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Nowosad A, Besson A. Lysosomes at the Crossroads of Cell Metabolism, Cell Cycle, and Stemness. Int J Mol Sci 2022; 23:ijms23042290. [PMID: 35216401 PMCID: PMC8879101 DOI: 10.3390/ijms23042290] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
Initially described as lytic bodies due to their degradative and recycling functions, lysosomes play a critical role in metabolic adaptation to nutrient availability. More recently, the contribution of lysosomal proteins to cell signaling has been established, and lysosomes have emerged as signaling hubs that regulate diverse cellular processes, including cell proliferation and cell fate. Deciphering these signaling pathways has revealed an extensive crosstalk between the lysosomal and cell cycle machineries that is only beginning to be understood. Recent studies also indicate that a number of lysosomal proteins are involved in the regulation of embryonic and adult stem cell fate and identity. In this review, we will focus on the role of the lysosome as a signaling platform with an emphasis on its function in integrating nutrient sensing with proliferation and cell cycle progression, as well as in stemness-related features, such as self-renewal and quiescence.
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Affiliation(s)
- Ada Nowosad
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France;
- Department of Oncology, KULeuven, Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France;
- Correspondence: ; Tel.: +33-561558486
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Piedrafita G, Varma SJ, Castro C, Messner CB, Szyrwiel L, Griffin JL, Ralser M. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure. PLoS Biol 2021; 19:e3001468. [PMID: 34860829 PMCID: PMC8673631 DOI: 10.1371/journal.pbio.3001468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 12/15/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken–egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a “metabolism first” theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network. The evolutionary origins of metabolism are largely unknown. This study shows that the prebiotically available proteinogenic amino acid cysteine can promote the metabolism-like rate-limiting formation of ribose-5-phosphate, suggesting that early metabolic pathways could have emerged thought the stepwise enzymatization of non-enzymatic reaction sequences.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Sreejith J. Varma
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Castro
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Christoph B. Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- The Rowett Institute, The University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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Nowacka-Chmielewska MM, Liśkiewicz D, Grabowska K, Liśkiewicz A, Marczak Ł, Wojakowska A, Pondel N, Grabowski M, Barski JJ, Małecki A. Effects of Simultaneous Exposure to a Western Diet and Wheel-Running Training on Brain Energy Metabolism in Female Rats. Nutrients 2021; 13:nu13124242. [PMID: 34959794 PMCID: PMC8707360 DOI: 10.3390/nu13124242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND In the pathogenesis of central nervous system disorders (e.g., neurodegenerative), an important role is attributed to an unhealthy lifestyle affecting brain energy metabolism. Physical activity in the prevention and treatment of lifestyle-related diseases is getting increasing attention. METHODS We performed a series of assessments in adult female Long Evans rats subjected to 6 weeks of Western diet feeding and wheel-running training. A control group of lean rats was fed with a standard diet. In all experimental groups, we measured physiological parameters (animal weights, body composition, serum metabolic parameters). We assessed the impact of simultaneous exposure to a Western diet and wheel-running on the cerebrocortical protein expression (global proteomic profiling), and in the second part of the experiment, we measured the cortical levels of protein related to brain metabolism (Western blot). RESULTS Western diet led to an obese phenotype and induced changes in the serum metabolic parameters. Wheel-running did not reduce animal weights or fat mass but significantly decreased serum glucose level. The global proteome analysis revealed that the altered proteins were functionally annotated as they were involved mostly in metabolic pathways. Western blot analysis showed the downregulation of the mitochondrial protein-Acyl-CoA dehydrogenase family member 9, hexokinase 1 (HK1)-enzyme involved in principal glucose metabolism pathways and monocarboxylate transporter 2 (MCT2). Wheel-running reversed this decline in the cortical levels of HK1 and MCT2. CONCLUSION The cerebrocortical proteome is affected by a combination of physical activity and Western diet in female rats. An analysis of the cortical proteins involved in brain energy metabolism provides a valuable basis for the deeper investigation of changes in the brain structure and function induced by simultaneous exposure to a Western diet and physical activity.
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Affiliation(s)
- Marta Maria Nowacka-Chmielewska
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, Academy of Physical Education, 40-065 Katowice, Poland; (D.L.); (N.P.); (A.M.)
- Correspondence: ; Tel.: +48-509-505-836
| | - Daniela Liśkiewicz
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, Academy of Physical Education, 40-065 Katowice, Poland; (D.L.); (N.P.); (A.M.)
| | - Konstancja Grabowska
- Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland; (K.G.); (M.G.); (J.J.B.)
| | - Arkadiusz Liśkiewicz
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland; (Ł.M.); (A.W.)
| | - Anna Wojakowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland; (Ł.M.); (A.W.)
| | - Natalia Pondel
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, Academy of Physical Education, 40-065 Katowice, Poland; (D.L.); (N.P.); (A.M.)
| | - Mateusz Grabowski
- Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland; (K.G.); (M.G.); (J.J.B.)
| | - Jarosław Jerzy Barski
- Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland; (K.G.); (M.G.); (J.J.B.)
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Andrzej Małecki
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, Academy of Physical Education, 40-065 Katowice, Poland; (D.L.); (N.P.); (A.M.)
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Jeong J, Lee J, Kim JH, Lim C. Metabolic flux from the Krebs cycle to glutamate transmission tunes a neural brake on seizure onset. PLoS Genet 2021; 17:e1009871. [PMID: 34714823 PMCID: PMC8555787 DOI: 10.1371/journal.pgen.1009871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/11/2021] [Indexed: 01/18/2023] Open
Abstract
Kohlschütter-Tönz syndrome (KTS) manifests as neurological dysfunctions, including early-onset seizures. Mutations in the citrate transporter SLC13A5 are associated with KTS, yet their underlying mechanisms remain elusive. Here, we report that a Drosophila SLC13A5 homolog, I'm not dead yet (Indy), constitutes a neurometabolic pathway that suppresses seizure. Loss of Indy function in glutamatergic neurons caused "bang-induced" seizure-like behaviors. In fact, glutamate biosynthesis from the citric acid cycle was limiting in Indy mutants for seizure-suppressing glutamate transmission. Oral administration of the rate-limiting α-ketoglutarate in the metabolic pathway rescued low glutamate levels in Indy mutants and ameliorated their seizure-like behaviors. This metabolic control of the seizure susceptibility was mapped to a pair of glutamatergic neurons, reversible by optogenetic controls of their activity, and further relayed onto fan-shaped body neurons via the ionotropic glutamate receptors. Accordingly, our findings reveal a micro-circuit that links neural metabolism to seizure, providing important clues to KTS-associated neurodevelopmental deficits.
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Affiliation(s)
- Jiwon Jeong
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Ji-hyung Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- * E-mail:
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Barmpatsalou V, Dubbelboer IR, Rodler A, Jacobson M, Karlsson E, Pedersen BL, Bergström CAS. Physiological properties, composition and structural profiling of porcine gastrointestinal mucus. Eur J Pharm Biopharm 2021; 169:156-167. [PMID: 34687897 DOI: 10.1016/j.ejpb.2021.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022]
Abstract
The gastrointestinal mucus is a hydrogel that lines the luminal side of the gastrointestinal epithelium, offering barrier protection from pathogens and lubrication of the intraluminal contents. These barrier properties likewise affect nutrients and drugs that need to penetrate the mucus to reach the epithelium prior to absorption. In order to assess the potential impact of the mucus on drug absorption, we need information about the nature of the gastrointestinal mucus. Today, most of the relevant available literature is mainly derived from rodent studies. In this work, we used a larger animal species, the pig model, to characterize the mucus throughout the length of the gastrointestinal tract. This is the first report of the physiological properties (physical appearance, pH and water content), composition (protein, lipid and metabolite content) and structural profiling (rheology and gel network) of the porcine gastrointestinal mucus. These findings allow for direct comparisons between the characteristics of mucus from various segments and can be further utilized to improve our understanding of the role of the mucus on region dependent drug absorption. Additionally, the present work is expected to contribute to the assessment of the porcine model as a preclinical species in the drug development process.
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Affiliation(s)
- Vicky Barmpatsalou
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, SE-751 23, Uppsala, Sweden
| | - Ilse R Dubbelboer
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, SE-751 23, Uppsala, Sweden
| | - Agnes Rodler
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, SE-751 23, Uppsala, Sweden; The Swedish Drug Delivery Center, Department of Medicinal Chemistry, Uppsala University, BMC P.O. Box 574, SE-751 23, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences, Faculty of Veterinary Medicine and Animal Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, SE-750 07, Uppsala, Sweden
| | - Eva Karlsson
- Oral Product Development, Pharmaceutical Technology & Development Operations, AstraZeneca, Gothenburg, Sweden
| | - Betty Lomstein Pedersen
- Product Development & Drug Delivery, Global Pharmaceutical R&D, Ferring Pharmaceuticals A/S, Kay Fiskers Plads 11, DK-2300, Copenhagen, Denmark
| | - Christel A S Bergström
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, SE-751 23, Uppsala, Sweden.
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Walke D, Schallert K, Ramesh P, Benndorf D, Lange E, Reichl U, Heyer R. MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. Int J Mol Sci 2021; 22:ijms222010992. [PMID: 34681649 PMCID: PMC8539661 DOI: 10.3390/ijms222010992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versality of microbial metabolism and a still-increasing number of newly biological pathways, linkage to standard pathway maps such as the KEGG central carbon metabolism is often problematic. We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called 'Pathway-Creator' and 'Pathway-Calculator'. The 'Pathway-Creator' enables an easy set-up of user-defined pathways with specific taxonomic constraints. The 'Pathway-Calculator' automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. The MPA_Pathway_Tool is implemented in Java and ReactJS.
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Affiliation(s)
- Daniel Walke
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Correspondence: (D.W.); (R.H.)
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
| | - Prasanna Ramesh
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Microbiology, Bernburger Straße 55, 06354 Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Emanuel Lange
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Correspondence: (D.W.); (R.H.)
