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Gao X, Pan T, Gao Y, Zhu W, Liu L, Duan W, Han C, Feng B, Yan W, Song Q, Liu Y, Yue L. Acetylation of PGK1 at lysine 323 promotes glycolysis, cell proliferation, and metastasis in luminal A breast cancer cells. BMC Cancer 2024; 24:1054. [PMID: 39192221 PMCID: PMC11348675 DOI: 10.1186/s12885-024-12792-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND In prior research employing iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) technology, we identified a range of proteins in breast cancer tissues exhibiting high levels of acetylation. Despite this advancement, the specific functions and implications of these acetylated proteins in the context of cancer biology have yet to be elucidated. This study aims to systematically investigate the functional roles of these acetylated proteins with the objective of identifying potential therapeutic targets within breast cancer pathophysiology. METHODS Acetylated targets were identified through bioinformatics, with their expression and acetylation subsequently confirmed. Proteomic analysis and validation studies identified potential acetyltransferases and deacetylases. We evaluated metabolic functions via assays for catalytic activity, glucose consumption, ATP levels, and lactate production. Cell proliferation and metastasis were assessed through viability, cycle analysis, clonogenic assays, PCNA uptake, wound healing, Transwell assays, and MMP/EMT marker detection. RESULTS Acetylated proteins in breast cancer were primarily involved in metabolism, significantly impacting glycolysis and the tricarboxylic acid cycle. Notably, PGK1 showed the highest acetylation at lysine 323 and exhibited increased expression and acetylation across breast cancer tissues, particularly in T47D and MCF-7 cells. Notably, 18 varieties acetyltransferases or deacetylases were identified in T47D cells, among which p300 and Sirtuin3 were validated for their interaction with PGK1. Acetylation at 323 K enhanced PGK1's metabolic role by boosting its activity, glucose uptake, ATP production, and lactate output. This modification also promoted cell proliferation, as evidenced by increased viability, S phase ratio, clonality, and PCNA levels. Furthermore, PGK1-323 K acetylation facilitated metastasis, improving wound healing, cell invasion, and upregulating MMP2, MMP9, N-cadherin, and Vimentin while downregulating E-cadherin. CONCLUSION PGK1-323 K acetylation was significantly elevated in T47D and MCF-7 luminal A breast cancer cells and this acetylation could be regulated by p300 and Sirtuin3. PGK1-323 K acetylation promoted cell glycolysis, proliferation, and metastasis, highlighting novel epigenetic targets for breast cancer therapy.
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Affiliation(s)
- Xiuli Gao
- Research Institute of Medicine and Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Ting Pan
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Yu Gao
- The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Wenbin Zhu
- Research Institute of Medicine and Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Likun Liu
- Research Institute of Medicine and Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Wenbo Duan
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Cuicui Han
- College of Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Bo Feng
- Dean's Office, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Wenjing Yan
- College of Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Qiuhang Song
- College of Basic Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yunlong Liu
- The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang, China.
| | - Liling Yue
- Research Institute of Medicine and Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang, China.
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Shebl N, El-Jaafary S, Saeed AA, Elkafrawy P, El-Sayed A, Shamma S, Elnemr R, Mekky J, Mohamed LA, Kittaneh O, El-Fawal H, Rizig M, Salama M. Metabolomic profiling reveals altered phenylalanine metabolism in Parkinson's disease in an Egyptian cohort. Front Mol Biosci 2024; 11:1341950. [PMID: 38516193 PMCID: PMC10955577 DOI: 10.3389/fmolb.2024.1341950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/18/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction: Parkinson's disease (PD) is the most common motor neurodegenerative disease worldwide. Given the complexity of PD etiology and the different metabolic derangements correlated to the disease, metabolomics profiling of patients is a helpful tool to identify patho-mechanistic pathways for the disease development. Dopamine metabolism has been the target of several previous studies, of which some have reported lower phenylalanine and tyrosine levels in PD patients compared to controls. Methods: In this study, we have collected plasma from 27 PD patients, 18 reference controls, and 8 high-risk controls to perform a metabolomic study using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Results: Our findings revealed higher intensities of trans-cinnamate, a phenylalanine metabolite, in patients compared to reference controls. Thus, we hypothesize that phenylalanine metabolism has been shifted to produce trans-cinnamate via L-phenylalanine ammonia lyase (PAL), instead of producing tyrosine, a dopamine precursor, via phenylalanine hydroxylase (PAH). Discussion: Given that these metabolites are precursors to several other metabolic pathways, the intensities of many metabolites such as dopamine, norepinephrine, and 3-hydroxyanthranilic acid, which connects phenylalanine metabolism to that of tryptophan, have been altered. Consequently, and in respect to Metabolic Control Analysis (MCA) theory, the levels of tryptophan metabolites have also been altered. Some of these metabolites are tryptamine, melatonin, and nicotinamide. Thus, we assume that these alterations could contribute to the dopaminergic, adrenergic, and serotonergic neurodegeneration that happen in the disease.
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Affiliation(s)
- Nourhan Shebl
- Institute of Global Health and Human Ecology (I-GHHE), The American University in Cairo, Cairo, Egypt
| | - Shaimaa El-Jaafary
- Neurology Department, Faculty of Medicine, Cairo University, Giza, Egypt
- Global Brain Health Institute (GBHI), Trinity College Dublin, Dublin, Ireland
| | - Ayman A Saeed
- Applied Organic Chemistry Department, Chemical Industries Research Institute, National Research Centre (NRC), Giza, Egypt
| | - Passent Elkafrawy
- Technology and Energy Research Center, Effat University-College of Engineering-NSMTU, Jeddah, Saudi Arabia
| | - Amr El-Sayed
- Social Research Center, The American University in Cairo, Cairo, Egypt
| | - Samir Shamma
- Institute of Global Health and Human Ecology (I-GHHE), The American University in Cairo, Cairo, Egypt
| | - Rasha Elnemr
- Climate Change Information Center & Expert Systems (CCICES), Agriculture Research Center, Giza, Egypt
| | - Jaidaa Mekky
- Neurology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Lobna A Mohamed
- Neurology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Omar Kittaneh
- Technology and Energy Research Center, Effat University-College of Engineering-NSMTU, Jeddah, Saudi Arabia
| | - Hassan El-Fawal
- Institute of Global Health and Human Ecology (I-GHHE), The American University in Cairo, Cairo, Egypt
| | - Mie Rizig
- Queen Square, Institute of Neurology, University College London, London, United Kingdom
| | - Mohamed Salama
- Institute of Global Health and Human Ecology (I-GHHE), The American University in Cairo, Cairo, Egypt
- Global Brain Health Institute (GBHI), Trinity College Dublin, Dublin, Ireland
- Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Ma XY, Coleman B, Prabhu P, Wen F. Segmentation and evaluation of pathway module efficiency: Quantitative approach to monitor and overcome evolving bottlenecks in xylose to ethanol pathway. BIORESOURCE TECHNOLOGY 2024; 395:130377. [PMID: 38278451 DOI: 10.1016/j.biortech.2024.130377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Engineering microbes that can efficiently ferment xylose to ethanol is critical to the development of renewable fuels from lignocellulosic biomass. To accelerate the strain optimization process, a method termed Segmentation and Evaluation of Pathway Module Efficiency (SEPME) was developed to enable rapid and iterative identification and removal of metabolic bottlenecks. Using SEPME, the overall pathway was segmented into two modules: the upstream xylose assimilation pathway and the downstream pentose phosphate pathway, glycolysis, and fermentation. The efficiencies of both modules were then quantified to identify the rate controlling module, followed by analyses of control coefficients, reaction rates, and byproduct concentrations to narrow down targets within the module. SEPME analysis revealed that as the strain was engineered with increasing xylose-to-ethanol yields, the bottlenecks shifted within a module and across the two modules. Guided by SEPME, these bottlenecks were removed one by one, and a strain approaching the theoretical ethanol yield was obtained.
