suppression strains with the competitive metabolic pathways inhibited revealed that the inhibited expressions of genes glmS, accB, and accA enhanced the β-alanine production. The introduction of heterologous phosphoenolpyruvate carboxylase increased the β-alanine production by 81.7%, which was 17-fold higher than that of the original strain. This was the first study using multiple molecular strategies to investigate the biosynthetic pathway of β-alanine in B. subtilis and to identify the genetic factors limiting the excessive synthesis of β-alanine by microorganisms.
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Affiliation(s)
- Shaomei Yang
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Jiachang Li
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Rong Meng
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Tingting Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Zengjian Wang
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China.
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, 346 Guanhai Road, Yantai, 256603, China.
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10
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AMPK inhibits liver gluconeogenesis: fact or fiction? Biochem J 2023; 480:105-125. [PMID: 36637190 DOI: 10.1042/bcj20220582] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023]
Abstract
Is there a role for AMPK in the control of hepatic gluconeogenesis and could targeting AMPK in liver be a viable strategy for treating type 2 diabetes? These are frequently asked questions this review tries to answer. After describing properties of AMPK and different small-molecule AMPK activators, we briefly review the various mechanisms for controlling hepatic glucose production, mainly via gluconeogenesis. The different experimental and genetic models that have been used to draw conclusions about the role of AMPK in the control of liver gluconeogenesis are critically discussed. The effects of several anti-diabetic drugs, particularly metformin, on hepatic gluconeogenesis are also considered. We conclude that the main effect of AMPK activation pertinent to the control of hepatic gluconeogenesis is to antagonize glucagon signalling in the short-term and, in the long-term, to improve insulin sensitivity by reducing hepatic lipid content.
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11
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Chai P, Lan P, Li S, Yao D, Chang C, Cao M, Shen Y, Ge S, Wu J, Lei M, Fan X. Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA. Mol Cell 2022; 82:4116-4130.e6. [DOI: 10.1016/j.molcel.2022.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/08/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
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12
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CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase. Nat Commun 2022; 13:6185. [PMID: 36261450 PMCID: PMC9581989 DOI: 10.1038/s41467-022-33987-2] [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: 05/30/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
Abstract
Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both reactions, an initial biotin carboxylation and the subsequent carboxyl transfer to pyruvate substrate to produce oxaloacetate. Reaction sites are at long distance, and there are several co-factors that play as allosteric regulators. Here, using cryoEM we explore the structure of active PC tetramers focusing on active sites and on the conformational space of the oligomers. The results capture the mobile domain at both active sites and expose catalytic steps of both reactions at high resolution, allowing the identification of substrates and products. The analysis of catalytically active PC tetramers reveals the role of certain motions during enzyme functioning, and the structural changes in the presence of additional cofactors expose the mechanism for allosteric regulation.
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13
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Granillo-Luna ON, Hernandez-Aguirre LE, Peregrino-Uriarte AB, Duarte-Gutierrez J, Contreras-Vergara CA, Gollas-Galvan T, Yepiz-Plascencia G. The anaplerotic pyruvate carboxylase from white shrimp Litopenaeus vannamei: Gene structure, molecular characterization, protein modelling and expression during hypoxia. Comp Biochem Physiol A Mol Integr Physiol 2022; 269:111212. [PMID: 35417748 DOI: 10.1016/j.cbpa.2022.111212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 10/18/2022]
Abstract
Hypoxic zones are spreading worldwide in marine environments affecting many organisms. Shrimp and other marine crustaceans can withstand environmental hypoxia using several strategies, including the regulation of energy producing metabolic pathways. Pyruvate carboxylase (PC) catalyzes the first reaction of gluconeogenesis to produce oxaloacetate from pyruvate. In mammals, PC also participates in lipogenesis, insulin secretion and other processes, but this enzyme has been scarcely studied in marine invertebrates. In this work, we characterized the gene encoding PC in the white shrimp Litopenaeus vannamei, modelled the protein structure and evaluated its gene expression in hepatopancreas during hypoxia, as well as glucose and lactate concentrations. The PC gene codes for a mitochondrial protein and has 21 coding exons and 4 non-coding exons that generate three transcript variants with differences only in the 5'-UTR. Total PC expression is more abundant in hepatopancreas compared to gills or muscle, indicating tissue-specific expression. Under hypoxic conditions of 1.53 mg/L dissolved oxygen, PC expression is maintained in hepatopancreas, indicating its key role even in energy-limited conditions. Finally, both glucose and lactate concentrations were maintained under hypoxia for 24-48 h in hepatopancreas.
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Affiliation(s)
- Omar N Granillo-Luna
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Laura E Hernandez-Aguirre
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Alma B Peregrino-Uriarte
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Jorge Duarte-Gutierrez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Carmen A Contreras-Vergara
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Teresa Gollas-Galvan
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Gloria Yepiz-Plascencia
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico.
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14
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Winkelman DC, Nikolau BJ. The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca. Front Mol Biosci 2022; 9:896226. [PMID: 35720111 PMCID: PMC9198275 DOI: 10.3389/fmolb.2022.896226] [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: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The aerobic, thermophilic Actinobacterium, Thermobifida fusca has been proposed as an organism to be used for the efficient conversion of plant biomass to fatty acid-derived precursors of biofuels or biorenewable chemicals. Despite the potential of T. fusca to catabolize plant biomass, there is remarkably little data available concerning the natural ability of this organism to produce fatty acids. Therefore, we determined the fatty acids that T. fusca produces when it is grown on different carbon sources (i.e., glucose, cellobiose, cellulose and avicel) and at two different growth temperatures, namely at the optimal growth temperature of 50°C and at a suboptimal temperature of 37°C. These analyses establish that T. fusca produces a combination of linear and branched chain fatty acids (BCFAs), including iso-, anteiso-, and 10-methyl BCFAs that range between 14- and 18-carbons in length. Although different carbon sources and growth temperatures both quantitatively and qualitatively affect the fatty acid profiles produced by T. fusca, growth temperature is the greater modifier of these traits. Additionally, genome scanning enabled the identification of many of the fatty acid biosynthetic genes encoded by T. fusca.
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Affiliation(s)
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology and the Center of Metabolic Biology, Iowa State University, Ames, IA, United States
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15
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Catalán Ú, Pedret A, Yuste S, Rubió L, Piñol C, Sandoval-Ramírez BA, Companys J, Foguet E, Herrero P, Canela N, Motilva MJ, Solà R. Red-Fleshed Apples Rich in Anthocyanins and White-Fleshed Apples Modulate the Aorta and Heart Proteome in Hypercholesterolaemic Rats: The AppleCOR Study. Nutrients 2022; 14:nu14051047. [PMID: 35268023 PMCID: PMC8912372 DOI: 10.3390/nu14051047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/27/2023] Open
Abstract
The impact of a red-fleshed apple (RFA) rich in anthocyanins (ACNs), a white-fleshed apple (WFA) without ACNs, and an extract infusion from Aronia fruit (AI) equivalent in dose of cyanidin-3-O-galactoside (main ACN) as RFA was determined by the proteome profile of aorta and heart as key cardiovascular tissues. Hypercholesterolaemic Wistar rats were separated into six groups (n = 6/group; three males and three females) and the proteomic profiles were analyzed using nanoliquid chromatography coupled to mass spectrometry. No adverse events were reported and all products were well tolerated. RFA downregulated C1QB and CFP in aorta and CRP in heart. WFA downregulated C1QB and CFP in aorta and C9 and C3 in aorta and heart, among other proteins. AI downregulated PRKACA, IQGAP1, and HSP90AB1 related to cellular signaling. Thus, both apples showed an anti-inflammatory effect through the complement system, while RFA reduced CRP. Regardless of the ACN content, an apple matrix effect was observed that involved different bioactive components, and inflammatory proteins were reduced.
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Affiliation(s)
- Úrsula Catalán
- Functional Nutrition, Oxidation, and CVD Research Group (NFOC-Salut), Medicine and Surgery Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, 43201 Reus, Spain; (Ú.C.); (B.A.S.-R.); (R.S.)
- Institut d’Investigació Sanitària Pere Virgili (IISPV), 43204 Reus, Spain
- Unitat de Nutrició i Salut, Eurecat, Centre Tecnològic de Catalunya, 43204 Reus, Spain;
| | - Anna Pedret
- Functional Nutrition, Oxidation, and CVD Research Group (NFOC-Salut), Medicine and Surgery Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, 43201 Reus, Spain; (Ú.C.); (B.A.S.-R.); (R.S.)