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Carnero EA, Bock CP, Distefano G, Corbin KD, Stephens NA, Pratley RE, Smith SR, Goodpaster BH, Sparks LM. Twenty-four hour assessments of substrate oxidation reveal differences in metabolic flexibility in type 2 diabetes that are improved with aerobic training. Diabetologia 2021; 64:2322-2333. [PMID: 34402932 DOI: 10.1007/s00125-021-05535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022]
Abstract
AIMS/HYPOTHESIS The aim of this study was to assess metabolic flexibility (MetFlex) in participants with type 2 diabetes within the physiologically relevant conditions of sleeping, the post-absorptive (fasting) state and during meals using 24 h whole-room indirect calorimetry (WRIC) and to determine the impact of aerobic training on these novel features of MetFlex. METHODS Normal-weight, active healthy individuals (active; n = 9), obese individuals without type 2 diabetes (ND; n = 9) and obese individuals with type 2 diabetes (n = 23) completed baseline metabolic assessments. The type 2 diabetes group underwent a 10 week supervised aerobic training intervention and repeated the metabolic assessments. MetFlex was assessed by indirect calorimetry in response to insulin infusion and during a 24 h period in a whole-room indirect calorimeter. Indices of MetFlex evaluated by WRIC included mean RQ and RQ kinetic responses after ingesting a standard high-carbohydrate breakfast (RQBF) and sleep RQ (RQsleep). Muscle mitochondrial energetics were assessed in the vastus lateralis muscle in vivo and ex vivo using 31P-magnetic resonance spectroscopy and high-resolution respirometry, respectively. RESULTS The three groups had significantly different RQsleep values (active 0.823 ± 0.04, ND 0.860 ± 0.01, type 2 diabetes 0.842 ± 0.03; p < 0.05). The active group had significantly faster RQBF and more stable RQsleep responses than the ND and type 2 diabetes groups, as demonstrated by steeper and flatter slopes, respectively. Following the training intervention, the type 2 diabetes group displayed significantly increased RQBF slope. Several indices of RQ kinetics had significant associations with in vivo and ex vivo muscle mitochondrial capacities. CONCLUSIONS/INTERPRETATION Twenty-four hour WRIC revealed that physiological RQ responses exemplify differences in MetFlex across a spectrum of metabolic health and correlated with skeletal muscle mitochondrial energetics. Defects in certain features of MetFlex were improved with aerobic training, emphasising the need to assess multiple aspects of MetFlex and disentangle insulin resistance from MetFlex in type 2 diabetes. TRIAL REGISTRATION ClinicalTrials.gov NCT01911104. FUNDING This study was funded by the ADA (grant no. 7-13-JF-53).
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Affiliation(s)
- Elvis A Carnero
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | | | | | - Karen D Corbin
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | | | | | - Steven R Smith
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | | | - Lauren M Sparks
- Translational Research Institute, AdventHealth, Orlando, FL, USA.
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Pareek V, Sha Z, He J, Wingreen NS, Benkovic SJ. Metabolic channeling: predictions, deductions, and evidence. Mol Cell 2021; 81:3775-3785. [PMID: 34547238 PMCID: PMC8485759 DOI: 10.1016/j.molcel.2021.08.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/19/2022]
Abstract
With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.
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Affiliation(s)
- Vidhi Pareek
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhou Sha
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Jingxuan He
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ned S Wingreen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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Shin JH, Andersen AJC, Achterberg P, Olsson L. Exploring functionality of the reverse β-oxidation pathway in Corynebacterium glutamicum for production of adipic acid. Microb Cell Fact 2021; 20:155. [PMID: 34348702 PMCID: PMC8336102 DOI: 10.1186/s12934-021-01647-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/29/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Adipic acid, a six-carbon platform chemical mainly used in nylon production, can be produced via reverse β-oxidation in microbial systems. The advantages posed by Corynebacterium glutamicum as a model cell factory for implementing the pathway include: (1) availability of genetic tools, (2) excretion of succinate and acetate when the TCA cycle becomes overflown, (3) initiation of biosynthesis with succinyl-CoA and acetyl-CoA, and (4) established succinic acid production. Here, we implemented the reverse β-oxidation pathway in C. glutamicum and assessed its functionality for adipic acid biosynthesis. RESULTS To obtain a non-decarboxylative condensation product of acetyl-CoA and succinyl-CoA, and to subsequently remove CoA from the condensation product, we introduced heterologous 3-oxoadipyl-CoA thiolase and acyl-CoA thioesterase into C. glutamicum. No 3-oxoadipic acid could be detected in the cultivation broth, possibly due to its endogenous catabolism. To successfully biosynthesize and secrete 3-hydroxyadipic acid, 3-hydroxyadipyl-CoA dehydrogenase was introduced. Addition of 2,3-dehydroadipyl-CoA hydratase led to biosynthesis and excretion of trans-2-hexenedioic acid. Finally, trans-2-enoyl-CoA reductase was inserted to yield 37 µg/L of adipic acid. CONCLUSIONS In the present study, we engineered the reverse β-oxidation pathway in C. glutamicum and assessed its potential for producing adipic acid from glucose as starting material. The presence of adipic acid, albeit small amount, in the cultivation broth indicated that the synthetic genes were expressed and functional. Moreover, 2,3-dehydroadipyl-CoA hydratase and β-ketoadipyl-CoA thiolase were determined as potential target for further improvement of the pathway.
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Affiliation(s)
- Jae Ho Shin
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Puck Achterberg
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.
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Yuan H, Wang X, Lin TY, Kim J, Liu WT. Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Sci Rep 2021; 11:15140. [PMID: 34302023 PMCID: PMC8302695 DOI: 10.1038/s41598-021-94628-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica's EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.
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Affiliation(s)
- Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
| | - Xuehao Wang
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
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11
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Chessa M, Panebianco M, Corbu S, Lussu M, Dessì A, Pintus R, Cesare Marincola F, Fanos V. Urinary Metabolomics Study of Patients with Bicuspid Aortic Valve Disease. Molecules 2021; 26:molecules26144220. [PMID: 34299495 PMCID: PMC8304733 DOI: 10.3390/molecules26144220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect responsible for valvular and aortic complications in affected patients. Causes and mechanisms of this pathology are still elusive and thus the lack of early detection biomarkers leads to challenges in its diagnosis and prevention of associated cardiovascular anomalies. The aim of this study was to explore the potential use of urine Nuclear Magnetic Resonance (NMR) metabolomics to evaluate a molecular fingerprint of BAV. Both multivariate and univariate statistical analyses were performed to compare the urinary metabolome of 20 patients with BAV with that of 24 matched controls. Orthogonal partial least squared discriminant analysis (OPLS-DA) showed statistically significant discrimination between cases and controls, suggesting seven metabolites (3-hydroxybutyrate, alanine, betaine, creatine, glycine, hippurate, and taurine) as potential biomarkers. Among these, glycine, hippurate and taurine individually displayed medium sensitivity and specificity by receiver operating characteristic (ROC) analysis. Pathway analysis indicated two metabolic pathways likely perturbed in BAV subjects. Possible contributions of gut microbiota activity and energy imbalance are also discussed. These results constitute encouraging preliminary findings in favor of the use of urine-based metabolomics for early diagnosis of BAV.
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Affiliation(s)
- Massimo Chessa
- Pediatric and Adult Congenital IRCCS, Policlinico San Donato, I-20097 San Donato Milanese, MI, Italy; (M.C.); (M.P.)
| | - Mario Panebianco
- Pediatric and Adult Congenital IRCCS, Policlinico San Donato, I-20097 San Donato Milanese, MI, Italy; (M.C.); (M.P.)
| | - Sara Corbu
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria, University of Cagliari, S.P. n° 8, Km 0.700, I-09042 Monserrato, CA, Italy; (S.C.); (M.L.); (A.D.); (R.P.); (V.F.)
| | - Milena Lussu
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria, University of Cagliari, S.P. n° 8, Km 0.700, I-09042 Monserrato, CA, Italy; (S.C.); (M.L.); (A.D.); (R.P.); (V.F.)
| | - Angelica Dessì
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria, University of Cagliari, S.P. n° 8, Km 0.700, I-09042 Monserrato, CA, Italy; (S.C.); (M.L.); (A.D.); (R.P.); (V.F.)
| | - Roberta Pintus
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria, University of Cagliari, S.P. n° 8, Km 0.700, I-09042 Monserrato, CA, Italy; (S.C.); (M.L.); (A.D.); (R.P.); (V.F.)
| | - Flaminia Cesare Marincola
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, CA, Italy
- Correspondence: ; Tel.: +39-070-675-4389
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria, University of Cagliari, S.P. n° 8, Km 0.700, I-09042 Monserrato, CA, Italy; (S.C.); (M.L.); (A.D.); (R.P.); (V.F.)
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12
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Xiao C, Rossignol F, Vaz FM, Ferreira CR. Inherited disorders of complex lipid metabolism: A clinical review. J Inherit Metab Dis 2021; 44:809-825. [PMID: 33594685 DOI: 10.1002/jimd.12369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Over 80 human diseases have been attributed to defects in complex lipid metabolism. A majority of them have been reported recently in the setting of rapid advances in genomic technology and their increased use in clinical settings. Lipids are ubiquitous in human biology and play roles in many cellular and intercellular processes. While inborn errors in lipid metabolism can affect every organ system with many examples of genetic heterogeneity and pleiotropy, the clinical manifestations of many of these disorders can be explained based on the disruption of the metabolic pathway involved. In this review, we will discuss the physiological function of major pathways in complex lipid metabolism, including nonlysosomal sphingolipid metabolism, acylceramide metabolism, de novo phospholipid synthesis, phospholipid remodeling, phosphatidylinositol metabolism, mitochondrial cardiolipin synthesis and remodeling, and ether lipid metabolism as well as common clinical phenotypes associated with each.
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Affiliation(s)
- Changrui Xiao
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Rossignol
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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13
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Xu X, Legay S, Sergeant K, Zorzan S, Leclercq CC, Charton S, Giarola V, Liu X, Challabathula D, Renaut J, Hausman JF, Bartels D, Guerriero G. Molecular insights into plant desiccation tolerance: transcriptomics, proteomics and targeted metabolite profiling in Craterostigma plantagineum. Plant J 2021; 107:377-398. [PMID: 33901322 PMCID: PMC8453721 DOI: 10.1111/tpj.15294] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/05/2021] [Accepted: 04/19/2021] [Indexed: 05/31/2023]
Abstract
The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long-term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and targeted metabolite profiling was carried out on leaves collected from different stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 39 metabolites were differentially abundant across the different sampling points. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post-transcriptional modification in metabolic reprogramming to prepare plants for desiccation and recovery. The integrative analysis of all three data sets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of precise changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. The maintenance of cyclic electron flow and photorespiration, and the switch from C3 to crassulacean acid metabolism photosynthesis, may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. Transcripts with a delayed translation, ATP-independent bypasses, alternative respiratory pathway and 4-aminobutyric acid shunt may all play a role in energy management, together conferring bioenergetic advantages to meet energy demands upon rehydration. This study provides a high-resolution map of the changes occurring in primary metabolism during dehydration and rehydration and enriches our understanding of the molecular mechanisms underpinning plant desiccation tolerance. The data sets provided here will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.