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Affiliation(s)
- Xiao Yin Ma
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Bryan Coleman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States; Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI 48109, United States.
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Schulz-Mirbach H, Dronsella B, He H, Erb TJ. Creating new-to-nature carbon fixation: A guide. Metab Eng 2024; 82:12-28. [PMID: 38160747 DOI: 10.1016/j.ymben.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Hai He
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35043, Marburg, Germany.
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Watkins BA, Smith BJ, Volpe SL, Shen CL. Exerkines, Nutrition, and Systemic Metabolism. Nutrients 2024; 16:410. [PMID: 38337694 PMCID: PMC10857119 DOI: 10.3390/nu16030410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The cornerstones of good health are exercise, proper food, and sound nutrition. Physical exercise should be a lifelong routine, supported by proper food selections to satisfy nutrient requirements based on energy needs, energy management, and variety to achieve optimal metabolism and physiology. The human body is sustained by intermediary and systemic metabolism integrating the physiologic processes for cells, tissues, organs, and systems. Recently, interest in specific metabolites, growth factors, cytokines, and hormones called exerkines has emerged to explain cooperation between nutrient supply organs and the brain during exercise. Exerkines consist of different compounds described as signaling moiety released during and after exercise. Examples of exerkines include oxylipin 12, 13 diHOME, lipid hormone adiponectin, growth factor BDNF, metabolite lactate, reactive oxygen species (ROS), including products of fatty acid oxidation, and cytokines such as interleukin-6. At this point, it is believed that exerkines are immediate, fast, and long-lasting factors resulting from exercise to support body energy needs with an emphasis on the brain. Although exerkines that are directly a product of macronutrient metabolism such as lactate, and result from catabolism is not surprising. Furthermore, other metabolites of macronutrient metabolism seem to be candidate exerkines. The exerkines originate from muscle, adipose, and liver and support brain metabolism, energy, and physiology. The purpose of this review is to integrate the actions of exerkines with respect to metabolism that occurs during exercise and propose other participating factors of exercise and brain physiology. The role of diet and macronutrients that influence metabolism and, consequently, the impact of exercise will be discussed. This review will also describe the evidence for PUFA, their metabolic and physiologic derivatives endocannabinoids, and oxylipins that validate them being exerkines. The intent is to present additional insights to better understand exerkines with respect to systemic metabolism.
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Affiliation(s)
- Bruce A. Watkins
- Department of Nutrition, University of California, Davis, CA 95616, USA
| | - Brenda J. Smith
- Department of Obstetrics and Gynecology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
- Indiana Center for Musculoskeletal Health, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Stella Lucia Volpe
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA;
| | - Chwan-Li Shen
- Department of Pathology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
- Center of Excellence for Integrative Health, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Singha B, Murmu S, Nair T, Rawat RS, Sharma AK, Soni V. Metabolic Rewiring of Mycobacterium tuberculosis upon Drug Treatment and Antibiotics Resistance. Metabolites 2024; 14:63. [PMID: 38248866 PMCID: PMC10820029 DOI: 10.3390/metabo14010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge, further compounded by the issue of antimicrobial resistance (AMR). AMR is a result of several system-level molecular rearrangements enabling bacteria to evolve with better survival capacities: metabolic rewiring is one of them. In this review, we present a detailed analysis of the metabolic rewiring of Mtb in response to anti-TB drugs and elucidate the dynamic mechanisms of bacterial metabolism contributing to drug efficacy and resistance. We have discussed the current state of AMR, its role in the prevalence of the disease, and the limitations of current anti-TB drug regimens. Further, the concept of metabolic rewiring is defined, underscoring its relevance in understanding drug resistance and the biotransformation of drugs by Mtb. The review proceeds to discuss the metabolic adaptations of Mtb to drug treatment, and the pleiotropic effects of anti-TB drugs on Mtb metabolism. Next, the association between metabolic changes and antimycobacterial resistance, including intrinsic and acquired drug resistance, is discussed. The review concludes by summarizing the challenges of anti-TB treatment from a metabolic viewpoint, justifying the need for this discussion in the context of novel drug discovery, repositioning, and repurposing to control AMR in TB.
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Affiliation(s)
- Biplab Singha
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Sumit Murmu
- Regional Centre of Biotechnology, Faridabad 121001, India;
| | - Tripti Nair
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA;
| | - Rahul Singh Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi 110067, India;
| | - Aditya Kumar Sharma
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
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Angarita-Rodríguez A, González-Giraldo Y, Rubio-Mesa JJ, Aristizábal AF, Pinzón A, González J. Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets. Int J Mol Sci 2023; 25:365. [PMID: 38203536 PMCID: PMC10778851 DOI: 10.3390/ijms25010365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Control theory, a well-established discipline in engineering and mathematics, has found novel applications in systems biology. This interdisciplinary approach leverages the principles of feedback control and regulation to gain insights into the complex dynamics of cellular and molecular networks underlying chronic diseases, including neurodegeneration. By modeling and analyzing these intricate systems, control theory provides a framework to understand the pathophysiology and identify potential therapeutic targets. Therefore, this review examines the most widely used control methods in conjunction with genomic-scale metabolic models in the steady state of the multi-omics type. According to our research, this approach involves integrating experimental data, mathematical modeling, and computational analyses to simulate and control complex biological systems. In this review, we find that the most significant application of this methodology is associated with cancer, leaving a lack of knowledge in neurodegenerative models. However, this methodology, mainly associated with the Minimal Dominant Set (MDS), has provided a starting point for identifying therapeutic targets for drug development and personalized treatment strategies, paving the way for more effective therapies.
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Affiliation(s)
- Andrea Angarita-Rodríguez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
| | - Juan J. Rubio-Mesa
- Departamento de Estadística, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Andrés Felipe Aristizábal
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
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Vázquez C, Encalada R, Belmont-Díaz J, Rivera M, Alvarez S, Nogueda-Torres B, Saavedra E. Metabolic control analysis of the transsulfuration pathway and the compensatory role of the cysteine transport in Trypanosoma cruzi. Biosystems 2023; 234:105066. [PMID: 37898397 DOI: 10.1016/j.biosystems.2023.105066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023]
Abstract
Trypanosoma cruzi is the causal agent of American Trypanosomiasis or Chagas Disease in humans. The current drugs for its treatment benznidazole and nifurtimox have inconveniences of toxicity and efficacy; therefore, the search for new therapies continues. Validation through genetic strategies of new drug targets against the parasite metabolism have identified numerous essential genes. Target validation can be further narrowed by applying Metabolic Control Analysis (MCA) to determine the flux control coefficients of the pathway enzymes. That coefficient is a quantitative value that represents the degree in which an enzyme/transporter determines the flux of a metabolic pathway; those with the highest coefficients can be promising drug targets. Previous studies have demonstrated that cysteine (Cys) is a key precursor for the synthesis of trypanothione, the main antioxidant metabolite in the parasite. In this research, MCA was applied in an ex vivo system to the enzymes of the reverse transsulfuration pathway (RTP) for Cys synthesis composed by cystathionine beta synthase (CBS) and cystathionine gamma lyase (CGL). The results indicated that CGL has 90% of the control of the pathway flux. Inhibition of CGL with propargylglycine (PAG) decreased the levels of Cys and trypanothione and depleted those of glutathione in epimastigotes (proliferative stage in the insect vector); these metabolite changes were prevented by supplementing with Cys, suggesting a compensatory role of the Cys transport (CysT). Indeed, Cys supplementation (but not PAG treatment) increased the activity of the CysT in epimastigotes whereas in trypomastigotes (infective stage in mammals) CysT was increased when they were incubated with PAG. Our results suggested that CGL could be a potential drug target given its high control on the RTP flux and its effects on the parasite antioxidant defense. However, the redundant Cys supply pathways in the parasite may require inhibition of the CysT as well. Our findings also suggest differential responses of the Cys supply pathways in different parasite stages.