- Unitat de Nutrició i Salut, Eurecat, Centre Tecnològic de Catalunya, 43204 Reus, Spain;
- Correspondence: ; Tel.: +34-977-75-9375
| | - Silvia Yuste
- Food Technology Department, Universitat de Lleida-AGROTECNIO Center, 25198 Lleida, Spain; (S.Y.); (L.R.)
| | - Laura Rubió
- Food Technology Department, Universitat de Lleida-AGROTECNIO Center, 25198 Lleida, Spain; (S.Y.); (L.R.)
| | - Carme Piñol
- Department of Medicine, Universitat de Lleida, 25008 Lleida, Spain;
- Institut de Recerca Biomèdica de Lleida, Fundació Dr. Pifarré-IRBLleida, 25198 Lleida, Spain
| | - Berner Andrée Sandoval-Ramírez
- Functional Nutrition, Oxidation, and CVD Research Group (NFOC-Salut), Medicine and Surgery Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, 43201 Reus, Spain; (Ú.C.); (B.A.S.-R.); (R.S.)
| | - Judit Companys
- Unitat de Nutrició i Salut, Eurecat, Centre Tecnològic de Catalunya, 43204 Reus, Spain;
| | - Elisabet Foguet
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, 43204 Reus, Spain; (E.F.); (P.H.); (N.C.)
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, 43204 Reus, Spain; (E.F.); (P.H.); (N.C.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, 43204 Reus, Spain; (E.F.); (P.H.); (N.C.)
| | - Maria-Jose Motilva
- Instituto de Ciencias de la Vid y del Vino (ICVV), Gobierno de La Rioja, CSIC, Universidad de La Rioja, 26007 Logroño, Spain;
| | - Rosa Solà
- Functional Nutrition, Oxidation, and CVD Research Group (NFOC-Salut), Medicine and Surgery Department, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, 43201 Reus, Spain; (Ú.C.); (B.A.S.-R.); (R.S.)
- Unitat de Nutrició i Salut, Eurecat, Centre Tecnològic de Catalunya, 43204 Reus, Spain;
- Hospital Universitari Sant Joan de Reus (HUSJR), 43204 Reus, Spain
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Exploring synthetic biology for the development of a sensor cell line for automated bioprocess control. Sci Rep 2022; 12:2268. [PMID: 35145179 PMCID: PMC8831625 DOI: 10.1038/s41598-022-06272-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
Unfavorable process conditions lead to adverse cultivation states, limited cell growth and thus hamper biotherapeutic protein production. Oxygen deficiency or hyperosmolality are among the most critical process conditions and therefore require continuous monitoring. We established a novel sensor CHO cell line with the ability to automatically sense and report unwanted process conditions by the expression of destabilized fluorescent proteins. To this end, an inducible real-time system to detect hypoxia by hypoxia response elements (HREs) of vascular endothelial growth factor (VEGF) origin reporting limitations by the expression of destabilized green fluorescent protein (GFP) was created. Additionally, we established a technique for observing hyperosmolality by exploiting osmotic response elements (OREs) for the expression of unstable blue fluorescent protein (BFP, FKBP-BFP), enabling the simultaneous automated supervision of two bioprocess parameters by using a dual sensor CHO cell line transfected with a multiplexable monitoring system. We finally also provided a fully automated in-line fluorescence microscopy-based setup to observe CHO cells and their response to varying culture conditions. In summary, we created the first CHO cell line, reporting unfavorable process parameters to the operator, and provided a novel and promising sensor technology accelerating the implementation of the process analytical technology (PAT) initiative by innovative solutions.
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17
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Ko S, Yeom E, Chun YL, Mun H, Howard-McGuire M, Millison NT, Jung J, Lee KP, Lee C, Lee KS, Delaney JR, Yoon JH. Profiling of RNA-binding Proteins Interacting With Glucagon and Adipokinetic Hormone mRNAs. J Lipid Atheroscler 2022; 11:55-72. [PMID: 35118022 PMCID: PMC8792818 DOI: 10.12997/jla.2022.11.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Glucagon in mammals and its homolog (adipokinetic hormone [AKH] in Drosophila melanogaster) are peptide hormones which regulate lipid metabolism by breaking down triglycerides. Although regulatory mechanisms of glucagon and AKH expression have been widely studied, post-transcriptional gene expression of glucagon has not been investigated thoroughly. In this study, we aimed to profile proteins binding with Gcg messenger RNA (mRNA) in mouse and Akh mRNA in Drosophila. METHODS Drosophila Schneider 2 (S2) and mouse 3T3-L1 cell lysates were utilized for affinity pull down of Akh and Gcg mRNA respectively using biotinylated anti-sense DNA oligoes against target mRNAs. Mass spectrometry and computational network analysis revealed mRNA-interacting proteins residing in functional proximity. RESULTS We observed that 1) 91 proteins interact with Akh mRNA from S2 cell lysates, 2) 34 proteins interact with Gcg mRNA from 3T3-L1 cell lysates. 3) Akh mRNA interactome revealed clusters of ribosomes and known RNA-binding proteins (RBPs). 4) Gcg mRNA interactome revealed mRNA-binding proteins including Plekha7, zinc finger protein, carboxylase, lipase, histone proteins and a cytochrome, Cyp2c44. 5) Levels of Gcg mRNA and its interacting proteins are elevated in skeletal muscles isolated from old mice compared to ones from young mice. CONCLUSION Akh mRNA in S2 cells are under active translation in a complex of RBPs and ribosomes. Gcg mRNA in mouse precursor adipocyte is in a condition distinct from Akh mRNA due to biochemical interactions with a subset of RBPs and histones. We anticipate that our study contributes to investigating regulatory mechanisms of Gcg and Akh mRNA decay, translation, and localization.
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Affiliation(s)
- Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Eunbyul Yeom
- Neurophysiology and Metabolism Research Group, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Yoo Lim Chun
- Department of Biomedical Science, Graduation School, Kyung Hee University, Seoul, Korea
| | - Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Marina Howard-McGuire
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Nathan T. Millison
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Junyang Jung
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Kwang-Pyo Lee
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kyu-Sun Lee
- Neurophysiology and Metabolism Research Group, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Joe R. Delaney
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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19
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González-Olalla JM, Medina-Sánchez JM, Norici A, Carrillo P. Regulation of Phagotrophy by Prey, Low Nutrients, and Low Light in the Mixotrophic Haptophyte Isochrysis galbana. MICROBIAL ECOLOGY 2021; 82:981-993. [PMID: 33661311 DOI: 10.1007/s00248-021-01723-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Mixotrophy combines autotrophy and phagotrophy in the same cell. However, it is not known to what extent the phagotrophy influences metabolism, cell composition, and growth. In this work, we assess, on the one hand (first test), the role of phagotrophy on the elemental and biochemical composition, cell metabolism, and enzymes related to C, N, and S metabolism of Isochrysis galbana Parke, 1949. On the other hand, we study how a predicted increase of phagotrophy under environmental conditions of low nutrients (second test) and low light (third test) can affect its metabolism and growth. Our results for the first test revealed that bacterivory increased the phosphorous and iron content per cell, accelerating cell division and improving the cell fitness; in addition, the stimulation of some C and N enzymatic routes help to maintain, to some degree, compositional homeostasis. Under nutrient or light scarcity, I. galbana grew more slowly despite greater bacterial consumption, and the activities of key enzymes involved in C, N, and S metabolism changed according to a predominantly phototrophic strategy of nutrition in this alga. Contrary to recent studies, the stimulation of phagotrophy under low nutrient and low irradiance did not imply greater and more efficient C flux.