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Affiliation(s)
- Xuan Xu
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Sylvain Legay
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Kjell Sergeant
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Simone Zorzan
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Céline C Leclercq
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Sophie Charton
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Xun Liu
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Dinakar Challabathula
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Jenny Renaut
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Jean-Francois Hausman
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Gea Guerriero
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
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14
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Lyu Y, Promislow DEL, Pletcher SD. Serotonin signaling modulates aging-associated metabolic network integrity in response to nutrient choice in Drosophila melanogaster. Commun Biol 2021; 4:740. [PMID: 34131274 PMCID: PMC8206115 DOI: 10.1038/s42003-021-02260-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/14/2021] [Indexed: 11/21/2022] Open
Abstract
Aging arises from complex interactions among multiple biochemical products. Systems-level analyses of biological networks may provide insights into the causes and consequences of aging that evade single-gene studies. We have previously found that dietary choice is sufficient to modulate aging in the vinegar fly, Drosophila melanogaster. Here we show that nutrient choice influenced several measures of metabolic network integrity, including connectivity, community structure, and robustness. Importantly, these effects are mediated by serotonin signaling, as a mutation in serotonin receptor 2A (5-HT2A) eliminated the effects of nutrient choice. Changes in network structure were associated with organism resilience and increased susceptibility to genetic perturbation. Our data suggest that the behavioral or perceptual consequences of exposure to individual macronutrients, involving serotonin signaling through 5-HT2A, qualitatively change the state of metabolic networks throughout the organism from one that is highly connected and robust to one that is fragmented, fragile, and vulnerable to perturbations.
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Affiliation(s)
- Yang Lyu
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel E L Promislow
- Department of Lab Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI, USA.
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15
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Abstract
This Review focuses on the mechanistic evidence for a link between obesity, dysregulated cellular metabolism and breast cancer. Strong evidence now links obesity with the development of 13 different types of cancer, including oestrogen receptor-positive breast cancer in postmenopausal women. A number of local and systemic changes are hypothesized to support this relationship, including increased circulating levels of insulin and glucose as well as adipose tissue-derived oestrogens, adipokines and inflammatory mediators. Metabolic pathways of energy production and utilization are dysregulated in tumour cells and this dysregulation is a newly accepted hallmark of cancer. Dysregulated metabolism is also hypothesized to be a feature of non-neoplastic cells in the tumour microenvironment. Obesity-associated factors regulate metabolic pathways in both breast cancer cells and cells in the breast microenvironment, which provides a molecular link between obesity and breast cancer. Consequently, interventions that target these pathways might provide a benefit in postmenopausal women and individuals with obesity, a population at high risk of breast cancer.
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Affiliation(s)
- Kristy A Brown
- Sandra and Edward Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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16
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Ling Q, Sadali NM, Soufi Z, Zhou Y, Huang B, Zeng Y, Rodriguez-Concepcion M, Jarvis RP. The chloroplast-associated protein degradation pathway controls chromoplast development and fruit ripening in tomato. Nat Plants 2021; 7:655-666. [PMID: 34007040 DOI: 10.1038/s41477-021-00916-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The maturation of green fleshy fruit to become colourful and flavoursome is an important strategy for plant reproduction and dispersal. In tomato (Solanum lycopersicum) and many other species, fruit ripening is intimately linked to the biogenesis of chromoplasts, the plastids that are abundant in ripe fruit and specialized for the accumulation of carotenoid pigments. Chromoplasts develop from pre-existing chloroplasts in the fruit, but the mechanisms underlying this transition are poorly understood. Here, we reveal a role for the chloroplast-associated protein degradation (CHLORAD) proteolytic pathway in chromoplast differentiation. Knockdown of the plastid ubiquitin E3 ligase SP1, or its homologue SPL2, delays tomato fruit ripening, whereas overexpression of SP1 accelerates ripening, as judged by colour changes. We demonstrate that SP1 triggers broader effects on fruit ripening, including fruit softening, and gene expression and metabolism changes, by promoting the chloroplast-to-chromoplast transition. Moreover, we show that tomato SP1 and SPL2 regulate leaf senescence, revealing conserved functions of CHLORAD in plants. We conclude that SP1 homologues control plastid transitions during fruit ripening and leaf senescence by enabling reconfiguration of the plastid protein import machinery to effect proteome reorganization. The work highlights the critical role of chromoplasts in fruit ripening, and provides a theoretical basis for engineering crop improvements.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Najiah Mohd Sadali
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ziad Soufi
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yuan Zhou
- Department of Plant Sciences, University of Oxford, Oxford, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Binquan Huang
- Department of Plant Sciences, University of Oxford, Oxford, UK
- School of Agriculture, Yunnan University, Kunming, China
| | - Yunliu Zeng
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Manuel Rodriguez-Concepcion
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, Spain
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford, UK.
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17
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Domenzain I, Li F, Kerkhoven EJ, Siewers V. Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. FEMS Yeast Res 2021; 21:foab002. [PMID: 33428734 PMCID: PMC7943257 DOI: 10.1093/femsyr/foab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public.
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Affiliation(s)
- Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Feiran Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
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18
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Abstract
The ability to ward off pathogens with minimal damage to the host determines the immune system's robustness. Multiple factors, including pathogen processing, identification, secretion of mediator and effector molecules, and immune cell proliferation and differentiation into various subsets, constitute the success of mounting an effective immune response. Cellular metabolism controls all of these intricate processes. Cells utilize diverse fuel sources and switch back and forth between different metabolic pathways depending on their energy needs. The three most critical metabolic pathways on which immune cells depend to meet their energy needs are oxidative metabolism, glycolysis, and glutaminolysis. Dynamic switching between these metabolic pathways is needed for optimal function of the immune cells. Moreover, switching between these metabolic pathways needs to be tightly regulated to achieve the best results. Immune cells depend on the Warburg effect for their growth, proliferation, secretory, and effector functions. Here, we hypothesize that the sirtuin, SIRT6, could be a negative regulator of the Warburg effect. We also postulate that SIRT6 could act as a master regulator of immune cell metabolism and function by regulating critical signaling pathways.
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Affiliation(s)
- Vinodkumar B Pillai
- Department of Surgery (Division of Cardiothoracic Surgery), Pritzker School of Medicine, Basic Science Division, University of Chicago, Chicago, Illinois
| | - Mahesh P Gupta
- Department of Surgery (Division of Cardiothoracic Surgery), Pritzker School of Medicine, Basic Science Division, University of Chicago, Chicago, Illinois
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19
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Ten Have GAM, Jansen L, Schooneman MG, Engelen MPKJ, Deutz NEP. Metabolic flux analysis of branched-chain amino and keto acids (BCAA, BCKA) and β-hydroxy β-methylbutyric acid across multiple organs in the pig. Am J Physiol Endocrinol Metab 2021; 320:E629-E640. [PMID: 33522397 DOI: 10.1152/ajpendo.00384.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Branched-chain amino acids (BCAA) and their metabolites the branched-chain keto acids (BCKA) and β-hydroxy β-methylbutyric acid (HMB) are involved in the regulation of key signaling pathways in the anabolic response to a meal. However, their (inter)organ kinetics remain unclear. Therefore, branched-chain amino acids (BCAA) [leucine (Leu), valine (Val), isoleucine (Ile)], BCKA [α-ketoisocaproic acid (KIC), 3-methyl-2-oxovaleric acid (KMV), 2-oxoisovalerate (KIV)], and HMB across organ net fluxes were measured. In multi-catheterized pigs (n = 12, ±25 kg), net fluxes across liver, portal drained viscera (PDV), kidney, and hindquarter (HQ, muscle compartment) were measured before and 4 h after bolus feeding of a complete meal (30% daily intake) in conscious state. Arterial and venous plasma were collected and concentrations were measured by LC- or GC-MS/MS. Data are expressed as mean [95% CI] and significance (P < 0.05) from zero by the Wilcoxon Signed Rank Test. In the postabsorptive state (in nmol/kg body wt/min), the kidney takes up HMB (3.2[1.3,5.0]) . BCKA is taken up by PDV (144[13,216]) but no release by other organs. In the postprandial state, the total net fluxes over 4 h (in µmol/kg body wt/4 h) showed a release of all BCKA by HQ (46.2[34.2,58.2]), KIC by the PDV (12.3[7.0,17.6]), and KIV by the kidney (10.0[2.3,178]). HMB was released by the liver (0.76[0.49,1.0]). All BCKA were taken up by the liver (200[133,268]). Substantial differences are present in (inter)organ metabolism and transport among the BCAA and its metabolites BCKA and HMB. The presented data in a translation animal model are relevant for the future development of optimized clinical nutrition.NEW & NOTEWORTHY Branched-chain amino acids (BCAA) and their metabolites the branched-chain keto acids (BCKA) and β-hydroxy β-methylbutyric acid (HMB) are involved in the regulation of key signaling pathways in the anabolic response to a meal. Substantial differences are present in (inter)organ metabolism and transport among the BCAA and its metabolites BCKA and HMB. The presented data in a translation animal model are relevant for the future development of optimized clinical nutrition.
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Affiliation(s)
- Gabriella A M Ten Have
- Center for Translational Research in Aging & Longevity, Department of Health & Kinesiology, Texas A&M University. College Station, Texas
| | - Lisa Jansen
- Center for Translational Research in Aging & Longevity, Department of Health & Kinesiology, Texas A&M University. College Station, Texas
| | - Marieke G Schooneman
- Department of Endocrinology and Metabolism, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marielle P K J Engelen
- Center for Translational Research in Aging & Longevity, Department of Health & Kinesiology, Texas A&M University. College Station, Texas
| | - Nicolaas E P Deutz
- Center for Translational Research in Aging & Longevity, Department of Health & Kinesiology, Texas A&M University. College Station, Texas
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20
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Fu S, Xue S, Chen J, Shang S, Xiao H, Zang Y, Tang X. Effects of Different Short-Term UV-B Radiation Intensities on Metabolic Characteristics of Porphyra haitanensis. Int J Mol Sci 2021; 22:ijms22042180. [PMID: 33671697 PMCID: PMC7927003 DOI: 10.3390/ijms22042180] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/03/2022] Open
Abstract
The effects of ultraviolet (UV) radiation, particularly UV-B on algae, have become an important issue as human-caused depletion of the protecting ozone layer has been reported. In this study, the effects of different short-term UV-B radiation on the growth, physiology, and metabolism of Porphyra haitanensis were examined. The growth of P. haitanensis decreased, and the bleaching phenomenon occurred in the thalli. The contents of total amino acids, soluble sugar, total protein, and mycosporine-like amino acids (MAAs) increased under different UV-B radiation intensities. The metabolic profiles of P. haitanensis differed between the control and UV-B radiation-treated groups. Most of the differential metabolites in P. haitanensis were significantly upregulated under UV-B exposure. Short-term enhanced UV-B irradiation significantly affected amino acid metabolism, carbohydrate metabolism, glutathione metabolism, and phenylpropane biosynthesis. The contents of phenylalanine, tyrosine, threonine, and serine were increased, suggesting that amino acid metabolism can promote the synthesis of UV-absorbing substances (such as phenols and MAAs) by providing precursor substances. The contents of sucrose, D-glucose-6-phosphate, and beta-D-fructose-6-phosphate were increased, suggesting that carbohydrate metabolism contributes to maintain energy supply for metabolic activity in response to UV-B exposure. Meanwhile, dehydroascorbic acid (DHA) was also significantly upregulated, denoting effective activation of the antioxidant system. To some extent, these results provide metabolic insights into the adaptive response mechanism of P. haitanensis to short-term enhanced UV-B radiation.