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Affiliation(s)
- Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico; Posgrado en Ciencias Químico Biológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, 11350, Mexico
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Javier Belmont-Díaz
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Moisés Rivera
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Samantha Alvarez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Benjamín Nogueda-Torres
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, 11350, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico.
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Mazat JP. The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation. Biosystems 2023; 234:105038. [PMID: 37838015 DOI: 10.1016/j.biosystems.2023.105038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 10/16/2023]
Abstract
Metabolic Control Theory (MCT) and Metabolic Control Analysis (MCA) are the two sides, theoretical and experimental, of the measurement of the sensitivity of metabolic networks in the vicinity of a steady state. We will describe the birth and the development of this theory from the first analyses of linear pathways up to a global mathematical theory applicable to any metabolic network. We will describe how the theory, given the global nature of mitochondrial oxidative phosphorylation, solved the problem of what controls mitochondrial ATP synthesis and then how it led to a better understanding of the differential tissue expression of human mitochondrial pathologies and of the heteroplasmy of mitochondrial DNA, leading to the concept of the threshold effect.
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Affiliation(s)
- Jean-Pierre Mazat
- IBGC CNRS UMR 5095 & Université de Bordeaux, 1, rue Camille Saint-Saëns, 33077, BORDEAUX Cedex, France.
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Kaste JAM, Green A, Shachar-Hill Y. Integrative teaching of metabolic modeling and flux analysis with interactive python modules. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:653-661. [PMID: 37584426 DOI: 10.1002/bmb.21777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/06/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The modeling of rates of biochemical reactions-fluxes-in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint-based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to-date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C-metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands-on computer laboratory component of a four-day metabolic modeling workshop and participant survey results showed improvements in learners' self-assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.
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Affiliation(s)
- Joshua A M Kaste
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Antwan Green
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
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Puurand M, Tepp K, Kaambre T. Diving into cancer OXPHOS - The application of metabolic control analysis to cell and tissue research. Biosystems 2023; 233:105032. [PMID: 37739307 DOI: 10.1016/j.biosystems.2023.105032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
Knowing how the oxidative phosphorylation (OXPHOS) system in cancer cells operates differently from that of normal cells would help find compounds that specifically paralyze the energy metabolism of cancer cells. The first experiments in the study of mitochondrial respiration using the metabolic control analysis (MCA) method were done with isolated liver mitochondria in the early 80s of the last century. Subsequent studies have shown that the regulation of mitochondrial respiration by ADP in isolated mitochondria differs significantly from a model of mitochondria in situ, where the contacts with components in the cytoplasm are largely preserved. The method of selective permeabilization of the outer membrane of the cells allows the application of MCA to evaluate the contribution of different components of the OXPHOS system to its functioning while mitochondria are in a natural state. In this review, we summarize the use of MCA to study OXPHOS in cancer using permeabilized cells and tissues. In addition, we give examples of how this data fits into cancer research with a completely different approach and methodology.
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Affiliation(s)
- Marju Puurand
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia.
| | - Kersti Tepp
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Tuuli Kaambre
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
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12
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Marín-Hernández Á, Saavedra E. Metabolic control analysis as a strategy to identify therapeutic targets, the case of cancer glycolysis. Biosystems 2023; 231:104986. [PMID: 37506818 DOI: 10.1016/j.biosystems.2023.104986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The use of kinetic modeling and metabolic control analysis (MCA) to identify possible therapeutic targets and to investigate the controlling and regulatory mechanisms in cancer glycolysis is here reviewed. The glycolytic pathway has been considered a target to decrease cancer cell growth; however, its occurrence in normal cells makes it difficult to design therapeutic strategies that target this pathway in pathological cells. Notwithstanding, the over-expression of all enzymes and transporters, as well as the expression of isoenzymes with different kinetic and regulatory properties in cancer cells, suggested a different distribution of the control of glycolytic flux than that observed in normal cells. Kinetic models of glycolysis are constructed with enzyme kinetics experimental data, validated with the steady-state metabolite concentrations and glycolytic fluxes; applying MCA, permitted us to identify the steps with the highest control of glycolysis in cancer cells, but low control in normal cells. The cancer glycolysis main controlling steps under several metabolic conditions were: glucose transport, hexokinase and hexose-6-phosphate isomerase (HPI); whereas in normal cells were: the first two and phosphofructokinase-1. HPI is the best therapeutic target because it exerts high control in cancer glycolytic flux, but not in normal cells. Furthermore, kinetic modeling also contributed to identifying new feed-back and feed-forward regulatory loops in cancer cells glycolysis, and to understanding the mode of metabolic action of glycolytic inhibitors. Thus, MCA and metabolic modeling allowed to propose new strategies for inhibiting glycolysis in cancer cells.
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Affiliation(s)
- Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico.
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
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13
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de Atauri P, Foguet C, Cascante M. Control analysis in the identification of key enzymes driving metabolic adaptations: Towards drug target discovery. Biosystems 2023; 231:104984. [PMID: 37506820 DOI: 10.1016/j.biosystems.2023.104984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Metabolic Control Analysis (MCA) marked a turning point in understanding the design principles of metabolic network control by establishing control coefficients as a means to quantify the degree of control that an enzyme exerts on flux or metabolite concentrations. MCA has demonstrated that control of metabolic pathways is distributed among many enzymes rather than depending on a single rate-limiting step. MCA also proved that this distribution depends not only on the stoichiometric structure of the network but also on other kinetic determinants, such as the degree of saturation of the enzyme active site, the distance to thermodynamic equilibrium, and metabolite feedback regulatory loops. Consequently, predicting the alterations that occur during metabolic adaptation in response to strong changes involving a redistribution in such control distribution can be challenging. Here, using the framework provided by MCA, we illustrate how control distribution in a metabolic pathway/network depends on enzyme kinetic determinants and to what extent the redistribution of control affects our predictions on candidate enzymes suitable as targets for small molecule inhibition in the drug discovery process. Our results uncover that kinetic determinants can lead to unexpected control distribution and outcomes that cannot be predicted solely from stoichiometric determinants. We also unveil that the inference of key enzyme-drivers of an observed metabolic adaptation can be dramatically improved using mean control coefficients and ruling out those enzyme activities that are associated with low control coefficients. As the use of constraint-based stoichiometric genome-scale metabolic models (GSMMs) becomes increasingly prevalent for identifying genes/enzymes that could be potential drug targets, we anticipate that incorporating kinetic determinants and ruling out enzymes with low control coefficients into GSMM workflows will facilitate more accurate predictions and reveal novel therapeutic targets.
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Affiliation(s)
- Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine & Institute of Biomedicine of Universitat de Barcelona, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, 28020, Spain.
| | - Carles Foguet
- British Heart Foundation Cardiovascular Epidemiology Unit and Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BD, United Kingdom
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine & Institute of Biomedicine of Universitat de Barcelona, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, 28020, Spain.
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14
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M. Glueck
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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15
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Moreno-Sánchez R, Robledo-Cadena DX, Pacheco-Velázquez SC, Vargas Navarro JL, Padilla-Flores JA, Rodríguez-Enríquez S. Estimation of energy pathway fluxes in cancer cells - Beyond the Warburg effect. Arch Biochem Biophys 2023; 739:109559. [PMID: 36906097 DOI: 10.1016/j.abb.2023.109559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/15/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
Glycolytic and respiratory fluxes were analyzed in cancer and non-cancer cells. The steady-state fluxes in energy metabolism were used to estimate the contributions of aerobic glycolytic and oxidative phosphorylation (OxPhos) pathways to the cellular ATP supply. The rate of lactate production - corrected for the fraction generated by glutaminolysis - is proposed as the appropriate way to estimate glycolytic flux. In general, the glycolytic rates estimated for cancer cells are higher than those found in non-cancer cells, as originally observed by Otto Warburg. The rate of basal or endogenous cellular O2 consumption corrected for non-ATP synthesizing O2 consumption, measured after inhibition by oligomycin (a specific, potent and permeable ATP synthase inhibitor), has been proposed as the appropriate way to estimate mitochondrial ATP synthesis-linked O2 flux or net OxPhos flux in living cells. Detecting non-negligible oligomycin-sensitive O2 consumption rates in cancer cells has revealed that the mitochondrial function is not impaired, as claimed by the Warburg effect. Furthermore, when calculating the relative contributions to cellular ATP supply, under a variety of environmental conditions and for different types of cancer cells, it was found that OxPhos pathway was the main ATP provider over glycolysis. Hence, OxPhos pathway targeting can be successfully used to block in cancer cells ATP-dependent processes such as migration. These observations may guide the re-design of novel targeted therapies.