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Affiliation(s)
- Juan Manuel González-Olalla
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
- University Institute of Water research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain.
| | - Juan Manuel Medina-Sánchez
- University Institute of Water research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
- Department of Ecology, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
| | - Alessandra Norici
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Presentación Carrillo
- University Institute of Water research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
- Department of Ecology, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
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20
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Rattanapornsompong K, Sirithanakorn C, Jitrapakdee S, Attwood PV. The role of the phosphate groups of trinitrophenyl adenosine 5'-triphosphate (TNP-ATP) in allosteric activation of pyruvate carboxylase and the inhibition of acetyl CoA-dependent activation. Arch Biochem Biophys 2021; 711:109017. [PMID: 34411580 DOI: 10.1016/j.abb.2021.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/26/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
A previous study showed that 2'-3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate (TNP-ATP) was a weak allosteric activator of Rhizobium etli pyruvate carboxylase (RePC) in the absence of acetyl-CoA. On the other hand, TNP-ATP inhibited the allosteric activation of RePC by acetyl-CoA. Here, we aimed to study the role of triphosphate group of TNP-ATP on its allosteric activation of the enzyme and inhibition of acetyl-CoA-dependent activation of RePC using TNP-ATP and its derivatives, including TNP-ADP, TNP-AMP and TNP-adenosine. The pyruvate carboxylation activity was assayed to determine the effect of reducing the number of phosphate groups in TNP-ATP derivatives on allosteric activation and inhibition of acetyl-CoA activation of RePC and chicken liver pyruvate carboxylase (CLPC). Reducing the number of phosphate groups in TNP-ATP derivatives decreased the activation efficacy for both RePC and CLPC compared to TNP-ATP. The apparent binding affinity and inhibition of activation of the enzymes by acetyl-CoA were also diminished when the number of phosphate groups in the TNP-ATP derivatives was reduced. Whilst TNP-AMP activated RePC, it did not activate CLPC, but it did inhibit acetyl-CoA activation of both RePC and CLPC. Similarly, TNP-adenosine did not activate RePC; however, it did inhibit acetyl-CoA activation using a different mechanism compared to phosphorylated TNP-derivatives. These findings indicate that mechanisms of PC activation and inhibition of acetyl-CoA activation by TNP-ATP and its derivatives are different. This study provides the basis for possible drug development for treatment of metabolic diseases and cancers with aberrant expression of PC.
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Affiliation(s)
| | - Chaiyos Sirithanakorn
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand; Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Paul V Attwood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
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21
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Arlt B, Mastrobuoni G, Wuenschel J, Astrahantseff K, Eggert A, Kempa S, Deubzer HE. Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect. J Enzyme Inhib Med Chem 2021; 36:1282-1289. [PMID: 34192988 PMCID: PMC8253182 DOI: 10.1080/14756366.2021.1935917] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The small-molecule inhibitor of phosphoglycerate dehydrogenase, NCT-503, reduces incorporation of glucose-derived carbons into serine in vitro. Here we describe an off-target effect of NCT-503 in neuroblastoma cell lines expressing divergent phosphoglycerate dehydrogenase (PHGDH) levels and single-cell clones with CRISPR-Cas9-directed PHGDH knockout or their respective wildtype controls. NCT-503 treatment strongly reduced synthesis of glucose-derived citrate in all cell models investigated compared to the inactive drug control and independent of PHGDH expression level. Incorporation of glucose-derived carbons entering the TCA cycle via pyruvate carboxylase was enhanced by NCT-503 treatment. The activity of citrate synthase was not altered by NCT-503 treatment. We also detected no change in the thermal stabilisation of citrate synthase in cellular thermal shift assays from NCT-503-treated cells. Thus, the direct cause of the observed off-target effect remains enigmatic. Our findings highlight off-target potential within a metabolic assessment of carbon usage in cells treated with the small-molecule inhibitor, NCT-503.
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Affiliation(s)
- Birte Arlt
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Neuroblastoma Research Group, Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Guido Mastrobuoni
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jasmin Wuenschel
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Neuroblastoma Research Group, Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Neuroblastoma Research Group, Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Kempa
- Berlin Institute of Health (BIH), Berlin, Germany.,Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany
| | - Hedwig E Deubzer
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Neuroblastoma Research Group, Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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22
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Lovio-Fragoso JP, de Jesús-Campos D, López-Elías JA, Medina-Juárez LÁ, Fimbres-Olivarría D, Hayano-Kanashiro C. Biochemical and Molecular Aspects of Phosphorus Limitation in Diatoms and Their Relationship with Biomolecule Accumulation. BIOLOGY 2021; 10:biology10070565. [PMID: 34206287 PMCID: PMC8301168 DOI: 10.3390/biology10070565] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary Phosphorus (P) is a key nutrient involved in the transfer of energy and the synthesis of several cellular components. It has been reported that P limitation in diatoms induces the synthesis of biomolecules and the accumulation of storage compounds, such as pigments, carbohydrates and lipids, with diverse biological activities, which can be used in diverse biotechnological applications. However, the molecular and biochemical mechanisms related to how diatoms cope with P deficiency are not clear, and research into this has been limited to a few species. The integration of results obtained from omics sciences could provide a broad understanding of the response of diatoms to P limitation, and the information obtained could help to solve challenges such as biomass production, by-products yield and genetic improvement of strains. Abstract Diatoms are the most abundant group of phytoplankton, and their success lies in their significant adaptation ability to stress conditions, such as nutrient limitation. Phosphorus (P) is a key nutrient involved in the transfer of energy and the synthesis of several cellular components. Molecular and biochemical mechanisms related to how diatoms cope with P deficiency are not clear, and research into this has been limited to a few species. Among the molecular responses that have been reported in diatoms cultured under P deficient conditions is the upregulation of genes encoding enzymes related to the transport, assimilation, remobilization and recycling of this nutrient. Regarding biochemical responses, due to the reduction of the requirements for carbon structures for the synthesis of proteins and phospholipids, more CO2 is fixed than is consumed by the Calvin cycle. To deal with this excess, diatoms redirect the carbon flow toward the synthesis of storage compounds such as triacylglycerides and carbohydrates, which are excreted as extracellular polymeric substances. This review aimed to gather all current knowledge regarding the biochemical and molecular mechanisms of diatoms related to managing P deficiency in order to provide a wider insight into and understanding of their responses, as well as the metabolic pathways affected by the limitation of this nutrient.
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Chilunga FP, Henneman P, Venema A, Meeks KAC, Requena-Méndez A, Beune E, Mockenhaupt FP, Smeeth L, Bahendeka S, Danquah I, Klipstein-Grobusch K, Adeyemo A, Mannens MMAM, Agyemang C. Genome-wide DNA methylation analysis on C-reactive protein among Ghanaians suggests molecular links to the emerging risk of cardiovascular diseases. NPJ Genom Med 2021; 6:46. [PMID: 34117263 PMCID: PMC8196035 DOI: 10.1038/s41525-021-00213-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/20/2021] [Indexed: 12/28/2022] Open
Abstract
Molecular mechanisms at the intersection of inflammation and cardiovascular diseases (CVD) among Africans are still unknown. We performed an epigenome-wide association study to identify loci associated with serum C-reactive protein (marker of inflammation) among Ghanaians and further assessed whether differentially methylated positions (DMPs) were linked to CVD in previous reports, or to estimated CVD risk in the same population. We used the Illumina Infinium® HumanMethylation450 BeadChip to obtain DNAm profiles of blood samples in 589 Ghanaians from the RODAM study (without acute infections, not taking anti-inflammatory medications, CRP levels < 40 mg/L). We then used linear models to identify DMPs associated with CRP concentrations. Post-hoc, we evaluated associations of identified DMPs with elevated CVD risk estimated via ASCVD risk score. We also performed subset analyses at CRP levels ≤10 mg/L and replication analyses on candidate probes. Finally, we assessed for biological relevance of our findings in public databases. We subsequently identified 14 novel DMPs associated with CRP. In post-hoc evaluations, we found that DMPs in PC, BTG4 and PADI1 showed trends of associations with estimated CVD risk, we identified a separate DMP in MORC2 that was associated with CRP levels ≤10 mg/L, and we successfully replicated 65 (24%) of previously reported DMPs. All DMPs with gene annotations (13) were biologically linked to inflammation or CVD traits. We have identified epigenetic loci that may play a role in the intersection between inflammation and CVD among Ghanaians. Further studies among other Africans are needed to confirm our findings.