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Affiliation(s)
- Shimei Fu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
| | - Song Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou 256600, China;
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266000, China
- Correspondence: (Y.Z.); (X.T.)
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Correspondence: (Y.Z.); (X.T.)
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21
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Rodríguez-Mier P, Poupin N, de Blasio C, Le Cam L, Jourdan F. DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. PLoS Comput Biol 2021; 17:e1008730. [PMID: 33571201 PMCID: PMC7904180 DOI: 10.1371/journal.pcbi.1008730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/24/2021] [Accepted: 01/21/2021] [Indexed: 11/18/2022] Open
Abstract
The correct identification of metabolic activity in tissues or cells under different conditions can be extremely elusive due to mechanisms such as post-transcriptional modification of enzymes or different rates in protein degradation, making difficult to perform predictions on the basis of gene expression alone. Context-specific metabolic network reconstruction can overcome some of these limitations by leveraging the integration of multi-omics data into genome-scale metabolic networks (GSMN). Using the experimental information, context-specific models are reconstructed by extracting from the generic GSMN the sub-network most consistent with the data, subject to biochemical constraints. One advantage is that these context-specific models have more predictive power since they are tailored to the specific tissue, cell or condition, containing only the reactions predicted to be active in such context. However, an important limitation is that there are usually many different sub-networks that optimally fit the experimental data. This set of optimal networks represent alternative explanations of the possible metabolic state. Ignoring the set of possible solutions reduces the ability to obtain relevant information about the metabolism and may bias the interpretation of the true metabolic states. In this work we formalize the problem of enumerating optimal metabolic networks and we introduce DEXOM, an unified approach for diversity-based enumeration of context-specific metabolic networks. We developed different strategies for this purpose and we performed an exhaustive analysis using simulated and real data. In order to analyze the extent to which these results are biologically meaningful, we used the alternative solutions obtained with the different methods to measure: 1) the improvement of in silico predictions of essential genes in Saccharomyces cerevisiae using ensembles of metabolic network; and 2) the detection of alternative enriched pathways in different human cancer cell lines. We also provide DEXOM as an open-source library compatible with COBRA Toolbox 3.0, available at https://github.com/MetExplore/dexom.
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Affiliation(s)
- Pablo Rodríguez-Mier
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Carlo de Blasio
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
- Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Laurent Le Cam
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
- Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- * E-mail:
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Abstract
The pituitary is a master endocrine gland that developed early in vertebrate evolution and therefore exists in all modern vertebrate classes. The last decade has transformed our view of this key organ. Traditionally, the pituitary has been viewed as a randomly organized collection of cells that respond to hypothalamic stimuli by secreting their content. However, recent studies have established that pituitary cells are organized in tightly wired large-scale networks that communicate with each other in both homo and heterotypic manners, allowing the gland to quickly adapt to changing physiological demands. These networks functionally decode and integrate the hypothalamic and systemic stimuli and serve to optimize the pituitary output into the generation of physiologically meaningful hormone pulses. The development of 3D imaging methods and transgenic models have allowed us to expand the research of functional pituitary networks into several vertebrate classes. Here we review the establishment of pituitary cell networks throughout vertebrate evolution and highlight the main perspectives and future directions needed to decipher the way by which pituitary networks serve to generate hormone pulses in vertebrates.
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Affiliation(s)
- Yorgui Santiago-Andres
- Laboratorio de Neuroendocrinología Comparada, Departamento de Ecología y Recursos Naturales, Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Matan Golan
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Rishon Lezion, Israel
| | - Tatiana Fiordelisio
- Laboratorio de Neuroendocrinología Comparada, Departamento de Ecología y Recursos Naturales, Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
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Diboun I, Al-Mansoori L, Al-Jaber H, Albagha O, Elrayess MA. Metabolomics of Lean/Overweight Insulin-Resistant Females Reveals Alterations in Steroids and Fatty Acids. J Clin Endocrinol Metab 2021; 106:e638-e649. [PMID: 33053159 DOI: 10.1210/clinem/dgaa732] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/08/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND The global diabetes epidemic is largely attributed to obesity-triggered metabolic syndrome. However, the impact of insulin resistance (IR) prior to obesity on the high prevalence of diabetes and the molecular mediators remain largely unknown. This study aims to compare the metabolic profiling of apparently healthy lean/overweight participants with IR and insulin sensitivity (IS), and identify the metabolic pathways underlying IR. METHODS In this cross-sectional study, clinical and metabolic data for 200 seemingly healthy young female participants (100 IR and 100 IS) was collected from Qatar Biobank. Orthogonal partial least square analysis was performed to assess the extent of separation between individuals from the 2 groups based on measured metabolites. Classical linear models were used to identify the metabolic signature of IR, followed by elastic-net-regularized generalized linear model (GLMNET) and receiver operating characteristic (ROC) analysis to determine top metabolites associated with IR. RESULTS Compared to lean/overweight participants with IS, those with IR showed increased androgenic steroids, including androsterone glucuronide, in addition to various microbiota byproducts, such as the phenylalanine derivative carboxyethylphenylalanine. On the other hand, participants with IS had elevated levels of long-chain fatty acids. A ROC analysis suggested better discriminatory performance using 20 metabolites selected by GLMNET in comparison to the classical clinical traits (area under curve: 0.93 vs 0.73, respectively). CONCLUSION Our data confirm the multifactorial mechanism of IR with a diverse spectrum of emerging potential biomarkers, including steroids, long-chain fatty acids, and microbiota metabolites. Further studies are warranted to validate these markers for diagnostic and therapeutic applications.
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Affiliation(s)
- Ilhame Diboun
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | | | - Hend Al-Jaber
- Biomedical Research Center (BRC), Qatar University, Doha, Qatar
| | - Omar Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
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Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. Plant Commun 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Kotapati HK, Bates PD. 14C-Tracing of Lipid Metabolism. Methods Mol Biol 2021; 2295:59-80. [PMID: 34047972 DOI: 10.1007/978-1-0716-1362-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipids are produced through a dynamic metabolic network involving branch points, cycles, reversible reactions, parallel reactions in different subcellular compartments, and distinct pools of the same lipid class involved in different parts of the network. For example, diacylglycerol (DAG) is a biosynthetic and catabolic intermediate of many different lipid classes. Triacylglycerol can be synthesized from DAG assembled de novo, or from DAG produced by catabolism of membrane lipids, most commonly phosphatidylcholine. Quantification of lipids provides a snapshot of the lipid abundance at the time they were extracted from the given tissue. However, quantification alone does not provide information on the path of carbon flux through the metabolic network to synthesize each lipid. Understanding lipid metabolic flux requires tracing lipid metabolism with isotopically labeled substrates over time in living tissue. [14C]acetate and [14C]glycerol are commonly utilized substrates to measure the flux of nascent fatty acids and glycerol backbones through the lipid metabolic network in vivo. When combined with mutant or transgenic plants, tracing of lipid metabolism can provide information on the molecular control of lipid metabolic flux. This chapter provides a method for tracing in vivo lipid metabolism in developing Arabidopsis thaliana seeds, including analysis of 14C labeled lipid classes and fatty acid regiochemistry through both thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) approaches.
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Affiliation(s)
- Hari Kiran Kotapati
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
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St-Jean M, Bourdeau I, Martin M, Lacroix A. Aldosterone is Aberrantly Regulated by Various Stimuli in a High Proportion of Patients with Primary Aldosteronism. J Clin Endocrinol Metab 2021; 106:e45-e60. [PMID: 33000146 PMCID: PMC7765652 DOI: 10.1210/clinem/dgaa703] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/28/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT In primary aldosteronism (PA), aldosterone secretion is relatively independent of the renin-angiotensin system, but can be regulated by several other stimuli. OBJECTIVE To evaluate aldosterone response to several stimuli in a series of patients with PA secondary either to bilateral adrenal hyperplasia (BAH) or unilateral aldosterone-producing adenoma (APA). DESIGN AND SETTING Prospective cohort study conducted in a university teaching hospital research center. PATIENTS Forty-three patients with confirmed PA and subtyped by adrenal vein sampling (n = 39) were studied, including 11 with BAH, 28 with APA, and 4 with undefined etiology. We also studied 4 other patients with aldosterone and cortisol cosecretion. INTERVENTIONS We systematically explored aberrant regulation of aldosterone using an in vivo protocol that included the following stimulation tests performed over 3 days under dexamethasone suppression: upright posture, mixed meal, adrenocorticotropin (ACTH) 1-24, gonadotropin-releasing hormone (GnRH), vasopressin, and serotonin R4 agonist. MAIN OUTCOME MEASURES Positive response was defined as >50% renin or ACTH-independent increase in plasma aldosterone/cortisol concentration following the various stimulation tests. RESULTS Renin-independent aldosterone secretion increased in response to several aberrant stimuli (upright posture, GnRH) in up to 83% of patients with APA or BAH in whom ACTH 1-24 and HT4R agonists also produced aldosterone oversecretion in all patients. The mean significant aberrant responses per patient was similar in BAH (4.6) and in APA (4.0). CONCLUSIONS Aldosterone secretion in PA is relatively autonomous from the renin-angiotensin system, but is highly regulated by several other stimuli, which contributes to the large variability of aldosterone levels in PA patients.