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Affiliation(s)
- Rafael Moreno-Sánchez
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Carrera de Biología, Laboratorio de Control Metabólico, Los Reyes Ixtacala, Hab. Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, Mexico.
| | | | | | - Jorge Luis Vargas Navarro
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Carrera de Biología, Laboratorio de Control Metabólico, Los Reyes Ixtacala, Hab. Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, Mexico
| | - Joaquín Alberto Padilla-Flores
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Carrera de Biología, Laboratorio de Control Metabólico, Los Reyes Ixtacala, Hab. Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, Mexico
| | - Sara Rodríguez-Enríquez
- Instituto Nacional de Cardiología, Departamento de Bioquímica, Ciudad de México, 14080, Mexico; Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Carrera de Medicina, Laboratorio de Control Metabólico, Los Reyes Ixtacala, Hab. Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, Mexico.
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16
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Hu M, Dinh HV, Shen Y, Suthers PF, Foster CJ, Call CM, Ye X, Pratas J, Fatma Z, Zhao H, Rabinowitz JD, Maranas CD. Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metab Eng 2023; 76:1-17. [PMID: 36603705 DOI: 10.1016/j.ymben.2023.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/04/2023]
Abstract
The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.
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Affiliation(s)
- Mengqi Hu
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Hoang V Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA; Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Charles J Foster
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Catherine M Call
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA; Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Xuanjia Ye
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jimmy Pratas
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA; Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Zia Fatma
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA; Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA.
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17
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Lu YA, Brien CMO, Mashek DG, Hu WS, Zhang Q. Kinetic-model-based pathway optimization with application to reverse glycolysis in mammalian cells. Biotechnol Bioeng 2023; 120:216-229. [PMID: 36184902 DOI: 10.1002/bit.28249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
Abstract
Over the last two decades, model-based metabolic pathway optimization tools have been developed for the design of microorganisms to produce desired metabolites. However, few have considered more complex cellular systems such as mammalian cells, which requires the use of nonlinear kinetic models to capture the effects of concentration changes and cross-regulatory interactions. In this study, we develop a new two-stage pathway optimization framework based on kinetic models that incorporate detailed kinetics and regulation information. In Stage 1, a set of optimization problems are solved to identify and rank the enzymes that contribute the most to achieving the metabolic objective. Stage 2 then determines the optimal enzyme interventions for specified desired numbers of enzyme adjustments. It also incorporates multi-scenario optimization, which allows the simultaneous consideration of multiple physiological conditions. We apply the proposed framework to find enzyme adjustments that enable a reverse glucose flow in cultured mammalian cells, thereby eliminating the need for glucose feed in the late culture stage and enhancing process robustness. The computational results demonstrate the efficacy of the proposed approach; it not only captures the important regulations and key enzymes for reverse glycolysis but also identifies differences and commonalities in the metabolic requirements for different carbon sources.
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Affiliation(s)
- Yen-An Lu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Conor M O' Brien
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qi Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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18
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Pacheco-Velázquez SC, Ortega-Mejía II, Vargas-Navarro JL, Padilla-Flores JA, Robledo-Cadena DX, Tapia-Martínez G, Peñalosa-Castro I, Aguilar-Ponce JL, Granados-Rivas JC, Moreno-Sánchez R, Rodríguez-Enríquez S. 17-β Estradiol up-regulates energy metabolic pathways, cellular proliferation and tumor invasiveness in ER+ breast cancer spheroids. Front Oncol 2022; 12:1018137. [PMID: 36419896 PMCID: PMC9676491 DOI: 10.3389/fonc.2022.1018137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/18/2022] [Indexed: 09/08/2024] Open
Abstract
Several biological processes related to cancer malignancy are regulated by 17-β estradiol (E2) in ER+-breast cancer. To establish the role of E2 on the atypical cancer energy metabolism, a systematic study analyzing transcription factors, proteins, and fluxes associated with energy metabolism was undertaken in multicellular tumor spheroids (MCTS) from human ER+ MCF-7 breast cancer cells. At E2 physiological concentrations (10 and 100 nM for 24 h), both ERα and ERβ receptors, and their protein target pS2, increased by 0.6-3.5 times vs. non-treated MCTS, revealing an activated E2/ER axis. E2 also increased by 30-470% the content of several transcription factors associated to mitochondrial biogenesis and oxidative phosphorylation (OxPhos) (p53, PGC1-α) and glycolytic pathways (HIF1-α, c-MYC). Several OxPhos and glycolytic proteins (36-257%) as well as pathway fluxes (48-156%) significantly increased being OxPhos the principal ATP cellular supplier (>75%). As result of energy metabolism stimulation by E2, cancer cell migration and invasion processes and related proteins (SNAIL, FN, MM-9) contents augmented by 24-189% vs. non-treated MCTS. Celecoxib at 10 nM blocked OxPhos (60%) as well as MCTS growth, cell migration and invasiveness (>40%); whereas the glycolytic inhibitor iodoacetate (0.5 µM) and doxorubicin (70 nM) were innocuous. Our results show for the first time using a more physiological tridimensional cancer model, resembling the initial stages of solid tumors, that anti-mitochondrial therapy may be useful to deter hormone-dependent breast carcinomas.
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Affiliation(s)
| | | | | | | | | | | | - Ignacio Peñalosa-Castro
- Laboratorio de Control Metabólico, Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab, Tlalnepantla, Mexico
| | | | - Juan Carlos Granados-Rivas
- Laboratorio de Control Metabólico, Carrera de Medicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab, Tlalnepantla, Mexico
| | - Rafael Moreno-Sánchez
- Laboratorio de Control Metabólico, Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab, Tlalnepantla, Mexico
| | - Sara Rodríguez-Enríquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Ciudad de México, Mexico
- Laboratorio de Control Metabólico, Carrera de Medicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab, Tlalnepantla, Mexico
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19
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Quantitative metabolic fluxes regulated by trans-omic networks. Biochem J 2022; 479:787-804. [PMID: 35356967 PMCID: PMC9022981 DOI: 10.1042/bcj20210596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 12/21/2022]
Abstract
Cells change their metabolism in response to internal and external conditions by regulating the trans-omic network, which is a global biochemical network with multiple omic layers. Metabolic flux is a direct measure of the activity of a metabolic reaction that provides valuable information for understanding complex trans-omic networks. Over the past decades, techniques to determine metabolic fluxes, including 13C-metabolic flux analysis (13C-MFA), flux balance analysis (FBA), and kinetic modeling, have been developed. Recent studies that acquire quantitative metabolic flux and multi-omic data have greatly advanced the quantitative understanding and prediction of metabolism-centric trans-omic networks. In this review, we present an overview of 13C-MFA, FBA, and kinetic modeling as the main techniques to determine quantitative metabolic fluxes, and discuss their advantages and disadvantages. We also introduce case studies with the aim of understanding complex metabolism-centric trans-omic networks based on the determination of metabolic fluxes.