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Affiliation(s)
- Felix P Chilunga
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ana Requena-Méndez
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Global Public Health, Karolinska Institutet, Solna, Sweden
| | - Erik Beune
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank P Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Silver Bahendeka
- Department of Medicine, MKPGMS-Uganda Martyrs University, Kampala, Uganda
| | - Ina Danquah
- Heidelberg Institute of Global Health (HIGH), Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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24
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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25
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Kiesel VA, Sheeley MP, Coleman MF, Cotul EK, Donkin SS, Hursting SD, Wendt MK, Teegarden D. Pyruvate carboxylase and cancer progression. Cancer Metab 2021; 9:20. [PMID: 33931119 PMCID: PMC8088034 DOI: 10.1186/s40170-021-00256-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/04/2021] [Indexed: 01/17/2023] Open
Abstract
Pyruvate carboxylase (PC) is a mitochondrial enzyme that catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate (OAA), serving to replenish the tricarboxylic acid (TCA) cycle. In nonmalignant tissue, PC plays an essential role in controlling whole-body energetics through regulation of gluconeogenesis in the liver, synthesis of fatty acids in adipocytes, and insulin secretion in pancreatic β cells. In breast cancer, PC activity is linked to pulmonary metastasis, potentially by providing the ability to utilize glucose, fatty acids, and glutamine metabolism as needed under varying conditions as cells metastasize. PC enzymatic activity appears to be of particular importance in cancer cells that are unable to utilize glutamine for anaplerosis. Moreover, PC activity also plays a role in lipid metabolism and protection from oxidative stress in cancer cells. Thus, PC activity may be essential to link energy substrate utilization with cancer progression and to enable the metabolic flexibility necessary for cell resilience to changing and adverse conditions during the metastatic process.
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Affiliation(s)
- Violet A Kiesel
- Department of Nutrition Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline P Sheeley
- Department of Nutrition Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael F Coleman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Eylem Kulkoyluoglu Cotul
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Shawn S Donkin
- Department of Animal Science, Purdue University, West Lafayette, USA
| | - Stephen D Hursting
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Dorothy Teegarden
- Department of Nutrition Sciences, Purdue University, West Lafayette, IN, 47907, USA.
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26
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Formation of Thiophene under Simulated Volcanic Hydrothermal Conditions on Earth-Implications for Early Life on Extraterrestrial Planets? Life (Basel) 2021; 11:life11020149. [PMID: 33669362 PMCID: PMC7920246 DOI: 10.3390/life11020149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 11/17/2022] Open
Abstract
Thiophene was detected on Mars during the Curiosity mission in 2018. The compound was even suggested as a biomarker due to its possible origin from diagenesis or pyrolysis of biological material. In the laboratory, thiophene can be synthesized at 400 °C by reacting acetylene and hydrogen sulfide on alumina. We here show that thiophene and thiophene derivatives are also formed abiotically from acetylene and transition metal sulfides such as NiS, CoS and FeS under simulated volcanic, hydrothermal conditions on Early Earth. Exactly the same conditions were reported earlier to have yielded a plethora of organic molecules including fatty acids and other components of extant metabolism. It is therefore tempting to suggest that thiophenes from abiotic formation could indicate sites and conditions well-suited for the evolution of metabolism and potentially for the origin-of-life on extraterrestrial planets.
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Köritzer J, Blenn C, Bürkle A, Beneke S. Mitochondria are devoid of poly(ADP-ribose)polymerase-1, but harbor its product oligo(ADP-ribose). J Cell Biochem 2021; 122:507-523. [PMID: 33417272 DOI: 10.1002/jcb.29887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022]
Abstract
There are conflicting data about localization of poly(ADP-ribose)polymerase-1 and its product poly(ADP-ribose) in mitochondria. To finally clarify the discussion, we investigated with biochemical and cell biological methods the potential presence of poly(ADP-ribose) polymerase-1 in these organelles. Our data show that endogenous and overexpressed poly(ADP-ribose)polymerase 1 is only localized to the nucleus with a clear exclusion of cytosolic compartments. In addition, highly purified mitochondria devoid of nuclear contaminations do not contain poly(ADP-ribose)polymerase-1. Although no poly(ADP-ribose)polymerase-1 enzyme is detectable in mitochondria, a shorter variant of its product poly(ADP-ribose) is present, associated specifically with a small subset of mitochondrial proteins as revealed by immunoprecipitation and protein fingerprint analysis. These proteins are located at key-points of the Krebs-cycle, are chaperones involved in mitochondrial functionality and quality-control, and are RNA-binding proteins important for transcript stability, respectively. Of note, despite the fact that especially poly(ADP-ribose)polymerase-1 is its own major target for modification, we could not detect this enzyme by mass spectrometry in these organelles. These data suggests a new way of targeted nuclear-mitochondrial signaling, mediated by nuclear poly(ADP-ribosyl)ation dependent on poly(ADP-ribose)polymerase-1.
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Affiliation(s)
- Julia Köritzer
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Christian Blenn
- Institute of Pharmacology and Toxicology, University of Zurich/Vetsuisse, Zurich, Switzerland
| | - Alexander Bürkle
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Sascha Beneke
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany.,Human and Environmental Toxicology Group, University of Konstanz, Konstanz, Germany
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28
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Britton S, Alber M, Cannon WR. Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell. J R Soc Interface 2020; 17:20200656. [PMID: 33050777 PMCID: PMC7653389 DOI: 10.1098/rsif.2020.0656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization-reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.
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Affiliation(s)
- Samuel Britton
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - William R. Cannon
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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29
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The osmo-metabolic approach: a novel and tantalizing glucose-sparing strategy in peritoneal dialysis. J Nephrol 2020; 34:503-519. [PMID: 32767274 PMCID: PMC8036224 DOI: 10.1007/s40620-020-00804-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Peritoneal dialysis (PD) is a viable but under-prescribed treatment for uremic patients. Concerns about its use include the bio-incompatibility of PD fluids, due to their potential for altering the functional and anatomical integrity of the peritoneal membrane. Many of these effects are thought to be due to the high glucose content of these solutions, with attendant issues of products generated during heat treatment of glucose-containing solutions. Moreover, excessive intraperitoneal absorption of glucose from the dialysate has many potential systemic metabolic effects. This article reviews the efforts to develop alternative PD solutions that obviate some of these side effects, through the replacement of part of their glucose content with other osmolytes which are at least as efficient in removing fluids as glucose, but less impactful on patient metabolism. In particular, we will summarize clinical studies on the use of alternative osmotic ingredients that are commercially available (icodextrin and amino acids) and preclinical studies on alternative solutions under development (taurine, polyglycerol, carnitine and xylitol). In addition to the expected benefit of a glucose-sparing approach, we describe an ‘osmo-metabolic’ approach in formulating novel PD solutions, in which there is the possibility of exploiting the pharmaco-metabolic properties of some of the osmolytes to attenuate the systemic side effects due to glucose. This approach has the potential to ameliorate pre-existing co-morbidities, including insulin resistance and type-2 diabetes, which have a high prevalence in the dialysis population, including in PD patients.
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30
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Spona-Friedl M, Braun A, Huber C, Eisenreich W, Griebler C, Kappler A, Elsner M. Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling. FEMS Microbiol Ecol 2020; 96:5828077. [DOI: 10.1093/femsec/fiaa080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/30/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTVirtually all heterotrophs incorporate carbon dioxide by anaplerotic fixation. Little explored, however, is the interdependency of pathways and rates of CO2fixation on the concurrent usage of organic substrate(s). Potentially, this could reveal which substrates out of a pool of dissolved organic carbon are utilised by environmental microorganisms. To explore this possibility, Bacillus subtilis W23 was grown in a minimal medium with normalised amounts of either glucose, lactate or malate as only organic substrates, each together with 1 g/L NaH13CO3. Incorporation of H13CO3− was traced by elemental analysis-isotope ratio mass spectrometry of biomass and gas chromatography-mass spectrometry of protein-derived amino acids. Until the late logarithmic phase, 13C incorporation into the tricarboxylic acid cycle increased with time and occurred via [4–13C]oxaloacetate formed by carboxylation of pyruvate. The levels of 13C incorporation were highest for growth on glucose and lowest on malate. Incorporation of 13C into gluconeogenesis products was mainly detected in the lactate and malate experiment, whereas glucose down-regulated this path. A proof-of-principle study with a natural groundwater community confirmed the ability to determine incorporation from H13CO3− by natural communities leading to specific labelling patterns. This underlines the potential of the labelling approach to characterise carbon sources of heterotrophic microorganisms in their natural environments.