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Affiliation(s)
- Matthieu St-Jean
- Division of Endocrinology, Department of Medicine and Research Center, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Isabelle Bourdeau
- Division of Endocrinology, Department of Medicine and Research Center, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Marc Martin
- Department of biochemistry, Clinical Department of Laboratory Medecine, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
| | - André Lacroix
- Division of Endocrinology, Department of Medicine and Research Center, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
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Yu C, Yan M, Dong H, Luo J, Ke Y, Guo A, Chen Y, Zhang J, Huang X. Maize bHLH55 functions positively in salt tolerance through modulation of AsA biosynthesis by directly regulating GDP-mannose pathway genes. Plant Sci 2021; 302:110676. [PMID: 33288001 DOI: 10.1016/j.plantsci.2020.110676] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 05/21/2023]
Abstract
Ascorbic acid (AsA) is an antioxidant and enzyme co-factor that is vital to plant development and abiotic stress tolerance. However, the regulation mechanisms of AsA biosynthesis in plants remain poorly understood. Here, we report a basic helix-loop-helix 55 (ZmbHLH55) transcription factor that regulates AsA biosynthesis in maize. Analysis of publicly available transcriptomic data revealed that ZmbHLH55 is co-expressed with several genes of the GDP-mannose pathway. Experimental data showed that ZmbHLH55 forms homodimers localized to the cell nuclei, and it exhibits DNA binding and transactivation activity in yeast. Under salt stress conditions, knock down mutant (zmbhlh55) in maize accumulated lower levels of AsA compared with wild type, accompanied by lower antioxidant enzymes activity, shorter root length, and higher malondialdehyde (MDA) level. Gene expression data from the WT and zmbhlh55 mutant, showed that ZmbHLH55 positively regulates the expression of ZmPGI2, ZmGME1, and ZmGLDH, but negatively regulates ZmGMP1 and ZmGGP. Furthermore, ZmbHLH55-overexpressing Arabidopsis, under salt conditions, showed higher AsA levels, increased rates of germination, and elevated antioxidant enzyme activities. In conclusion, these results have identified previously unknown regulation mechanisms for AsA biosynthesis, indicating that ZmbHLH55 may be a potential candidate to enhance plant salt stress tolerance in the future.
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Affiliation(s)
- Chunmei Yu
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Ming Yan
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Huizhen Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Luo
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Yongchao Ke
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Anfang Guo
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Yanhong Chen
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Jian Zhang
- Ministry of Agriculture Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, 226019, China
| | - Xiaosan Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Guo W, Wang Y, Fan M, Xie S, Zhao H, Wang J, Liu Y, Xu D, Xu Y. Integrating metabolomics and network pharmacology to explore the protective effect of gross saponins of Tribulus terrestris L. fruit against ischemic stroke in rat. J Ethnopharmacol 2020; 263:113202. [PMID: 32768639 DOI: 10.1016/j.jep.2020.113202] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/21/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Tribulus terrestris L. belongs to the family Zygophyllaceae and has been widely used as a folk medicine for a long history in Asian countries. Gross saponins of Tribulus terrestris L. fruit (GSTTF) has an obvious neuroprotective effect on the treatment of ischemic stroke, but its potential therapeutic mechanisms have not been thoroughly studied. AIM OF THE STUDY To investigate the protective effect of GSTTF against ischemic stroke in rat. MATERIALS AND METHODS The combination of metabolomics and network pharmacology analysis was applied to investigate the protective effects of GSTTF on ischemic stroke and its putative mechanism. The related pathway of the biomarkers highlighted from metabolomics analysis was explored, then the possible targets of GSTTF were further revealed by network pharmacology analysis. Molecular docking was conducted to investigate the interaction between the active compound and target protein. RESULTS Metabolomics analysis showed that metabolic disturbances were observed in serum for the rats in middle cerebral artery occlusion (MCAO). These MCAO-induced deviations in serum metabolism can be reversely changed by GSTTF via metabolic pathways regulation. Twenty-four proteins with the connectivity degree larger than 15 were selected by the network pharmacology analysis, which are considered as the possible therapeutic targets of the GSTTF against ischemic stroke. The results of molecular docking showed that the active compounds were capable of binding to the representative potential targets HSD11B1 and AR, respectively. And the docking mode of two compounds with the lowest binding energy to their target protein was illustrated by the ribbon binding map. CONCLUSION The present study combines metabolomics and network pharmacology analysis to investigate the mechanism of MCAO-induced ischemic stroke and reveal the efficiency and possible mechanisms of GSTTF for ischemic stroke. Further studies on the bioactive saponin as well as their synergistic action on ischemic stroke will be conducted to better reveal the underlying mechanisms.
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Affiliation(s)
- Wenjun Guo
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China; Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China
| | - Yang Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, 999078, China.
| | - Meiling Fan
- Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China
| | - Shengxu Xie
- Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China
| | - Hongyu Zhao
- Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China
| | - Jifeng Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Yue Liu
- Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China
| | - Dongming Xu
- Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China
| | - Yajuan Xu
- Key Laboratory of Medicinal Materials, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, 130021, China.
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Socaciu AI, Ionuţ R, Socaciu MA, Ungur AP, Bârsan M, Chiorean A, Socaciu C, Râjnoveanu AG. Melatonin, an ubiquitous metabolic regulator: functions, mechanisms and effects on circadian disruption and degenerative diseases. Rev Endocr Metab Disord 2020; 21:465-478. [PMID: 32691289 DOI: 10.1007/s11154-020-09570-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The last four decades, we assist to an increasing scientific interest on melatonin, a circadian hormone, a metabolic regulator which influences not only plants' metabolism and their defense against pathogens but mostly the animals and humans' metabolic pathways, their response to circadian disruption, stress and burnout syndrome. In humans, as a hormonal regulator, produced in the pineal grand as well in mitochondria, melatonin is involved in different, complex intracellular signaling pathways, with antioxidant and immune stimulating effects, proving to act as a circadian synchronizer, as a preventive and therapeutic agent in many degenerative diseases, and especially in hormone-dependent cancers. Preclinical or clinical studies showed recently the mechanisms involved in regulating the cellular activity, its role in aging and circadian disturbances and impact on degenerative diseases. Melatonin proved to have an anti-inflammatory, antiapoptotic and powerful antioxidant effect by subtle mechanisms in mitochondrial metabolic pathways. This overview includes recent and relevant literature data related to the impact of endogenous and exogeneous melatonin on the prevention of cancer progression and treatment of various degenerative diseases. Metabolomics, an emerging new omics' technology, based on high performance liquid chromatography coupled with mass spectrometry is presented as an encouraging technique to fingerprint and realize a precise evaluation and monitoring of the turnover of melatonin and its metabolites in different pathological circumstances.
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Affiliation(s)
- Andreea Iulia Socaciu
- Department of Occupational Health, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
| | - Răzvan Ionuţ
- Department of Occupational Health, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
| | - Mihai Adrian Socaciu
- Department of Medical Imaging, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
| | - Andreea Petra Ungur
- Department of Occupational Health, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
| | - Maria Bârsan
- Department of Occupational Health, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
| | - Angelica Chiorean
- Department of Radiology, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
| | - Carmen Socaciu
- Department of Biochemistry, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania.
| | - Armand Gabriel Râjnoveanu
- Department of Occupational Health, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania
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Shanmugalingam R, Wang X, Motum P, Fulcher I, Lee G, Kumar R, Hennessy A, Makris A. The 15-Epilipoxin-A4 Pathway with Prophylactic Aspirin in Preventing Preeclampsia: A Longitudinal Cohort Study. J Clin Endocrinol Metab 2020; 105:5905864. [PMID: 32930782 DOI: 10.1210/clinem/dgaa642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/11/2020] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The benefit of aspirin in preventing preeclampsia is increasingly recognized; however, its mechanism of action remains unclear. Nonobstetric studies have described an anti-inflammatory effect of aspirin through the 15-epilipoxin-A4 pathway (aspirin-triggered lipoxin [ATL]). However, the anti-inflammatory mechanism of aspirin in the prevention of preeclampsia remains unknown. OBJECTIVE/HYPOTHESIS To examine (1) the difference in longitudinal endogenous lipoxin-A4 (En-Lipoxin-A4) concentration in low-risk (LR) and high-risk (HR) pregnancies, and (2) the effect of aspirin on endogenous ATL concentration and the associated effect on cytokine profile of HR women. METHODS Plasma from 220 HR women was collected at 12, 16, 20, 24, 28, 32, and 36 weeks of gestation. Adherence to aspirin was biochemically verified. Plasma En-Lipoxin-A4 and ATL concentrations were analyzed using liquid chromatography mass spectrometry, and cytokines, interleukin (IL)-10, tumor necrosis factor-α, interferon-γ, IL-8, and IL-1β, with the high-sensitivity multibead Luminex® assay. RESULTS HR women have up to 70% lower plasma concentration of En-Lipoxin-A4 (P < 0.001) than LR women. HR women with adequate aspirin adherence (HR-AA) (n = 82) had higher plasma concentration of ATL (P < .001), lower concentration of IL-8 from 16 to 36 weeks of gestation (P < .001), and increased IL-10 concentration from 16 to 28 weeks of gestation (P = .03) compared with high-risk women who were not on aspirin (HR-NA). HR-AA who did not develop preeclampsia had higher plasma En-lipoxin-A4 (P < .001), ATL (P = .02), and IL-10 concentrations (P < .001) with lower IL-8 concentration (P = .004) than HR women who developed preeclampsia. DISCUSSION Plasma concentration of En-Lipoxin-A4 is lower in HR women than in LR controls. Adequate adherence with aspirin results in an increase in ATL and IL-10 with reduced IL-8 plasma concentration. This study suggests a potential anti-inflammatory role of aspirin through the ATL pathway with prophylactic aspirin in HR pregnant women.
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Affiliation(s)
- Renuka Shanmugalingam
- Department of Renal Medicine, South Western Sydney Local Health District, NSW, Australia
- School of Medicine, Western Sydney University, NSW, Australia
- Women's Health Initiative Translational Unit (WHITU), Ingham Institute For Applied Medical Research and South Western Sydney Local Health District, NSW, Australia
- Vascular Immunology Research Group, Heart Research Institute (HRI), Sydney, NSW, Australia
| | - XiaoSuo Wang
- Bosch Mass Spectrometry Faculty, University of Sydney, NSW, Australia
- Freedman Foundation Metabolomics Facility, Innovation Centre, Victor Chang Cardiac Research Institute, NSW, Australia
| | - Penelope Motum
- Women's Health Initiative Translational Unit (WHITU), Ingham Institute For Applied Medical Research and South Western Sydney Local Health District, NSW, Australia
- Department of Haematology, South Western Sydney Local Health District, NSW, Australia
| | - Ian Fulcher
- Department of Obstetrics and Gynaecology, South Western Sydney Local Health District, NSW, Australia
| | - Gaksoo Lee
- Women's Health Initiative Translational Unit (WHITU), Ingham Institute For Applied Medical Research and South Western Sydney Local Health District, NSW, Australia
- Department of Obstetrics and Gynaecology, South Western Sydney Local Health District, NSW, Australia
| | - Roshika Kumar
- South Western Sydney Clinical School, University of New South Wales (UNSW), NSW, Australia
| | - Annemarie Hennessy
- Department of Renal Medicine, South Western Sydney Local Health District, NSW, Australia
- School of Medicine, Western Sydney University, NSW, Australia
- Women's Health Initiative Translational Unit (WHITU), Ingham Institute For Applied Medical Research and South Western Sydney Local Health District, NSW, Australia
- Vascular Immunology Research Group, Heart Research Institute (HRI), Sydney, NSW, Australia
| | - Angela Makris
- Department of Renal Medicine, South Western Sydney Local Health District, NSW, Australia
- School of Medicine, Western Sydney University, NSW, Australia
- Women's Health Initiative Translational Unit (WHITU), Ingham Institute For Applied Medical Research and South Western Sydney Local Health District, NSW, Australia
- Vascular Immunology Research Group, Heart Research Institute (HRI), Sydney, NSW, Australia
- South Western Sydney Clinical School, University of New South Wales (UNSW), NSW, Australia
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Hsu CN, Tain YL. Developmental Programming and Reprogramming of Hypertension and Kidney Disease: Impact of Tryptophan Metabolism. Int J Mol Sci 2020; 21:E8705. [PMID: 33218054 PMCID: PMC7698939 DOI: 10.3390/ijms21228705] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/08/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
The concept that hypertension and chronic kidney disease (CKD) originate in early life has emerged recently. During pregnancy, tryptophan is crucial for maternal protein synthesis and fetal development. On one hand, impaired tryptophan metabolic pathway in pregnancy impacts fetal programming, resulting in the developmental programming of hypertension and kidney disease in adult offspring. On the other hand, tryptophan-related interventions might serve as reprogramming strategies to prevent a disease from occurring. In the present review, we aim to summarize (1) the three major tryptophan metabolic pathways, (2) the impact of tryptophan metabolism in pregnancy, (3) the interplay occurring between tryptophan metabolites and gut microbiota on the production of uremic toxins, (4) the role of tryptophan-derived metabolites-induced hypertension and CKD of developmental origin, (5) the therapeutic options in pregnancy that could aid in reprogramming adverse effects to protect offspring against hypertension and CKD, and (6) possible mechanisms linking tryptophan metabolism to developmental programming of hypertension and kidney disease.