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20
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Santin A, Russo MT, Ferrante MI, Balzano S, Orefice I, Sardo A. Highly Valuable Polyunsaturated Fatty Acids from Microalgae: Strategies to Improve Their Yields and Their Potential Exploitation in Aquaculture. Molecules 2021; 26:7697. [PMID: 34946780 PMCID: PMC8707597 DOI: 10.3390/molecules26247697] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microalgae have a great potential for the production of healthy food and feed supplements. Their ability to convert carbon into high-value compounds and to be cultured in large scale without interfering with crop cultivation makes these photosynthetic microorganisms promising for the sustainable production of lipids. In particular, microalgae represent an alternative source of polyunsaturated fatty acids (PUFAs), whose consumption is related to various health benefits for humans and animals. In recent years, several strategies to improve PUFAs' production in microalgae have been investigated. Such strategies include selecting the best performing species and strains and the optimization of culturing conditions, with special emphasis on the different cultivation systems and the effect of different abiotic factors on PUFAs' accumulation in microalgae. Moreover, developments and results obtained through the most modern genetic and metabolic engineering techniques are described, focusing on the strategies that lead to an increased lipid production or an altered PUFAs' profile. Additionally, we provide an overview of biotechnological applications of PUFAs derived from microalgae as safe and sustainable organisms, such as aquafeed and food ingredients, and of the main techniques (and their related issues) for PUFAs' extraction and purification from microalgal biomass.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (A.S.); (M.T.R.); (S.B.); (I.O.)
| | - Monia Teresa Russo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (A.S.); (M.T.R.); (S.B.); (I.O.)
| | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (A.S.); (M.T.R.); (S.B.); (I.O.)
| | - Sergio Balzano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (A.S.); (M.T.R.); (S.B.); (I.O.)
- Department of Marine Microbiology and Biogeochemistry, Netherland Institute for Sea Research, Landsdiep 4, 1793 AB Texel, The Netherlands
| | - Ida Orefice
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (A.S.); (M.T.R.); (S.B.); (I.O.)
| | - Angela Sardo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (A.S.); (M.T.R.); (S.B.); (I.O.)
- Istituto di Scienze Applicate e Sistemi Intelligenti “Eduardo Caianiello”, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
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21
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Marín-Hernández Á, Rodríguez-Zavala JS, Jasso-Chávez R, Saavedra E, Moreno-Sánchez R. Protein acetylation effects on enzyme activity and metabolic pathway fluxes. J Cell Biochem 2021; 123:701-718. [PMID: 34931340 DOI: 10.1002/jcb.30197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/11/2022]
Abstract
Acetylation of proteins seems a widespread process found in the three domains of life. Several studies have shown that besides histones, acetylation of lysine residues also occurs in non-nuclear proteins. Hence, it has been suggested that this covalent modification is a mechanism that might regulate diverse metabolic pathways by modulating enzyme activity, stability, and/or subcellular localization or interaction with other proteins. However, protein acetylation levels seem to have low correlation with modification of enzyme activity and pathway fluxes. In addition, the results obtained with mutant enzymes that presumably mimic acetylation have frequently been over-interpreted. Moreover, there is a generalized lack of rigorous enzyme kinetic analysis in parallel to acetylation level determinations. The purpose of this review is to analyze the current findings on the impact of acetylation on metabolic enzymes and its repercussion on metabolic pathways function/regulation.
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Affiliation(s)
| | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
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22
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Moreno-Sánchez R, Gallardo-Pérez JC, Pacheco-Velazquez SC, Robledo-Cadena DX, Rodríguez-Enríquez S, Encalada R, Saavedra E, Marín-Hernández Á. Regulatory role of acetylation on enzyme activity and fluxes of energy metabolism pathways. Biochim Biophys Acta Gen Subj 2021; 1865:130021. [PMID: 34597724 DOI: 10.1016/j.bbagen.2021.130021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Most of the enzymes involved in the central carbon metabolism are acetylated in Lys residues. It has been claimed that this covalent modification represents a novel regulatory mechanism by which both enzyme/transporter activities and pathway fluxes can be modulated. METHODS To establish which enzymes are regulated by acetylation, a systematic experimental analysis of activities and acetylation profile for several energy metabolism enzymes and pathway fluxes was undertaken in cells and mitochondria. RESULTS The majority of the glycolytic and neighbor enzymes as well as mitochondrial enzymes indeed showed Lys-acetylation, with GLUT1, HPI, CS, ATP synthase displaying comparatively lower acetylation patterns. The incubation of cytosolic and mitochondrial fractions with recombinant Sirt-3 produced lower acetylation signals, whereas incubation with acetyl-CoA promoted protein acetylation. Significant changes in acetylation levels of MDH and IDH-2 from rat liver mitochondria revealed no change in their activities. Similar observations were attained for the cytosolic enzymes from AS-30D and HeLa cells. A minor but significant (23%) increase in the AAT-MDH complex activity induced by acetylation was observed. To examine this question further, AS-30D and HeLa cells were treated with nicotinamide and valproic acid. These compounds promoted changes in the acetylation patterns of glycolytic proteins, although their activities and the glycolytic flux (as well as the OxPhos flux) revealed no clear correlation with acetylation. CONCLUSION Acetylation seems to play no predominant role in the control of energy metabolism enzyme activities and pathway fluxes. GENERAL SIGNIFICANCE The physiological function of protein acetylation on energy metabolism pathways remains to be elucidated.
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Affiliation(s)
- Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City 14080, Mexico
| | | | | | | | | | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City 14080, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City 14080, Mexico
| | - Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City 14080, Mexico.
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23
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Munro LJ, Kell DB. Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Affiliation(s)
- Lachlan J. Munro
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Douglas B. Kell
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, U.K
- Mellizyme Biotechnology Ltd, IC1, Liverpool Science Park, 131 Mount Pleasant, Liverpool L3 5TF, U.K
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24
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Kozaeva E, Volkova S, Matos MRA, Mezzina MP, Wulff T, Volke DC, Nielsen LK, Nikel PI. Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A-dependent bioproduction in rewired Pseudomonas putida. Metab Eng 2021; 67:373-386. [PMID: 34343699 DOI: 10.1016/j.ymben.2021.07.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023]
Abstract
Pseudomonas putida is evolutionarily endowed with features relevant for bioproduction, especially under harsh operating conditions. The rich metabolic versatility of this species, however, comes at the price of limited formation of acetyl-coenzyme A (CoA) from sugar substrates. Since acetyl-CoA is a key metabolic precursor for a number of added-value products, in this work we deployed an in silico-guided rewiring program of central carbon metabolism for upgrading P. putida as a host for acetyl-CoA-dependent bioproduction. An updated kinetic model, integrating fluxomics and metabolomics datasets in addition to manually-curated information of enzyme mechanisms, identified targets that would lead to increased acetyl-CoA levels. Based on these predictions, a set of plasmids based on clustered regularly interspaced short palindromic repeats (CRISPR) and dead CRISPR-associated protein 9 (dCas9) was constructed to silence genes by CRISPR interference (CRISPRi). Dynamic reduction of gene expression of two key targets (gltA, encoding citrate synthase, and the essential accA gene, encoding subunit A of the acetyl-CoA carboxylase complex) mediated an 8-fold increase in the acetyl-CoA content of rewired P. putida. Poly(3-hydroxybutyrate) (PHB) was adopted as a proxy of acetyl-CoA availability, and two synthetic pathways were engineered for biopolymer accumulation. By including cell morphology as an extra target for the CRISPRi approach, fully rewired P. putida strains programmed for PHB accumulation had a 5-fold increase in PHB titers in bioreactor cultures using glucose. Thus, the strategy described herein allowed for rationally redirecting metabolic fluxes in P. putida from central metabolism towards product biosynthesis-especially relevant when deletion of essential pathways is not an option.