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Affiliation(s)
- Marina Spona-Friedl
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Alexander Braun
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Claudia Huber
- Chair of Biochemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Chair of Biochemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Department of Functional and Evolutionary Ecology, Universität Wien, Althanstr. 14, A-1090 Wien, Austria
| | - Andreas Kappler
- Geomicrobiology, Eberhard-Karls-University Tuebingen, Sigwartstr. 10, 72076 Tuebingen, Germany
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technische Universität München, Marchioninistr. 17, 81377 München, Germany
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31
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Pinweha P, Phillips CA, Gregory PA, Li X, Chuayboonya P, Mongkolsiri P, Goodall GJ, Jitrapakdee S. MicroRNA-143-3p targets pyruvate carboxylase expression and controls proliferation and migration of MDA-MB-231 cells. Arch Biochem Biophys 2019; 677:108169. [DOI: 10.1016/j.abb.2019.108169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 01/06/2023]
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32
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Chandler TL, White HM. Glucose metabolism is differentially altered by choline and methionine in bovine neonatal hepatocytes. PLoS One 2019; 14:e0217160. [PMID: 31141525 PMCID: PMC6541273 DOI: 10.1371/journal.pone.0217160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/06/2019] [Indexed: 02/06/2023] Open
Abstract
Choline and methionine serve essential roles in the liver that may interact with glucose metabolism. Our objectives were to quantify glucose export, cellular glycogen, and expression of genes controlling oxidation and gluconeogenesis in primary bovine neonatal hepatocytes exposed to increasing concentrations of choline chloride (CC) and D,L-methionine (DLM) with or without fatty acids (FA). Primary hepatocytes isolated from 3 Holstein calves were maintained as monolayer cultures for 24 h before treatment with CC (61, 128, 2028, 4528 μmol/L) and DLM (16, 30, 100, 300 μmol/L) with or without a 1 mmol/L FA cocktail in a factorial design. After 24 h, media was harvested to quantify glucose, β-hydroxybutyrate (BHB), and cells harvested to quantify glycogen, DNA, and gene expression. No interactions between CC and DLM were detected. The potential two-way interaction between CC or DLM and FA was partitioned into three contrasts when P ≤ 0.20: linear without FA, linear with FA, difference of slope. Fatty acids did not affect glucose or cellular glycogen but increased pyruvate carboxylase (PC), cytosolic and mitochondrial phosphoenolpyruvate carboxykinase (PEPCKc, PEPCKm), and glucose-6-phosphatase (G6PC) expression. Increasing CC decreased glucose but increased cellular glycogen. Expression of PC and PEPCKc was increased by CC during FA treatment. Increasing DLM did not affect metabolites or PC expression, although PEPCKc was marginally decreased. Methionine did not affect G6PC, while CC had a marginal quadratic effect on G6PC. Oxidative and gluconeogenic enzymes appear to respond to FA in primary bovine neonatal hepatocytes. Increased PC and PEPCKc by CC during FA treatment suggest increased gluconeogenic capacity. Changes in G6PC may have shifted glucose-6-phosphate towards cellular glycogen; however, subsequent examination of G6PC protein is needed. Unaltered PC and marginally decreased PEPCKc suggest increased oxidative capacity with DLM, although BHB export was unaltered. The differential regulation supports unique effects of CC and DLM within bovine hepatocytes.
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Affiliation(s)
- Tawny L. Chandler
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Heather M. White
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, United States of America
- * E-mail:
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33
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Characterization of the kinetics and activation thermodynamics of intra- and inter-organism hybrid tetramers of pyruvate carboxylase. Arch Biochem Biophys 2019; 665:87-95. [DOI: 10.1016/j.abb.2019.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 11/18/2022]
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34
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Lee STM, Keshavmurthy S, Fontana S, Takuma M, Chou WH, Chen CA. Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations. BMC Res Notes 2018; 11:119. [PMID: 29426371 PMCID: PMC5807827 DOI: 10.1186/s13104-018-3230-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 02/06/2018] [Indexed: 11/13/2022] Open
Abstract
Objective Global climate change has resulted in the decline of health and condition of various coral reefs worldwide. Here, we describe expression profiles of Acropora muricata collected during opposing seasons in Otsuki, Kochi, Japan to define the capacity of corals to cope with changing environmental conditions. Coral communities in Otsuki experience large temperature fluctuations between the winter (~ 16 °C) and summer (~ 27 °C). Results Coral nubbins that were collected in the summer showed no change in photochemical efficiency when exposed to thermal or cold stress, while winter samples showed a decrease in photochemical health when subjected to thermal stress. Under cold stress, corals that were collected in the summer showed an up-regulation of actin-related protein and serine/threonine protein kinase, while corals collected during the winter did not show any cellular stress. On the other hand, under thermal stress, the most notable change was the up-regulation of phosphoenolpyruvate carboxykinase in corals that were collected during the winter season. Our observations in the differential genes expressed under temperature-derived stress suggest that A. muricata from Kochi may maintain physiological resilience due to the frequently encountered environmental stress, and this may play a role in the coral’s thermal tolerance. Electronic supplementary material The online version of this article (10.1186/s13104-018-3230-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonny T M Lee
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Chicago Medicine, Chicago, IL, USA
| | | | - Silvia Fontana
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Taipei, Taiwan.,National Taiwan Normal University, Taipei, Taiwan
| | - Mezaki Takuma
- Biological Institute on Kuroshio, Otsuki, Kochi, Japan
| | - Wen-Hua Chou
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Taipei, Taiwan.,National Taiwan Normal University, Taipei, Taiwan
| | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. .,Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Taipei, Taiwan. .,Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
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35
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Gupta SK, Srivastava SK, Sharma A, Nalage VHH, Salvi D, Kushwaha H, Chitnis NB, Shukla P. Metabolic engineering of CHO cells for the development of a robust protein production platform. PLoS One 2017; 12:e0181455. [PMID: 28763459 PMCID: PMC5538670 DOI: 10.1371/journal.pone.0181455] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/01/2017] [Indexed: 12/12/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are the most preferred mammalian host used for the bio-pharmaceutical production. A major challenge in metabolic engineering is to balance the flux of the tuned heterogonous metabolic pathway and achieve efficient metabolic response in a mammalian cellular system. Pyruvate carboxylase is an important network element for the cytoplasmic and mitochondrial metabolic pathway and efficiently contributes in enhancing the energy metabolism. The lactate accumulation in cell culture can be reduced by re-wiring of the pyruvate flux in engineered cells. In the present work, we over-expressed the yeast cytosolic pyruvate carboxylase (PYC2) enzyme in CHO cells to augment pyruvate flux towards the TCA cycle. The dual selection strategy is adopted for the screening and isolation of CHO clones containing varying number of PYC2 gene load and studied their cellular kinetics. The enhanced PYC2 expression has led to enhanced pyruvate flux which, thus, allowed reduced lactate accumulation up to 4 folds and significant increase in the cell density and culture longevity. With this result, engineered cells have shown a significant enhanced antibody expression up to 70% with improved product quality (~3 fold) as compared to the parental cells. The PYC2 engineering allowed overall improved cell performance with various advantages over parent cells in terms of pyruvate, glucose, lactate and cellular energy metabolism. This study provides a potential expression platform for a bio-therapeutic protein production in a controlled culture environment.
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Affiliation(s)
- Sanjeev Kumar Gupta
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana-India
| | - Santosh K. Srivastava
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
| | - Ankit Sharma
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
| | - Vaibhav H. H. Nalage
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
| | - Darshita Salvi
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
| | - Hiralal Kushwaha
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
| | - Nikhil B. Chitnis
- Advanced Biotech Lab, Ipca Laboratories Ltd., Plot#125, Kandivli Industrial Estate, Kandivli (west), Mumbai, Maharashtra, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana-India
- * E-mail:
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Gupta SK, Sharma A, Kushwaha H, Shukla P. Over-expression of a Codon Optimized Yeast Cytosolic Pyruvate Carboxylase (PYC2) in CHO Cells for an Augmented Lactate Metabolism. Front Pharmacol 2017; 8:463. [PMID: 28769797 PMCID: PMC5511841 DOI: 10.3389/fphar.2017.00463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023] Open
Abstract
Monoclonal antibodies are the most demanding biotherapeutic drugs now a days used for the cure of various critical illnesses. Chinese hamster ovary (CHO) cells are one of the main hosts used for the large scale production of these antibodies. However, the cell line and production processes are the key factors to determine the cost and affordability of these antibodies. The metabolic waste lactic acid and ammonium are accumulated during a cell culture process and adversely affects productivity as well as product quality. To control the lactate metabolism of mAb (IgG1-kappa) producing CHO clones, we super-transfected the cells with a mammalian construct bearing codon optimized yeast cytosolic pyruvate carboxylase (PYC2) and a strong fusion promoter for optimal expression of PYC2 enzyme. A pool study was also performed for the assessment of cell’s performance, post-translational modification of a mAb and its expression in a CHO clone. The current study resulted an improved mAb titer up to 5%, galactosylation up to 2.5-folds, mannosylation up to twofold and marginal improved main and basic peaks in the charge variant profile at the cell pool stage. Such, approach may be suitable for the implementation in CHO cells producing recombinant protein for a better process control for the production of biotherapeutics.