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Affiliation(s)
- Chien-Ning Hsu
- Department of Pharmacy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan;
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - You-Lin Tain
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan
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Xu X, Niu L, Liu Y, Pang M, Lu W, Xia C, Zhu Y, Yang B, Wang Q. Study on the mechanism of Gegen Qinlian Decoction for treating type II diabetes mellitus by integrating network pharmacology and pharmacological evaluation. J Ethnopharmacol 2020; 262:113129. [PMID: 32730886 DOI: 10.1016/j.jep.2020.113129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 06/13/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gegen Qinlian Decoction (GQD) is a classic traditional Chinese medicine prescription that is widely used to clinically treat diabetes mellitus. It is composed of Pueraria lobata (Willd.) Ohwi (ge gen), Scutellaria baicalensis Georgi (huang qin), Coptidis chinensis Franch. (huang lian), and Glycyrrhiza uralensis Fisch. (gan cao). However, the active ingredients in GQD and their mechanism of action are unclear. AIM OF THE STUDY In this study, we aimed to verify the efficacy of GQD in improving insulin resistance (IR) in diabetic mice and used network pharmacology to identify potential targets and pathways underlying its mechanism of action. MATERIALS AND METHODS A mouse model of diabetes was created by feeding mice a high-fat diet followed by an intraperitoneal injection of streptozotocin. These type II diabetic mice were administered either a clinical dose or a high dose of GQD, after which blood glucose and serum insulin levels were measured to assess its effects on IR. Network pharmacology was used to construct a 'component-pathway-target' network to elucidate the likely targets and pathways modulated in common by GQD components. Furthermore, mRNA transcript levels and protein expression levels of oestrogen receptor alpha (ESR1) were determined. RESULTS The in vivo experiment showed that GQD markedly decreased blood glucose and increased serum insulin levels in type II diabetic mice. Network pharmacology and bioinformatics analysis indicated that GQD regulated 82 corresponding proteins and 59 relevant biological pathways associated with diabetes. One such target was ESR1, which was significantly decreased at both the mRNA and protein levels in diabetic mice, but whose levels were significantly increased by GQD treatment. CONCLUSIONS This project provides a scientific basis for understanding the effectiveness of multi-component, multi-target compound formulas, as well as a new strategy for investigating therapeutic drugs for type II diabetes and other diseases.
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Affiliation(s)
- Xinyi Xu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Lulu Niu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Yan Liu
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Meilu Pang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Wanying Lu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Cong Xia
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Yuxuan Zhu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
| | - Qi Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China.
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Vogel K, Greinert T, Reichard M, Held C, Harms H, Maskow T. Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry. Int J Mol Sci 2020; 21:ijms21218341. [PMID: 33172189 PMCID: PMC7664384 DOI: 10.3390/ijms21218341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022] Open
Abstract
In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner.
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Affiliation(s)
- Kristina Vogel
- UFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
- Institute for Drug Development, Leipzig University Medical School, Leipzig University, Bruederstr. 34, 04103 Leipzig, Germany
| | - Thorsten Greinert
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany; (T.G.); (C.H.)
| | - Monique Reichard
- UFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany; (T.G.); (C.H.)
| | - Hauke Harms
- UFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
| | - Thomas Maskow
- UFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
- Correspondence:
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Karimi R, Cleven A, Elbarbry F, Hoang H. The Impact of Fasting on Major Metabolic Pathways of Macronutrients and Pharmacokinetics Steps of Drugs. Eur J Drug Metab Pharmacokinet 2020; 46:25-39. [PMID: 33151502 DOI: 10.1007/s13318-020-00656-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this review, we have investigated how fasting promotes an adaptive cross-talk between different hormones and metabolic pathways to supply and meet the body's daily energy demands. We highlight in biochemical terms and mechanisms how fasting impacts four metabolic pathways-glycogenolysis, gluconeogenesis, amino acid oxidation, and fatty acid β-oxidation-that are actively engaged in the metabolism of carbohydrates, proteins, and lipids. Fasting results in reduced insulin secretion and increased glucagon and epinephrine release to prevent or stimulate metabolic reaction(s). Fasting stimulates glycogenolysis, amino acid and glucose oxidation, aminotransferase reactions in skeletal muscle, and promotes gluconeogenesis and urea production in the liver. In addition, fasting promotes gene expression of lipid metabolism in skeletal muscle, the synthesis of ketone bodies in the liver, and intracellular hormone-sensitive lipase activity in adipose tissue. Furthermore, the impact of fasting on reducing cellular damage by mitochondrial reactive oxygen species is discussed. Lastly, we briefly describe the impact of fasting on the four steps of pharmacokinetics-the absorption, distribution, metabolism, and excretion of a few select drugs-with an emphasis on the elimination of drugs related to the cytochrome-P450 family of enzymes.
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Affiliation(s)
- Reza Karimi
- Pacific University Oregon School of Pharmacy, 222 SE 8th Avenue, HPC-Ste 451, Hillsboro, OR, 97123, USA.
| | - Anita Cleven
- Pacific University Oregon School of Pharmacy, 222 SE 8th Avenue, HPC-Ste 451, Hillsboro, OR, 97123, USA
| | - Fawzy Elbarbry
- Pacific University Oregon School of Pharmacy, 222 SE 8th Avenue, HPC-Ste 451, Hillsboro, OR, 97123, USA
| | - Huy Hoang
- Pacific University Oregon School of Pharmacy, 222 SE 8th Avenue, HPC-Ste 451, Hillsboro, OR, 97123, USA
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Iglesias-Pedraz JM, Fossatti-Jara DM, Valle-Riestra-Felice V, Cruz-Visalaya SR, Ayala Felix JA, Comai L. WRN modulates translation by influencing nuclear mRNA export in HeLa cancer cells. BMC Mol Cell Biol 2020; 21:71. [PMID: 33054770 PMCID: PMC7557079 DOI: 10.1186/s12860-020-00315-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/01/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The Werner syndrome protein (WRN) belongs to the RecQ family of helicases and its loss of function results in the premature aging disease Werner syndrome (WS). We previously demonstrated that an early cellular change induced by WRN depletion is a posttranscriptional decrease in the levels of enzymes involved in metabolic pathways that control macromolecular synthesis and protect from oxidative stress. This metabolic shift is tolerated by normal cells but causes mitochondria dysfunction and acute oxidative stress in rapidly growing cancer cells, thereby suppressing their proliferation. RESULTS To identify the mechanism underlying this metabolic shift, we examined global protein synthesis and mRNA nucleocytoplasmic distribution after WRN knockdown. We determined that WRN depletion in HeLa cells attenuates global protein synthesis without affecting the level of key components of the mRNA export machinery. We further observed that WRN depletion affects the nuclear export of mRNAs and demonstrated that WRN interacts with mRNA and the Nuclear RNA Export Factor 1 (NXF1). CONCLUSIONS Our findings suggest that WRN influences the export of mRNAs from the nucleus through its interaction with the NXF1 export receptor thereby affecting cellular proteostasis. In summary, we identified a new partner and a novel function of WRN, which is especially important for the proliferation of cancer cells.
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Affiliation(s)
- Juan Manuel Iglesias-Pedraz
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Diego Matia Fossatti-Jara
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
- Present address: National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic
| | - Valeria Valle-Riestra-Felice
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Sergio Rafael Cruz-Visalaya
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Jose Antonio Ayala Felix
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Biochemistry and Molecular Medicine, Keck School of Medicine, Longevity Institute, Davis School of Gerontology, University of Southern California, Los Angeles, CA 90033 USA
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Sailani MR, Metwally AA, Zhou W, Rose SMSF, Ahadi S, Contrepois K, Mishra T, Zhang MJ, Kidziński Ł, Chu TJ, Snyder MP. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Nat Commun 2020; 11:4933. [PMID: 33004787 PMCID: PMC7529769 DOI: 10.1038/s41467-020-18758-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
The influence of seasons on biological processes is poorly understood. In order to identify biological seasonal patterns based on diverse molecular data, rather than calendar dates, we performed a deep longitudinal multiomics profiling of 105 individuals over 4 years. Here, we report more than 1000 seasonal variations in omics analytes and clinical measures. The different molecules group into two major seasonal patterns which correlate with peaks in late spring and late fall/early winter in California. The two patterns are enriched for molecules involved in human biological processes such as inflammation, immunity, cardiovascular health, as well as neurological and psychiatric conditions. Lastly, we identify molecules and microbes that demonstrate different seasonal patterns in insulin sensitive and insulin resistant individuals. The results of our study have important implications in healthcare and highlight the value of considering seasonality when assessing population wide health risk and management.