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Affiliation(s)
- Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Svetlana Volkova
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Marta R A Matos
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mariela P Mezzina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Lars K Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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25
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Klaus VS, Schriever SC, Monroy Kuhn JM, Peter A, Irmler M, Tokarz J, Prehn C, Kastenmüller G, Beckers J, Adamski J, Königsrainer A, Müller TD, Heni M, Tschöp MH, Pfluger PT, Lutter D. Correlation guided Network Integration (CoNI) reveals novel genes affecting hepatic metabolism. Mol Metab 2021; 53:101295. [PMID: 34271221 PMCID: PMC8361260 DOI: 10.1016/j.molmet.2021.101295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
Objective Technological advances have brought a steady increase in the availability of various types of omics data, from genomics to metabolomics. Integrating these multi-omics data is a chance and challenge for systems biology; yet, tools to fully tap their potential remain scarce. Methods We present here a fully unsupervised and versatile correlation-based method – termed Correlation guided Network Integration (CoNI) – to integrate multi-omics data into a hypergraph structure that allows for the identification of effective modulators of metabolism. Our approach yields single transcripts of potential relevance that map to specific, densely connected, metabolic subgraphs or pathways. Results By applying our method on transcriptomics and metabolomics data from murine livers under standard Chow or high-fat diet, we identified eleven genes with potential regulatory effects on hepatic metabolism. Five candidates, including the hepatokine INHBE, were validated in human liver biopsies to correlate with diabetes-related traits such as overweight, hepatic fat content, and insulin resistance (HOMA-IR). Conclusion Our method's successful application to an independent omics dataset confirmed that the novel CoNI framework is a transferable, entirely data-driven, flexible, and versatile tool for multiple omics data integration and interpretation.
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Affiliation(s)
- Valentina S Klaus
- Computational Discovery Research Unit, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany; TUM School of Medicine, Neurobiology of Diabetes, Technical University Munich, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany
| | - Sonja C Schriever
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany; Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, Neuherberg, Germany
| | - José Manuel Monroy Kuhn
- Computational Discovery Research Unit, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany
| | - Andreas Peter
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tübingen, Tübingen, Germany; Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Janina Tokarz
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gabi Kastenmüller
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Beckers
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Neuherberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Neuherberg, Germany
| | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Germany
| | - Timo D Müller
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany; Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Eberhard Karls University Hospitals and Clinics, Tübingen, Germany
| | - Martin Heni
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tübingen, Tübingen, Germany; Department of Internal Medicine, Division of Endocrinology, Diabetology, and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Matthias H Tschöp
- TUM School of Medicine, Neurobiology of Diabetes, Technical University Munich, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany; Division of Metabolic Diseases, Department of Medicine, Technical University Munich, Munich, Germany
| | - Paul T Pfluger
- TUM School of Medicine, Neurobiology of Diabetes, Technical University Munich, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany; Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dominik Lutter
- Computational Discovery Research Unit, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Germany.
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26
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Gao P, Huang X, Fang XY, Zheng H, Cai SL, Sun AJ, Zhao L, Zhang Y. Application of metabolomics in clinical and laboratory gastrointestinal oncology. World J Gastrointest Oncol 2021; 13:536-549. [PMID: 34163571 PMCID: PMC8204353 DOI: 10.4251/wjgo.v13.i6.536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/09/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Metabolites are versatile bioactive molecules. They are not only the substrates and/or the products of enzymatic reactions but also act as the regulators in the systemic metabolism. Metabolomics is a high-throughput analytical strategy to qualify or quantify as many metabolites as possible in the metabolomes. It is an indispensable part of systems biology. The leading techniques in this field are mainly based on mass spectrometry and nuclear magnetic resonance spectroscopy. The metabolomic analysis has gained wide use in bioscience fields. In the tumor research arena, metabolomics can be employed to identify biomarkers for prediction, diagnosis, and prognosis. Chemotherapeutic effect evaluation and personalized medicine decision-making can also benefit from metabolomic analysis of patient biofluid or biopsy samples. Many cell-level studies can help in disease exploration. In this review, the basic features and principles of varied metabolomic analysis are introduced. The value of metabolomics in clinical and laboratory gastrointestinal cancer studies is discussed, especially for mass spectrometry applications. Besides, combined use of metabolomics and other tools to solve problems in cancer practice is briefly illustrated. In summary, metabolomics paves a new way to explore cancerous diseases in the light of small molecules.
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Affiliation(s)
- Peng Gao
- Department ofClinical Laboratory, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Xin Huang
- Department of Internal Medicine, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Xue-Yan Fang
- Department of Nursing, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Hui Zheng
- Clinical Research Center, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Shu-Ling Cai
- Clinical Research Center, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Ai-Jun Sun
- Clinical Research Center, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Liang Zhao
- Department of Internal Medicine, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Yong Zhang
- Department of Surgery, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
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27
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Cloutier M, Xiang D, Gao P, Kochian LV, Zou J, Datla R, Wang E. Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642938. [PMID: 33889166 PMCID: PMC8056077 DOI: 10.3389/fpls.2021.642938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Fatty acids in crop seeds are a major source for both vegetable oils and industrial applications. Genetic improvement of fatty acid composition and oil content is critical to meet the current and future demands of plant-based renewable seed oils. Addressing this challenge can be approached by network modeling to capture key contributors of seed metabolism and to identify underpinning genetic targets for engineering the traits associated with seed oil composition and content. Here, we present a dynamic model, using an Ordinary Differential Equations model and integrated time-course gene expression data, to describe metabolic networks during Arabidopsis thaliana seed development. Through in silico perturbation of genes, targets were predicted in seed oil traits. Validation and supporting evidence were obtained for several of these predictions using published reports in the scientific literature. Furthermore, we investigated two predicted targets using omics datasets for both gene expression and metabolites from the seed embryo, and demonstrated the applicability of this network-based model. This work highlights that integration of dynamic gene expression atlases generates informative models which can be explored to dissect metabolic pathways and lead to the identification of causal genes associated with seed oil traits.
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Affiliation(s)
- Mathieu Cloutier
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edwin Wang
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
- Centre for Health Genomics and Informatics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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28
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Millard P, Enjalbert B, Uttenweiler-Joseph S, Portais JC, Létisse F. Control and regulation of acetate overflow in Escherichia coli. eLife 2021; 10:63661. [PMID: 33720011 PMCID: PMC8021400 DOI: 10.7554/elife.63661] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
Overflow metabolism refers to the production of seemingly wasteful by-products by cells during growth on glucose even when oxygen is abundant. Two theories have been proposed to explain acetate overflow in Escherichia coli – global control of the central metabolism and local control of the acetate pathway – but neither accounts for all observations. Here, we develop a kinetic model of E. coli metabolism that quantitatively accounts for observed behaviours and successfully predicts the response of E. coli to new perturbations. We reconcile these theories and clarify the origin, control, and regulation of the acetate flux. We also find that, in turns, acetate regulates glucose metabolism by coordinating the expression of glycolytic and TCA genes. Acetate should not be considered a wasteful end-product since it is also a co-substrate and a global regulator of glucose metabolism in E. coli. This has broad implications for our understanding of overflow metabolism.
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Affiliation(s)
- Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Brice Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Jean-Charles Portais
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, INSERM U1031, CNRS 5070, Université Toulouse III - Paul Sabatier, EFS, Toulouse, France
| | - Fabien Létisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,Université Toulouse III - Paul Sabatier, Toulouse, France
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29
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Utomo JC, Chaves FC, Bauchart P, Martin VJJ, Ro DK. Developing a Yeast Platform Strain for an Enhanced Taxadiene Biosynthesis by CRISPR/Cas9. Metabolites 2021; 11:147. [PMID: 33802586 PMCID: PMC8000486 DOI: 10.3390/metabo11030147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022] Open
Abstract
Paclitaxel is an important diterpenoid commonly used as an anticancer drug. Although the paclitaxel biosynthetic pathway has been mostly revealed, some steps remain to be elucidated. The difficulties in plant transformations and the scarcity of the precursor of paclitaxel, (+)-taxa-4(5), 11(12)-diene (taxadiene), have hindered the full comprehension of paclitaxel biochemistry and, therefore, its production by biotechnological approaches. One solution is to use the budding yeast, Saccharomyces cerevisiae, as a platform to elucidate the paclitaxel biosynthesis. As taxadiene is a diterpenoid, its common precursor, geranylgeranyl pyrophosphate (GGPP), needs to be increased in yeast. In this study, we screened various GGPP synthases (GGPPS) to find the most suitable GGPPS for taxadiene production in yeast. We also optimized the taxadiene production by increasing the flux toward the terpenoid pathway. Finally, to remove selection markers, we integrated the required genes using a CRISPR/Cas9 system in the yeast genome. Our result showed that a titer of 2.02 ± 0.40 mg/L (plasmid) and 0.41 ± 0.06 mg/L (integrated) can be achieved using these strategies. This platform strain can be used to readily test the gene candidates for microbial paclitaxel biosynthesis in the future.