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Affiliation(s)
- Sanjeev K Gupta
- Advanced Biotech Lab, Ipca Laboratories Ltd.Mumbai, India.,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
| | - Ankit Sharma
- Advanced Biotech Lab, Ipca Laboratories Ltd.Mumbai, India
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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Wang X, Zhang Y, Zhang X, Wang D, Jin G, Li B, Xu F, Cheng J, Zhang F, Wu S, Rui S, He J, Zhang R, Liu W. The comprehensive liver transcriptome of two cattle breeds with different intramuscular fat content. Biochem Biophys Res Commun 2017; 490:1018-1025. [PMID: 28669724 DOI: 10.1016/j.bbrc.2017.06.157] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
Intramuscular fat (IMF) content is an important determinant factor of meat quality in cattle. There is significant difference in IMF content between Jinnan and Simmental cattle. Here, to identify candidate genes and networks associated with IMF deposition, we deeply explored the transcriptome architecture of liver in these two cattle breeds. We sequenced the liver transcriptome of five Jinnan and three Simmental cattle, yielding about 413.9 million sequencing reads. 124 differentially expressed genes (DEGs) were detected, of which 53 were up-regulated and 71 were down-regulated in Jinnan cattle. 1282 potentially novel genes were also identified. Gene ontology analysis revealed these DEGs (including CYP21A2, PC, ACACB, APOA1, and FADS2) were significantly enriched in lipid biosynthetic process, regulation of cholesterol esterification, reverse cholesterol transport, and regulation of lipoprotein lipase activity. Genes involved in pyruvate metabolism pathway were also significantly overrepresented. Moreover, we identified an interaction network which related to lipid metabolism, which might be contributed to the IMF deposition in cattle. We concluded that the DEGs involved in the regulation of lipid metabolism could play an important role in IMF deposition. Overall, we proposed a new panel of candidate genes and interaction networks that can be associated with IMF deposition and used as biomarkers in cattle breeding.
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Affiliation(s)
- Xi Wang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China; Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Yuanqing Zhang
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Xizhong Zhang
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Dongcai Wang
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Guang Jin
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Bo Li
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Fang Xu
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Jing Cheng
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Feng Zhang
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Sujun Wu
- Institute of Animal Husbandry and Veterinary, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032, Shanxi, China
| | - Su Rui
- School of Chemical and Environmental Engineering, North University of China, Taiyuan, 030051, Shanxi, China
| | - Jiang He
- Center of Shanxi Animal Genetics and Breeding, Taiyuan, 030001, Shanxi, China
| | - Ronghua Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Wenzhong Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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Weber C, Schäff C, Kautzsch U, Börner S, Erdmann S, Bruckmaier R, Röntgen M, Kuhla B, Hammon H. Variable liver fat concentration as a proxy for body fat mobilization postpartum has minor effects on insulin-induced changes in hepatic gene expression related to energy metabolism in dairy cows. J Dairy Sci 2017; 100:1507-1520. [DOI: 10.3168/jds.2016-11808] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022]
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Yip J, Geng X, Shen J, Ding Y. Cerebral Gluconeogenesis and Diseases. Front Pharmacol 2017; 7:521. [PMID: 28101056 PMCID: PMC5209353 DOI: 10.3389/fphar.2016.00521] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/15/2016] [Indexed: 01/08/2023] Open
Abstract
The gluconeogenesis pathway, which has been known to normally present in the liver, kidney, intestine, or muscle, has four irreversible steps catalyzed by the enzymes: pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose 1,6-bisphosphatase, and glucose 6-phosphatase. Studies have also demonstrated evidence that gluconeogenesis exists in brain astrocytes but no convincing data have yet been found in neurons. Astrocytes exhibit significant 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 activity, a key mechanism for regulating glycolysis and gluconeogenesis. Astrocytes are unique in that they use glycolysis to produce lactate, which is then shuttled into neurons and used as gluconeogenic precursors for reduction. This gluconeogenesis pathway found in astrocytes is becoming more recognized as an important alternative glucose source for neurons, specifically in ischemic stroke and brain tumor. Further studies are needed to discover how the gluconeogenesis pathway is controlled in the brain, which may lead to the development of therapeutic targets to control energy levels and cellular survival in ischemic stroke patients, or inhibit gluconeogenesis in brain tumors to promote malignant cell death and tumor regression. While there are extensive studies on the mechanisms of cerebral glycolysis in ischemic stroke and brain tumors, studies on cerebral gluconeogenesis are limited. Here, we review studies done to date regarding gluconeogenesis to evaluate whether this metabolic pathway is beneficial or detrimental to the brain under these pathological conditions.
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Affiliation(s)
- James Yip
- Department of Neurosurgery, Wayne State University School of Medicine Detroit, MI, USA
| | - Xiaokun Geng
- Department of Neurosurgery, Wayne State University School of MedicineDetroit, MI, USA; China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical UniversityBeijing, China; Department of Neurology, Beijing Luhe Hospital, Capital Medical UniversityBeijing, China
| | - Jiamei Shen
- Department of Neurosurgery, Wayne State University School of MedicineDetroit, MI, USA; China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical UniversityBeijing, China
| | - Yuchuan Ding
- Department of Neurosurgery, Wayne State University School of MedicineDetroit, MI, USA; China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical UniversityBeijing, China
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Delgado-Goni T, Miniotis MF, Wantuch S, Parkes HG, Marais R, Workman P, Leach MO, Beloueche-Babari M. The BRAF Inhibitor Vemurafenib Activates Mitochondrial Metabolism and Inhibits Hyperpolarized Pyruvate-Lactate Exchange in BRAF-Mutant Human Melanoma Cells. Mol Cancer Ther 2016; 15:2987-2999. [PMID: 27765851 PMCID: PMC5136471 DOI: 10.1158/1535-7163.mct-16-0068] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 11/16/2022]
Abstract
Understanding the impact of BRAF signaling inhibition in human melanoma on key disease mechanisms is important for developing biomarkers of therapeutic response and combination strategies to improve long-term disease control. This work investigates the downstream metabolic consequences of BRAF inhibition with vemurafenib, the molecular and biochemical processes that underpin them, their significance for antineoplastic activity, and potential as noninvasive imaging response biomarkers. 1H NMR spectroscopy showed that vemurafenib decreases the glycolytic activity of BRAF-mutant (WM266.4 and SKMEL28) but not BRAFWT (CHL-1 and D04) human melanoma cells. In WM266.4 cells, this was associated with increased acetate, glycine, and myo-inositol levels and decreased fatty acyl signals, while the bioenergetic status was maintained. 13C NMR metabolic flux analysis of treated WM266.4 cells revealed inhibition of de novo lactate synthesis and glucose utilization, associated with increased oxidative and anaplerotic pyruvate carboxylase mitochondrial metabolism and decreased lipid synthesis. This metabolic shift was associated with depletion of hexokinase 2, acyl-CoA dehydrogenase 9, 3-phosphoglycerate dehydrogenase, and monocarboxylate transporters (MCT) 1 and 4 in BRAF-mutant but not BRAFWT cells and, interestingly, decreased BRAF-mutant cell dependency on glucose and glutamine for growth. Further, the reduction in MCT1 expression observed led to inhibition of hyperpolarized 13C-pyruvate-lactate exchange, a parameter that is translatable to in vivo imaging studies, in live WM266.4 cells. In conclusion, our data provide new insights into the molecular and metabolic consequences of BRAF inhibition in BRAF-driven human melanoma cells that may have potential for combinatorial therapeutic targeting as well as noninvasive imaging of response. Mol Cancer Ther; 15(12); 2987-99. ©2016 AACR.
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Affiliation(s)
- Teresa Delgado-Goni
- Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research, London, United Kingdom
| | - Maria Falck Miniotis
- Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research, London, United Kingdom
| | - Slawomir Wantuch
- Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research, London, United Kingdom
| | - Harold G Parkes
- Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research, London, United Kingdom
| | - Richard Marais
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Martin O Leach
- Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Mounia Beloueche-Babari
- Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research, London, United Kingdom.