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Affiliation(s)
- M Reza Sailani
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Ahmed A Metwally
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | | | - Sara Ahadi
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Martin Jinye Zhang
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Łukasz Kidziński
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Theodore J Chu
- Department of Pediatrics, Division of Allergy and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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Abstract
The critical role of phosphate (Pi) in countless biological processes requires the ability to control its concentration both intracellularly and extracellularly. At the body level, this concentration is finely regulated by numerous hormones, primarily parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23). While this control of the body's Pi homeostasis is now well documented, knowledge of the mechanisms that allow the cell and the body to detect extracellular Pi variations is much less known. These systems are well described in bacteria, yeasts and plants, but as will be discussed in this review, knowledge obtained from these organisms is not entirely relevant to the requirements of Pi biology in mammals. In this review, we present the latest findings on extracellular Pi sensing in mammals, and describe the mammalian Pi sensors identified to date, such as SLC20A1 (PIT1)/SLC20A2 (PIT2) heterodimers and the calcium-sensing receptor (CaSR). While there are many questions remaining to be resolved, a clarification of the Pi sensing mechanisms in mammals is critical to understanding the deregulation of Pi balance in certain life-threatening disease states, such as end-stage renal disease and associated vascular calcifications, and to proposing relevant therapeutic approaches.
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Affiliation(s)
- Laurent Beck
- INSERM, UMR 1229, RMeS, Regenerative Medicine and Skeleton, Université de Nantes, ONIRIS, Nantes, France
- Université de Nantes, UFR Odontologie, Nantes, France
| | - Sarah Beck-Cormier
- INSERM, UMR 1229, RMeS, Regenerative Medicine and Skeleton, Université de Nantes, ONIRIS, Nantes, France
- Université de Nantes, UFR Odontologie, Nantes, France
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O'Brien CM, Mulukutla BC, Mashek DG, Hu WS. Regulation of Metabolic Homeostasis in Cell Culture Bioprocesses. Trends Biotechnol 2020; 38:1113-1127. [PMID: 32941791 DOI: 10.1016/j.tibtech.2020.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/26/2022]
Abstract
Mammalian cells are the main tool for the production of therapeutic proteins, viruses for gene therapy, and cells for cell therapy. In production processes cell metabolism is the main driver that causes changes in the growth environment and affects productivity and product quality. Of all nutrients, glucose has the most prominent impact on bioprocesses. We summarize recent findings on the regulation of glucose and energy metabolism in cultured cells. Local allosteric regulations and post-translational modifications of enzymes in metabolic networks interplay with global signaling and transcriptional regulation. These regulatory networks sustain homeostasis across the cytosolic and mitochondrial compartments. Understanding the regulation of glucose metabolism and metabolic state is crucial for enhancing process productivity and product quality.
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Affiliation(s)
- Conor M O'Brien
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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Abstract
PURPOSE OF REVIEW To summarize the underlying biochemical basis for low-carbohydrate and ketogenic diets (LC/KD) and provide mechanisms to account for demonstrated effectiveness. RECENT FINDINGS LC/KD continue to have success, to outperform other diets as well as most drugs for weight loss and diabetes treatment. In many cases, LC/KD can effect remission (absence of drugs) or reversal (only metformin or nondiabetes drugs) of type 2 diabetes and can provide a significant adjunct to pharmacology in type 1. Medication is reduced or eliminated in most cases. The results are consistent with the biochemical rationale which stresses the global effects of the glucose-insulin axis. SUMMARY Evidence for the superior effectiveness of LC/KD for metabolic disease is now overwhelming. At the same time, the approach has received only limited support, and in many cases, persistence of the traditional opposition. Clinical practice or research must confront this crisis in order to bring practice in line with current science and to avoid continued harm to medicine and ultimately, the patient.
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Affiliation(s)
- Richard D Feinman
- State University of New York Downstate Health Sciences University, Brooklyn, New York, USA
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Bagamery LE, Justman QA, Garner EC, Murray AW. A Putative Bet-Hedging Strategy Buffers Budding Yeast against Environmental Instability. Curr Biol 2020; 30:4563-4578.e4. [PMID: 32976801 DOI: 10.1016/j.cub.2020.08.092] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/20/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022]
Abstract
To grow and divide, cells must extract resources from dynamic and unpredictable environments. Many organisms use different metabolic strategies for distinct contexts. Budding yeast can produce ATP from carbon sources by mechanisms that prioritize either speed (fermentation) or yield (respiration). Withdrawing glucose from exponentially growing cells reveals variability in their ability to switch from fermentation to respiration. We observe two subpopulations of glucose-starved cells: recoverers, which rapidly adapt and resume growth, and arresters, which enter a shock state characterized by deformation of many cellular structures, including mitochondria. These states are heritable, and on high glucose, arresters grow and divide faster than recoverers. Recoverers have a fitness advantage during a carbon source shift but are less fit in a constant, high-glucose environment, and we observe natural variation in the frequency of the two states across wild yeast strains. These experiments suggest that bet hedging has evolved in budding yeast.
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Affiliation(s)
- Laura E Bagamery
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Quincey A Justman
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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Wang Y, Sha W, Wang H, Howard AG, Tsilimigras MCB, Zhang J, Su C, Wang Z, Zhang B, Fodor AA, Gordon-Larsen P. Urbanization in China is associated with pronounced perturbation of plasma metabolites. Metabolomics 2020; 16:103. [PMID: 32951074 PMCID: PMC7707273 DOI: 10.1007/s11306-020-01724-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/12/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Urbanization is associated with major changes in environmental and lifestyle exposures that may influence metabolic signatures. OBJECTIVES We investigated cross-sectional urban and rural differences in plasma metabolome analyzed by liquid chromatography/mass spectrometry platform in 500 Chinese adults aged 25-68 years from two neighboring southern Chinese provinces. METHODS We first examined the overall metabolome differences by urban and rural residential location, using Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) and random forest classification. We then tested the association between urbanization status and individual metabolites using a linear regression adjusting for age, sex, and province and conducted pathway analysis (Fisher's exact test) to identify metabolic pathways differed by urbanization status. RESULTS We observed distinct overall metabolome by urbanization status in OPLS-DA and random forest classification. Using linear regression, out of a total of 1108 unique metabolite features identified in this sample, we found that 266 metabolites were differed by urbanization status (positive false discovery rate-adjusted p-value, q-value < 0.05). For example, the following metabolites were positively associated with urbanization status: caffeine metabolites from xanthine metabolism, hazardous pollutants like 4-hydroxychlorothalonil and perfluorooctanesulfonate, and metabolites implicated in cardiometabolic diseases, such as branched-chain amino acids. In pathway analysis, we found that xanthine metabolism pathways differed by urbanization status (q-value = 1.64E-04). CONCLUSION We detected profound differences in host metabolites by urbanization status. Urban residents were characterized by metabolites signaling caffeine metabolism and toxic pollutants and metabolites on known pathways to cardiometabolic disease risks, compared to their rural counterparts. Our findings highlight the importance of considering urbanization in metabolomics analysis.
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Affiliation(s)
- Yiqing Wang
- Department of Nutrition, Gillings School of Global Public Health & School of Medicine, University of North Carolina at Chapel Hill (UNC-Chapel Hill), Chapel Hill, NC, USA
| | - Wei Sha
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
- Department of Cancer Biostatistics, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Huijun Wang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Annie Green Howard
- Carolina Population Center, UNC-Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - Matthew C B Tsilimigras
- Department of Nutrition, Gillings School of Global Public Health & School of Medicine, University of North Carolina at Chapel Hill (UNC-Chapel Hill), Chapel Hill, NC, USA
- Carolina Population Center, UNC-Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - Jiguo Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Chang Su
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Zhihong Wang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Bing Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health & School of Medicine, University of North Carolina at Chapel Hill (UNC-Chapel Hill), Chapel Hill, NC, USA.
- Carolina Population Center, UNC-Chapel Hill, Chapel Hill, NC, USA.
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Abstract
Cells adjust their metabolism in response to mutations, but how this reprogramming depends on the genetic context is not well known. Specifically, the absence of individual enzymes can affect reprogramming, and thus the impact of mutations in cell growth. Here, we examine this issue with an in silico model of Saccharomyces cerevisiae's metabolism. By quantifying the variability in the growth rate of 10000 different mutant metabolisms that accumulated changes in their reaction fluxes, in the presence, or absence, of a specific enzyme, we distinguish a subset of modifier genes serving as buffers or potentiators of variability. We notice that the most potent modifiers refer to the glycolysis pathway and that, more broadly, they show strong pleiotropy and epistasis. Moreover, the evidence that this subset depends on the specific growing condition strengthens its systemic underpinning, a feature only observed before in a toy model of a gene-regulatory network. Some of these enzymes also modulate the effect that biochemical noise and environmental fluctuations produce in growth. Thus, the reorganization of metabolism induced by mutations has not only direct physiological implications but also transforms the influence that other mutations have on growth. This is a general result with implications in the development of cancer therapies based on metabolic inhibitors.
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Affiliation(s)
- Juan F. Poyatos
- Logic of Genomic Systems Lab (CNB-CSIC), Madrid, Spain
- Center for Genomics and Systems Biology (NYU), New York, United States of America
- * E-mail:
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Abstract
Ketone bodies - 3-hydroxybutyrate (3-OHB), acetoacetate, and acetone - are ancient, evolutionarily preserved, small fuel substrates, which uniquely can substitute and alternate with glucose under conditions of fuel and food deficiency. Once canonized as a noxious, toxic pathogen leading to ketoacidosis in patients with diabetes, it is now becoming increasingly clear that 3-OHB possesses a large number of beneficial, life-preserving effects in the fields of clinical science and medicine. 3-OHB, the most prominent ketone body, binds to specific hydroxyl-carboxylic acid receptors and inhibits histone deacetylase enzymes, free fatty acid receptors, and the NOD-like receptor protein 3 inflammasome, tentatively inhibiting lipolysis, inflammation, oxidative stress, cancer growth, angiogenesis, and atherosclerosis, and perhaps contributing to the increased longevity associated with exercise and caloric restriction. Clinically ketone bodies/ketogenic diets have for a long time been used to reduce the incidence of seizures in epilepsy and may have a role in the treatment of other neurological diseases such as dementia. 3-OHB also acts to preserve muscle protein during systemic inflammation and is an important component of the metabolic defense against insulin-induced hypoglycemia. Most recently, a number of studies have reported that 3-OHB dramatically increases myocardial blood flow and cardiac output in control subjects and patients with heart failure. At the moment, scientific interest in ketone bodies, in particular 3-OHB, is in a hectic transit and, hopefully, future, much needed, controlled clinical studies will reveal and determine to which extent the diverse biological manifestations of 3-OHB should be introduced medically.