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Affiliation(s)
- Joseph C. Utomo
- Department of Biological Science, University of Calgary, Calgary, AB T2N1N4, Canada;
| | - Fabio C. Chaves
- Programa de Pós-graduação em Ciência e Tecnologia de Alimentos, Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Caixa Postal 354, Pelotas CEP 96010-900, Brazil;
| | - Philippe Bauchart
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC H4B1R6, Canada; (P.B.); (V.J.J.M.)
| | - Vincent J. J. Martin
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC H4B1R6, Canada; (P.B.); (V.J.J.M.)
| | - Dae-Kyun Ro
- Department of Biological Science, University of Calgary, Calgary, AB T2N1N4, Canada;
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30
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Yang H, Song L, Zou Y, Sun D, Wang L, Yu Z, Guo J. Role of Hyaluronic Acids and Potential as Regenerative Biomaterials in Wound Healing. ACS APPLIED BIO MATERIALS 2021; 4:311-324. [PMID: 35014286 DOI: 10.1021/acsabm.0c01364] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The skin can protect the body from external harm, sense environmental changes, and maintain physiological homeostasis. Cutaneous repair and regeneration associated with surgical wounds, acute traumas, and chronic diseases are a central concern of healthcare. Patients may experience the failure of current treatments due to the complexity of the healing process; therefore, emerging strategies are needed. Hyaluronic acids (HAs, also known as hyaluronan), a glycosaminoglycan (GAG) of the extracellular matrix (ECM), play key roles in cell differentiation, proliferation, and migration throughout tissue development and regeneration. Recently, HA derivatives have been developed as regenerative biomaterials for treating skin damage and injury. In this review, the healing process, namely, hemostasis, inflammation, proliferation, and maturation, is described and the role of HAs in the healing process is discussed. This review also provides recent examples in the development of HA derivatives for wound healing.
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Affiliation(s)
- Hao Yang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Liu Song
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Yifang Zou
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Dandan Sun
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Limei Wang
- Department of Pharmacy, The General Hospital of FAW, Changchun 130011, China
| | - Zhuo Yu
- Department of Hepatopathy, Shuguang Hospital, Affiliated with Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianfeng Guo
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
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31
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Voit EO. Metabolic Systems. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11619-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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32
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Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms 2020; 8:E2050. [PMID: 33371386 PMCID: PMC7767376 DOI: 10.3390/microorganisms8122050] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines are driven by predictive design tools, these tools have been difficult to build for biological design due to the complexity of biological systems and many unknowns of their quantitative behavior. However, due to many recent advances, the gap between design in biology and other engineering fields is closing. In this work, we discuss promising areas of development of computational tools for engineering microbial strains. We define five frontiers of active research: (1) Constraint-based modeling and metabolic network reconstruction, (2) Kinetics and thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence analysis, and (5) Regulatory network analysis. Experimental and machine learning drivers have enabled these methods to improve by leaps and bounds in both scope and accuracy. Modern strain design projects will require these tools to be comprehensively applied to the entire cell and efficiently integrated within a single workflow. We expect that these frontiers, enabled by the ongoing revolution of big data science, will drive forward more advanced and powerful strain engineering strategies.
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Affiliation(s)
- Daniel Craig Zielinski
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Balasubramanian S, Chandrasekran P, Yesudhas AJR, Ganapathyraman P, Eiteman MA, Subramanian R. In vivo interpretation of model predicted inhibition in acrylate pathway engineered
Lactococcus lactis. Biotechnol Bioeng 2020; 117:3785-3798. [DOI: 10.1002/bit.27517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering University of Georgia Athens Georgia
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Lo-Thong O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F. Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches. Sci Rep 2020; 10:13446. [PMID: 32778715 PMCID: PMC7417601 DOI: 10.1038/s41598-020-70295-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 07/27/2020] [Indexed: 11/29/2022] Open
Abstract
Metabolic pathway modeling plays an increasing role in drug design by allowing better understanding of the underlying regulation and controlling networks in the metabolism of living organisms. However, despite rapid progress in this area, pathway modeling can become a real nightmare for researchers, notably when few experimental data are available or when the pathway is highly complex. Here, three different approaches were developed to model the second part of glycolysis of E. histolytica as an application example, and have succeeded in predicting the final pathway flux: one including detailed kinetic information (white-box), another with an added adjustment term (grey-box) and the last one using an artificial neural network method (black-box). Afterwards, each model was used for metabolic control analysis and flux control coefficient determination. The first two enzymes of this pathway are identified as the key enzymes playing a role in flux control. This study revealed the significance of the three methods for building suitable models adjusted to the available data in the field of metabolic pathway modeling, and could be useful to biologists and modelers.
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Affiliation(s)
- Ophélie Lo-Thong
- University of Paris, UMR_S1134, BIGR, Inserm, 75015, Paris, France.,DSIMB, UMR_S1134, BIGR, Inserm, Laboratory of Excellence GR-Ex, Faculty of Sciences and Technology, University of La Reunion, 97715, Saint-Denis, France
| | - Philippe Charton
- University of Paris, UMR_S1134, BIGR, Inserm, 75015, Paris, France.,DSIMB, UMR_S1134, BIGR, Inserm, Laboratory of Excellence GR-Ex, Faculty of Sciences and Technology, University of La Reunion, 97715, Saint-Denis, France
| | - Xavier F Cadet
- PEACCEL, Artificial Intelligence Department, 6 square Albin Cachot, box 42, 75013, Paris, France
| | - Brigitte Grondin-Perez
- LE2P, Laboratory of Energy, Electronics and Processes EA 4079, Faculty of Sciences and Technology, University of La Reunion, 97444, St Denis cedex, France
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, 14080, Mexico City, Mexico
| | - Cédric Damour
- LE2P, Laboratory of Energy, Electronics and Processes EA 4079, Faculty of Sciences and Technology, University of La Reunion, 97444, St Denis cedex, France
| | - Frédéric Cadet
- University of Paris, UMR_S1134, BIGR, Inserm, 75015, Paris, France. .,DSIMB, UMR_S1134, BIGR, Inserm, Laboratory of Excellence GR-Ex, Faculty of Sciences and Technology, University of La Reunion, 97715, Saint-Denis, France.
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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A combined experimental and modelling approach for the Weimberg pathway optimisation. Nat Commun 2020; 11:1098. [PMID: 32107375 PMCID: PMC7046635 DOI: 10.1038/s41467-020-14830-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/31/2020] [Indexed: 02/06/2023] Open
Abstract
The oxidative Weimberg pathway for the five-step pentose degradation to α-ketoglutarate is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. The oxidative pathway from Caulobacter crescentus has been employed in in-vivo metabolic engineering with intact cells and in in-vitro enzyme cascades. The performance of such engineering approaches is often hampered by systems complexity, caused by non-linear kinetics and allosteric regulatory mechanisms. Here we report an iterative approach to construct and validate a quantitative model for the Weimberg pathway. Two sensitive points in pathway performance have been identified as follows: (1) product inhibition of the dehydrogenases (particularly in the absence of an efficient NAD+ recycling mechanism) and (2) balancing the activities of the dehydratases. The resulting model is utilized to design enzyme cascades for optimized conversion and to analyse pathway performance in C. cresensus cell-free extracts.