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Heo HJ, Tozour JN, Delahaye F, Zhao Y, Cui L, Barzilai N, Einstein FH. Advanced aging phenotype is revealed by epigenetic modifications in rat liver after in utero malnutrition. Aging Cell 2016; 15:964-72. [PMID: 27470058 PMCID: PMC5013021 DOI: 10.1111/acel.12505] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 02/06/2023] Open
Abstract
Adverse environmental exposures of mothers during fetal period predispose offspring to a range of age-related diseases earlier in life. Here, we set to determine whether a deregulated epigenetic pattern is similar in young animals whose mothers' nutrition was modulated during fetal growth to that acquired during normal aging in animals. Using a rodent model of maternal undernutrition (UN) or overnutrition (ON), we examined cytosine methylation profiles of liver from young female offspring and compared them to age-matched young controls and aged (20-month-old) animals. HELP-tagging, a genomewide restriction enzyme and sequencing assay demonstrates that fetal exposure to two different maternal diets is associated with nonrandom dysregulation of methylation levels with profiles similar to those seen in normal aging animals and occur in regions mapped to genes relevant to metabolic diseases and aging. Functional consequences were assessed by gene expression at 9 weeks old with more significant changes at 6 months of age. Early developmental exposures to unfavorable maternal diets result in altered methylation profiles and transcriptional dysregulation in Prkcb, Pc, Ncor2, and Smad3 that is also seen with normal aging. These Notch pathway and lipogenesis genes may be useful for prediction of later susceptibility to chronic disease.
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Affiliation(s)
- Hye J. Heo
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Jessica N. Tozour
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Fabien Delahaye
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Yongmei Zhao
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Lingguang Cui
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Nir Barzilai
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Medicine Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Francine Hughes Einstein
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Medicine Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
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Westerhold LE, Adams SL, Bergman HL, Zeczycki TN. Pyruvate Occupancy in the Carboxyl Transferase Domain of Pyruvate Carboxylase Facilitates Product Release from the Biotin Carboxylase Domain through an Intermolecular Mechanism. Biochemistry 2016; 55:3447-60. [PMID: 27254467 DOI: 10.1021/acs.biochem.6b00372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein structure, ligand binding, and catalytic turnover contributes to the governance of catalytic events occurring at spatially distinct domains in multifunctional enzymes. Coordination of these catalytic events partially rests on the ability of spatially discrete active sites to communicate with other allosteric and active sites on the same polypeptide chain (intramolecular) or on different polypeptide chains (intermolecular) within the holoenzyme. Often, communication results in long-range effects on substrate binding or product release. For example, pyruvate binding to the carboxyl transferase (CT) domain of pyruvate carboxylase (PC) increases the rate of product release in the biotin carboxylase (BC) domain. In order to address how CT domain ligand occupancy is "sensed" by other domains, we generated functional, mixed hybrid tetramers using the E218A (inactive BC domain) and T882S (low pyruvate binding, low activity) mutant forms of PC. The apparent Ka pyruvate for the pyruvate-stimulated release of Pi catalyzed by the T882S:E218A[1:1] hybrid tetramer was comparable to the wild-type enzyme and nearly 10-fold lower than that for the T882S homotetramer. In addition, the ratio of the rates of oxaloacetate formation to Pi release for the WT:T882S[1:1] and E218A:T882S[1:1] hybrid tetramer-catalyzed reactions was 0.5 and 0.6, respectively, while the T882S homotetramer exhibited a near 1:1 coupling of the two domains, suggesting that the mechanisms coordinating catalytic events is more complicated that we initially assumed. The results presented here are consistent with an intermolecular communication mechanism, where pyruvate binding to the CT domain is "sensed" by domains on a different polypeptide chain within the tetramer.
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Affiliation(s)
- Lauren E Westerhold
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Stephanie L Adams
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Hanna L Bergman
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
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Hussein AH, Batista ED, Miesner MD, Titgemeyer EC. Effect of ruminal ammonia supply on lysine utilization by growing steers. J Anim Sci 2016; 94:656-64. [PMID: 27065136 DOI: 10.2527/jas.2015-9717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Six ruminally cannulated Holstein steers (202 ± 15 kg) were used to study the effects of ruminal ammonia loading on whole-body lysine (Lys) utilization. Steers were housed in metabolism crates and used in a 6 × 6 Latin square design. All steers received 2.52 kg DM/d of a diet (10.1% CP) containing 82% soybean hulls, 8% wheat straw, 5% cane molasses, and 5% vitamins and minerals, and 10 g/d of urea (considered to be part of the basal diet) was ruminally infused continuously to ensure adequate ruminal ammonia concentrations. All steers were ruminally infused continuously with 200 g/d of acetic acid, 200 g/d of propionic acid, and 50 g/d of butyric acid and abomasally infused with 300 g/d of glucose continuously to increase energy supply without increasing microbial protein supply. Steers were also abomasally infused continuously with an excess of all essential AA except Lys to ensure that Lys was the only limiting AA. Treatments were arranged as a 3 × 2 factorial with 3 levels of urea (0, 40, or 80 g/d) continuously infused ruminally to induce ammonia loading and 2 levels of Lys (0 or 6 g/d) continuously infused abomasally. Treatments did not affect fecal N output ( = 0.37). Lysine supplementation decreased ( < 0.01) urinary N excretion from 51.9 g/d to 44.3 g/d, increased ( < 0.01) retained N from 24.8 to 33.8 g/d, increased ( < 0.01) plasma Lys, and decreased ( ≤ 0.05) plasma serine, tyrosine, valine, leucine, and phenylalanine. Lysine supplementation also tended ( = 0.09) to reduce plasma urea-N. Urea infusions linearly increased ( = 0.05) retained N (27.1, 29.3, and 31.5 g/d) and also linearly increased ( < 0.01) urinary N excretion (31.8, 48.1, and 64.4 g/d), urinary urea (21.9, 37.7, and 54.3 g/d), urinary ammonia (1.1, 1.4, and 1.9 g/d), and plasma urea (2.7, 4.0, and 5.1 mM), and linearly decreased plasma alanine ( = 0.04) and plasma glycine ( < 0.01). Assuming that retained protein is 6.25 × retained N and contains 6.4% Lys, the incremental efficiencies of infused Lys utilization were 51%, 59%, and 69% for steers receiving 0, 40, and 80 g/d of urea, respectively, indicating that ruminal ammonia loads may improve the efficiency of Lys utilization. This is supported by observed increases in whole body-protein deposition in response to ammonia loading of our steers that were, by design, Lys deficient.
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Regulation of Glucose Homeostasis by Glucocorticoids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015. [PMID: 26215992 DOI: 10.1007/978-1-4939-2895-8_5] [Citation(s) in RCA: 383] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glucocorticoids are steroid hormones that regulate multiple aspects of glucose homeostasis. Glucocorticoids promote gluconeogenesis in liver, whereas in skeletal muscle and white adipose tissue they decrease glucose uptake and utilization by antagonizing insulin response. Therefore, excess glucocorticoid exposure causes hyperglycemia and insulin resistance. Glucocorticoids also regulate glycogen metabolism. In liver, glucocorticoids increase glycogen storage, whereas in skeletal muscle they play a permissive role for catecholamine-induced glycogenolysis and/or inhibit insulin-stimulated glycogen synthesis. Moreover, glucocorticoids modulate the function of pancreatic α and β cells to regulate the secretion of glucagon and insulin, two hormones that play a pivotal role in the regulation of blood glucose levels. Overall, the major glucocorticoid effect on glucose homeostasis is to preserve plasma glucose for brain during stress, as transiently raising blood glucose is important to promote maximal brain function. In this chapter we will discuss the current understanding of the mechanisms underlying different aspects of glucocorticoid-regulated mammalian glucose homeostasis.
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45
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Cardaci S, Zheng L, MacKay G, van den Broek NJ, MacKenzie ED, Nixon C, Stevenson D, Tumanov S, Bulusu V, Kamphorst JJ, Vazquez A, Fleming S, Schiavi F, Kalna G, Blyth K, Strathdee D, Gottlieb E. Pyruvate carboxylation enables growth of SDH-deficient cells by supporting aspartate biosynthesis. Nat Cell Biol 2015; 17:1317-26. [PMID: 26302408 PMCID: PMC4591470 DOI: 10.1038/ncb3233] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 07/29/2015] [Indexed: 12/13/2022]
Abstract
Succinate dehydrogenase (SDH) is a heterotetrameric nuclear-encoded complex responsible for the oxidation of succinate to fumarate in the tricarboxylic acid cycle. Loss-of-function mutations in any of the SDH genes are associated with cancer formation. However, the impact of SDH loss on cell metabolism and the mechanisms enabling growth of SDH-defective cells are largely unknown. Here, we generated Sdhb-ablated kidney mouse cells and used comparative metabolomics and stable-isotope-labelling approaches to identify nutritional requirements and metabolic adaptations to SDH loss. We found that lack of SDH activity commits cells to consume extracellular pyruvate, which sustains Warburg-like bioenergetic features. We further demonstrated that pyruvate carboxylation diverts glucose-derived carbons into aspartate biosynthesis, thus sustaining cell growth. By identifying pyruvate carboxylase as essential for the proliferation and tumorigenic capacity of SDH-deficient cells, this study revealed a metabolic vulnerability for potential future treatment of SDH-associated malignancies.