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Affiliation(s)
- Niels Møller
- Department of Clinical Medicine, Medical/Steno Aarhus Research Laboratory, Aarhus University, Aarhus N, Denmark
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus N, Denmark
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44
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Herencias C, Salgado-Briegas S, Prieto MA, Nogales J. Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling. PLoS Comput Biol 2020; 16:e1007646. [PMID: 32925899 PMCID: PMC7529429 DOI: 10.1371/journal.pcbi.1007646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 10/01/2020] [Accepted: 07/20/2020] [Indexed: 12/30/2022] Open
Abstract
In this study we analyze the growth-phase dependent metabolic states of Bdellovibrio bacteriovorus by constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide computational evidences supporting potential axenic growth of B. bacteriovorus's in a rich medium based on its encoded metabolic capabilities. Our systems-level analysis confirms the presence of "energy-saving" mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacteria's metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications.
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Affiliation(s)
- Cristina Herencias
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Sergio Salgado-Briegas
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Juan Nogales
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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45
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Abstract
The coordination of nutrient sensing, delivery, uptake and utilization is essential for maintaining cellular, tissue and whole-body homeostasis. Such synchronization can be achieved only if metabolic information is communicated between the cells and tissues of the entire organism. During intense exercise, the metabolic demand of the body can increase approximately 100-fold. Thus, exercise is a physiological state in which intertissue communication is of paramount importance. In this Review, we discuss the physiological processes governing intertissue communication during exercise and the molecules mediating such cross-talk.
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Affiliation(s)
- Robyn M Murphy
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Matthew J Watt
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Febbraio
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia.
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46
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Bennett NK, Nguyen MK, Darch MA, Nakaoka HJ, Cousineau D, Ten Hoeve J, Graeber TG, Schuelke M, Maltepe E, Kampmann M, Mendelsohn BA, Nakamura JL, Nakamura K. Defining the ATPome reveals cross-optimization of metabolic pathways. Nat Commun 2020; 11:4319. [PMID: 32859923 PMCID: PMC7455733 DOI: 10.1038/s41467-020-18084-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 08/04/2020] [Indexed: 12/24/2022] Open
Abstract
Disrupted energy metabolism drives cell dysfunction and disease, but approaches to increase or preserve ATP are lacking. To generate a comprehensive metabolic map of genes and pathways that regulate cellular ATP-the ATPome-we conducted a genome-wide CRISPR interference/activation screen integrated with an ATP biosensor. We show that ATP level is modulated by distinct mechanisms that promote energy production or inhibit consumption. In our system HK2 is the greatest ATP consumer, indicating energy failure may not be a general deficiency in producing ATP, but rather failure to recoup the ATP cost of glycolysis and diversion of glucose metabolites to the pentose phosphate pathway. We identify systems-level reciprocal inhibition between the HIF1 pathway and mitochondria; glycolysis-promoting enzymes inhibit respiration even when there is no glycolytic ATP production, and vice versa. Consequently, suppressing alternative metabolism modes paradoxically increases energy levels under substrate restriction. This work reveals mechanisms of metabolic control, and identifies therapeutic targets to correct energy failure.
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Affiliation(s)
- Neal K Bennett
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Mai K Nguyen
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Maxwell A Darch
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Hiroki J Nakaoka
- Department of Radiation Oncology, University of California, San Francisco, CA, 94158, USA
| | - Derek Cousineau
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Johanna Ten Hoeve
- UCLA Metabolomics Center, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Thomas G Graeber
- UCLA Metabolomics Center, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Markus Schuelke
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Emin Maltepe
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Bryce A Mendelsohn
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Jean L Nakamura
- Department of Radiation Oncology, University of California, San Francisco, CA, 94158, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.
- Department of Neurology, University of California, San Francisco, CA, 94158, USA.
- Graduate Program in Biomedical Sciences, University of California, San Francisco, CA, USA.
- Graduate Program in Neuroscience, University of California, San Francisco, CA, USA.
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47
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Zhang W, Chen X, Sun W, Nie T, Quanquin N, Sun Y. Escherichia Coli Increases its ATP Concentration in Weakly Acidic Environments Principally through the Glycolytic Pathway. Genes (Basel) 2020; 11:genes11090991. [PMID: 32854287 PMCID: PMC7563387 DOI: 10.3390/genes11090991] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.
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Affiliation(s)
- Wenbin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510640, China;
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Xin Chen
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou 510006, China;
| | - Wei Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Tao Nie
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Natalie Quanquin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA;
| | - Yirong Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
- Correspondence:
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48
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Liu B, Li J, Lin X, Hu J, Lou S. The metabolic changes in the hippocampus of an atherosclerotic rat model and the regulation of aerobic training. Metab Brain Dis 2020; 35:1017-1034. [PMID: 32240489 DOI: 10.1007/s11011-020-00566-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/17/2020] [Indexed: 01/17/2023]
Abstract
Atherosclerosis has been associated with the progression of cognitive impairment and the effect of metabolic changes in the brain on cognitive function may be pronounced. The aim is to reveal the metabolic changes during atherosclerosis and clarify the possible role of exercise in regulating hippocampal metabolism. Hence, A rat model of atherosclerosis was established by high-fat diet feeding in combination with vitamin D3 intraperitoneal injection, then 4 weeks of aerobic exercise was conducted. Metabolomics based on GC-MS was applied to detect small molecules metabolites and western blot was used to detect the concentration of enzymes involved in metabolic changes in rat hippocampus. Compared to the control group, metabolites including xylulose 5-phosphate, threonine, succinate, and nonanoic acid were markedly elevated, whereas methyl arachidonic acid and methyl stearate decreased in the AS group, accompanied by a raised concentration of aldose reductase and glucose 6-phosphate dehydrogenase as well as a declined concentration of acetyl-CoA carboxylase and fatty acid synthase. After 4 weeks' aerobic exercise, the levels of succinic acid, branched chain amino acids, nonanoic acid, desmosterol, and aldose reductase decreased, whereas methyl arachidonic acid, methyl stearate, and glyceraldehyde-3-phosphate elevated in the hippocampus of the TAS group in comparison with the AS group. These results suggest that atherosclerosis could cause a severe metabolic disturbance, and aerobic exercise plays an important role in regulating atherosclerosis-induced disorder of glucose metabolism in the hippocampus.
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Affiliation(s)
- Beibei Liu
- Key Laboratory of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
- Department of Rehabilitation Medicine, Weifang Medical University, Weifang, 261053, China
| | - Jingjing Li
- Post-doctoral station of clinical medicine, Tongji Hospital, medical school of Tongji University, Shanghai, 200092, China
| | - Xiaojing Lin
- Key Laboratory of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Jingyun Hu
- Key Laboratory of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Shujie Lou
- Key Laboratory of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China.
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49
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Choi JY, Choi CY. Gonadotropin-releasing hormone-independent effects of recombinant vertebrate ancient long opsin in the goldfish Carassius auratus reveal alternative reproduction pathways. Fish Physiol Biochem 2020; 46:1219-1227. [PMID: 32146552 DOI: 10.1007/s10695-020-00784-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Vertebrate ancient long (VAL)-opsin is a green-sensitive photoreceptor that shows high sequence similarity to vertebrate ancient opsin, which is considered to play a role in sexual maturation via gonadotropin-releasing hormone (GnRH); however, the role of VAL-opsin in vertebrate sexual maturity remains unclear. Therefore, we investigated the possible role of VAL-opsin in reproduction in the goldfish Carassius auratus under a state of GnRH inhibition. Goldfish were injected with recombinant VAL-opsin protein (0.5 μg/g body mass) and/or the GnRH antagonist cetrorelix (0.5 μg/fish), and changes in the mRNA expression levels of genes associated with goldfish reproduction were measured by quantitative polymerase chain reaction, including those involved in the hypothalamus-pituitary-gonad (HPG) axis, VAL-opsin, GnRH, the gonadotropins (GTHs) luteinizing hormone and follicle-stimulating hormone, and estrogen receptor (ER). Moreover, the fish were irradiated with a green light-emitting diode (520 nm) to observe the synergistic effect on the HPG axis with VAL-opsin. Green LED exposure significantly and slightly increased the VAL-opsin and GnRH levels, respectively; however, these effects were blocked in groups injected with cetrorelix at all time points. Cetrorelix significantly decreased the mRNA levels of GTHs and ER, whereas these hormones recovered by co-treatment with VAL-opsin. These results indicate that green LED is an effective light source to promote the expression of sex hormones in fish. Moreover, VAL-opsin not only affects activity of the HPG axis but also appears to act on the pituitary gland directly to stimulate a new sexual maturation pathway that promotes the secretion of GTHs independent of GnRH.
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Affiliation(s)
- Ji Yong Choi
- Division of Marine BioScience, National Korea Maritime and Ocean University, Busan, 49112, Republic of Korea
| | - Cheol Young Choi
- Division of Marine BioScience, National Korea Maritime and Ocean University, Busan, 49112, Republic of Korea.
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50
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Tian L, Pu J, Liu Y, Gui S, Zhong X, Song X, Xu S, Zhang H, Wang H, Zhou W, Xie P. Metabolomic analysis of animal models of depression. Metab Brain Dis 2020; 35:979-990. [PMID: 32440806 DOI: 10.1007/s11011-020-00574-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/14/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Our understanding of the molecular mechanisms of depression remains largely unclear. Previous studies have shown that the prefrontal cortex (PFC) is among most important brain regions that exhibits metabolic changes in depression. A comprehensive analysis based on candidate metabolites in the PFC of animal models of depression will provide valuable information for understanding the pathogenic mechanism underlying depression. METHODS Candidate metabolites that are potentially involved in the metabolic changes of the PFC in animal models of depression were retrieved from the Metabolite Network of Depression Database. The significantly altered metabolic pathways were revealed by canonical pathway analysis, and the relationships among altered pathways were explored by pathway crosstalk analysis. Additionally, drug-associated pathways were investigated using drug-associated metabolite set enrichment analysis. The interrelationships among metabolites, proteins, and other molecules were analyzed by molecular network analysis. RESULTS Among 88 candidate metabolites, 87 altered canonical pathways were identified, and the top five ranked pathways were tRNA charging, the endocannabinoid neuronal synapse pathway, (S)-reticuline biosynthesis II, catecholamine biosynthesis, and GABA receptor signaling. Pathway crosstalk analysis revealed that these altered pathways were grouped into three interlinked modules involved in amino acid metabolism, nervous system signaling/neurotransmitters, and nucleotide metabolism. In the drug-associated metabolite set enrichment analysis, the main enriched drug pathways were opioid-related and antibiotic-related action pathways. Furthermore, the most significantly altered molecular network was involved in amino acid metabolism, molecular transport, and small molecule biochemistry. CONCLUSIONS This study provides important clues for the metabolic characteristics of the PFC in depression.
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Affiliation(s)
- Lu Tian
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Yiyun Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Siwen Gui
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaogang Zhong
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Xuemian Song
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Shaohua Xu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Hanpin Zhang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Haiyang Wang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Wei Zhou
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Peng Xie
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China.
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China.
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
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