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MESH Headings
- Animals
- Aspartic Acid/biosynthesis
- Carboxylic Acids/metabolism
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Cell Line, Transformed
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cells, Cultured
- Humans
- Immunoblotting
- Kidney/cytology
- Kidney/metabolism
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Male
- Metabolomics/methods
- Mice, 129 Strain
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Nude
- Pyruvate Carboxylase/metabolism
- Pyruvic Acid/metabolism
- RNA Interference
- Succinate Dehydrogenase/genetics
- Succinate Dehydrogenase/metabolism
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Affiliation(s)
- Simone Cardaci
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Liang Zheng
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Gillian MacKay
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | | | | | - Colin Nixon
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - David Stevenson
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Sergey Tumanov
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Vinay Bulusu
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Jurre J. Kamphorst
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Alexei Vazquez
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Stewart Fleming
- Department of Pathology, University of Dundee, Ninewells Hospital, Dundee, DD1 9SY, UK
| | - Francesca Schiavi
- Veneto Institute of Oncology IRCCS, Familial cancer clinic and oncoendocrinology, Via Gattamelata 64, 35128 Padova, Italy
| | - Gabriela Kalna
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Karen Blyth
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Douglas Strathdee
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
| | - Eyal Gottlieb
- Cancer Research UK, Beatson Institute, Switchback Rd, Glasgow, G61 1BD, UK
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46
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Nicolae A, Wahrheit J, Nonnenmacher Y, Weyler C, Heinzle E. Identification of active elementary flux modes in mitochondria using selectively permeabilized CHO cells. Metab Eng 2015; 32:95-105. [PMID: 26417715 DOI: 10.1016/j.ymben.2015.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 12/23/2022]
Abstract
Metabolic compartmentation is a key feature of mammalian cells. Mitochondria are the powerhouse of eukaryotic cells, responsible for respiration and the TCA cycle. We accessed the mitochondrial metabolism of the economically important Chinese hamster ovary (CHO) cells using selective permeabilization. We tested key substrates without and with addition of ADP. Based on quantified uptake and production rates, we could determine the contribution of different elementary flux modes to the metabolism of a substrate or substrate combination. ADP stimulated the uptake of most metabolites, directly by serving as substrate for the respiratory chain, thus removing the inhibitory effect of NADH, or as allosteric effector. Addition of ADP favored substrate metabolization to CO2 and did not enhance the production of other metabolites. The controlling effect of ADP was more pronounced when we supplied metabolites to the first part of the TCA cycle: pyruvate, citrate, α-ketoglutarate and glutamine. In the second part of the TCA cycle, the rates were primarily controlled by the concentrations of C4-dicarboxylates. Without ADP addition, the activity of the pyruvate carboxylase-malate dehydrogenase-malic enzyme cycle consumed the ATP produced by oxidative phosphorylation, preventing its accumulation and maintaining metabolic steady state conditions. Aspartate was taken up only in combination with pyruvate, whose uptake also increased, a fact explained by complex regulatory effects. Isocitrate dehydrogenase and α-ketoglutarate dehydrogenase were identified as the key regulators of the TCA cycle, confirming existent knowledge from other cells. We have shown that selectively permeabilized cells combined with elementary mode analysis allow in-depth studying of the mitochondrial metabolism and regulation.
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Affiliation(s)
- Averina Nicolae
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Judith Wahrheit
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Yannic Nonnenmacher
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Christian Weyler
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Elmar Heinzle
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany.
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Yang L, Lübeck M, Lübeck PS. Effects of heterologous expression of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase on organic acid production in Aspergillus carbonarius. J Ind Microbiol Biotechnol 2015; 42:1533-45. [PMID: 26403577 PMCID: PMC4607725 DOI: 10.1007/s10295-015-1688-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/11/2015] [Indexed: 11/25/2022]
Abstract
Aspergillus carbonarius has a potential as a cell factory for production of various organic acids. In this study, the organic acid profile of A. carbonarius was investigated under different cultivation conditions. Moreover, two heterologous genes, pepck and ppc, which encode phosphoenolpyruvate carboxykinase in Actinobacillus succinogenes and phosphoenolpyruvate carboxylase in Escherichia coli, were inserted individually and in combination in A. carbonarius to enhance the carbon flux toward the reductive TCA branch. Results of transcription analysis and measurement of enzyme activities of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase in the corresponding single and double transformants demonstrated that the two heterologous genes were successfully expressed in A. carbonarius. The production of citric acid increased in all the transformants in both glucose- and xylose-based media at pH higher than 3 but did not increase in the pH non-buffered cultivation compared with the wild type.
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Affiliation(s)
- Lei Yang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark.
| | - Mette Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark.
| | - Peter S Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark.
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48
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Choosangtong K, Sirithanakorn C, Adina-Zada A, Wallace JC, Jitrapakdee S, Attwood PV. Residues in the acetyl CoA binding site of pyruvate carboxylase involved in allosteric regulation. FEBS Lett 2015; 589:2073-9. [PMID: 26149215 DOI: 10.1016/j.febslet.2015.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
We have examined the roles of Asp1018, Glu1027, Arg469 and Asp471 in the allosteric domain of Rhizobium etli pyruvate carboxylase. Arg469 and Asp471 interact directly with the allosteric activator acetyl coenzyme A (acetyl CoA) and the R469S and R469K mutants showed increased enzymic activity in the presence and absence of acetyl CoA, whilst the D471A mutant exhibited no acetyl CoA-activation. E1027A, E1027R and D1018A mutants had increased activity in the absence of acetyl CoA, but not in its presence. These results suggest that most of these residues impose restrictions on the structure and/or dynamics of the enzyme to affect activity.
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Affiliation(s)
- Kamonman Choosangtong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Chaiyos Sirithanakorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Abdul Adina-Zada
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - John C Wallace
- School of Molecular and Biomedical Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Paul V Attwood
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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49
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Insights into Transcriptional Regulation of Hepatic Glucose Production. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 318:203-53. [DOI: 10.1016/bs.ircmb.2015.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Sureka K, Choi PH, Precit M, Delince M, Pensinger DA, Huynh TN, Jurado AR, Goo YA, Sadilek M, Iavarone AT, Sauer JD, Tong L, Woodward JJ. The cyclic dinucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function. Cell 2014; 158:1389-1401. [PMID: 25215494 DOI: 10.1016/j.cell.2014.07.046] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/09/2014] [Accepted: 07/29/2014] [Indexed: 12/13/2022]
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a broadly conserved second messenger required for bacterial growth and infection. However, the molecular mechanisms of c-di-AMP signaling are still poorly understood. Using a chemical proteomics screen for c-di-AMP-interacting proteins in the pathogen Listeria monocytogenes, we identified several broadly conserved protein receptors, including the central metabolic enzyme pyruvate carboxylase (LmPC). Biochemical and crystallographic studies of the LmPC-c-di-AMP interaction revealed a previously unrecognized allosteric regulatory site 25 Å from the active site. Mutations in this site disrupted c-di-AMP binding and affected catalytic activity of LmPC as well as PC from pathogenic Enterococcus faecalis. C-di-AMP depletion resulted in altered metabolic activity in L. monocytogenes. Correction of this metabolic imbalance rescued bacterial growth, reduced bacterial lysis, and resulted in enhanced bacterial burdens during infection. These findings greatly expand the c-di-AMP signaling repertoire and reveal a central metabolic regulatory role for a cyclic dinucleotide.
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Affiliation(s)
- Kamakshi Sureka
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Philip H Choi
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Mimi Precit
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Matthieu Delince
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel A Pensinger
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - TuAnh Ngoc Huynh
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Ashley R Jurado
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21201, USA
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, CA 94720, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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