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Krycer JR, Quek LE, Francis D, Fazakerley DJ, Elkington SD, Diaz-Vegas A, Cooke KC, Weiss FC, Duan X, Kurdyukov S, Zhou PX, Tambar UK, Hirayama A, Ikeda S, Kamei Y, Soga T, Cooney GJ, James DE. Lactate production is a prioritized feature of adipocyte metabolism. J Biol Chem 2020; 295:83-98. [PMID: 31690627 PMCID: PMC6952601 DOI: 10.1074/jbc.ra119.011178] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Adipose tissue is essential for whole-body glucose homeostasis, with a primary role in lipid storage. It has been previously observed that lactate production is also an important metabolic feature of adipocytes, but its relationship to adipose and whole-body glucose disposal remains unclear. Therefore, using a combination of metabolic labeling techniques, here we closely examined lactate production of cultured and primary mammalian adipocytes. Insulin treatment increased glucose uptake and conversion to lactate, with the latter responding more to insulin than did other metabolic fates of glucose. However, lactate production did not just serve as a mechanism to dispose of excess glucose, because we also observed that lactate production in adipocytes did not solely depend on glucose availability and even occurred independently of glucose metabolism. This suggests that lactate production is prioritized in adipocytes. Furthermore, knocking down lactate dehydrogenase specifically in the fat body of Drosophila flies lowered circulating lactate and improved whole-body glucose disposal. These results emphasize that lactate production is an additional metabolic role of adipose tissue beyond lipid storage and release.
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Affiliation(s)
- James R Krycer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lake-Ee Quek
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia; School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Deanne Francis
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Daniel J Fazakerley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia; Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Sarah D Elkington
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexis Diaz-Vegas
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kristen C Cooke
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fiona C Weiss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Xiaowen Duan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sergey Kurdyukov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ping-Xin Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038; School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Uttam K Tambar
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-Ku, Tokyo 100-0004, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Yushi Kamei
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-Ku, Tokyo 100-0004, Japan
| | - Gregory J Cooney
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia; Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
| | - David E James
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia; Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
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38
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González-Chávez Z, Vázquez C, Moreno-Sánchez R, Saavedra E. Metabolic Control Analysis for Drug Target Prioritization in Trypanosomatids. Methods Mol Biol 2020; 2116:689-718. [PMID: 32221950 DOI: 10.1007/978-1-0716-0294-2_41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To validate therapeutic targets in metabolic pathways of trypanosomatids, the criterion of enzyme essentiality determined by gene knockout or knockdown is usually being applied. Since, it is often found that most of the enzymes/proteins analyzed are essential, additional criteria have to be implemented for drug target prioritization. Metabolic control analysis (MCA), often in conjunction with kinetic pathway modeling, offers such possibility for prioritization. MCA is a theoretical and experimental approach to analyze how metabolic pathways are controlled. It involves strategies to perform quantitative analyses to determine the degree in which an enzyme controls a pathway flux, a value called flux control coefficient ([Formula: see text]). By determining the [Formula: see text] of individual steps in a metabolic pathway, the distribution of control of the pathway is established, that is, the identification of the main flux-controlling steps. Therefore, MCA can help in ranking pathway enzymes as drug targets from a metabolic perspective. In this chapter, three approaches to determine [Formula: see text] are reviewed: (1) In vitro pathway reconstitution, (2) manipulation of enzyme activities within parasites, and (3) in silico kinetic modeling of the metabolic pathway. To perform these methods, accurate experimental data of enzyme activities, metabolite concentrations and pathway fluxes are necessary. The methodology is illustrated with the example of trypanothione metabolism of Trypanosoma cruzi and protocols to determine such experimental data for this metabolic process are also described. However, the MCA strategy can be applied to any metabolic pathway in the parasite and general directions to perform it are provided in this chapter.
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Affiliation(s)
- Zabdi González-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico.
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Saavedra E, González-Chávez Z, Moreno-Sánchez R, Michels PA. Drug Target Selection for Trypanosoma cruzi Metabolism by Metabolic Control Analysis and Kinetic Modeling. Curr Med Chem 2019; 26:6652-6671. [DOI: 10.2174/0929867325666180917104242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/22/2022]
Abstract
In the search for therapeutic targets in the intermediary metabolism of trypanosomatids
the gene essentiality criterion as determined by using knock-out and knock-down genetic
strategies is commonly applied. As most of the evaluated enzymes/transporters have
turned out to be essential for parasite survival, additional criteria and approaches are clearly
required for suitable drug target prioritization. The fundamentals of Metabolic Control
Analysis (MCA; an approach in the study of control and regulation of metabolism) and kinetic
modeling of metabolic pathways (a bottom-up systems biology approach) allow quantification
of the degree of control that each enzyme exerts on the pathway flux (flux control coefficient)
and metabolic intermediate concentrations (concentration control coefficient). MCA
studies have demonstrated that metabolic pathways usually have two or three enzymes with
the highest control of flux; their inhibition has more negative effects on the pathway function
than inhibition of enzymes exerting low flux control. Therefore, the enzymes with the highest
pathway control are the most convenient targets for therapeutic intervention. In this review,
the fundamentals of MCA as well as experimental strategies to determine the flux control coefficients
and metabolic modeling are analyzed. MCA and kinetic modeling have been applied
to trypanothione metabolism in Trypanosoma cruzi and the model predictions subsequently
validated in vivo. The results showed that three out of ten enzyme reactions analyzed
in the T. cruzi anti-oxidant metabolism were the most controlling enzymes. Hence, MCA and
metabolic modeling allow a further step in target prioritization for drug development against
trypanosomatids and other parasites.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Zabdi González-Chávez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Paul A.M. Michels
- Centre for Immunity, Infection and Evolution (CIIE) and Centre for Translational and Chemical Biology (CTCB), School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
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Sorochynska OM, Bayliak MM, Gospodaryov DV, Vasylyk YV, Kuzniak OV, Pankiv TM, Garaschuk O, Storey KB, Lushchak VI. Every-Other-Day Feeding Decreases Glycolytic and Mitochondrial Energy-Producing Potentials in the Brain and Liver of Young Mice. Front Physiol 2019; 10:1432. [PMID: 31824339 PMCID: PMC6883932 DOI: 10.3389/fphys.2019.01432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/04/2019] [Indexed: 01/02/2023] Open
Abstract
Intermittent fasting is used to reduce body mass in obese adult humans and animals. However, information on the impact of one type of intermittent fasting (IF) called every-other-day feeding (EODF) on young animals is scarce. In this study, 1-month-old mice of both sexes were subjected to a 4-week regimen of EODF using age-matched counterparts fed ad libitum as controls. At the end of EODF exposure, experimental male and female mice weighed 14 and 13% less than the control counterparts. The EODF regimen resulted in lower liver levels of glycogen, glucose, and lactate, but did not affect lactate level in mouse cerebral cortex of both sexes. Activities of key glycolytic enzymes (hexokinase, phosphofructokinase, and pyruvate kinase) in liver of experimental mice were lower than those in controls. In the cerebral cortex, only hexokinase and pyruvate kinase activities were lower than in controls, but phosphofructokinase activity was not affected in IF females and was higher in IF males as compared with ad libitum fed males. Mitochondria isolated from liver of IF mice had lower respiratory control ratios, but those from the cortex had the same values as control animals. The concentration of β-hydroxybutyrate and the activity of β-hydroxybutyrate dehydrogenase were lower in the IF mouse liver, but not changed or enhanced in the IF cerebral cortex. Thus, animal responses to IF do not depend significantly on sex and are directed to decrease energy metabolism to save resources, and the effects are more pronounced in the liver than in the brain.
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Affiliation(s)
- Oksana M Sorochynska
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Maria M Bayliak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Dmytro V Gospodaryov
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Yulia V Vasylyk
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Oksana V Kuzniak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Tetiana M Pankiv
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Olga Garaschuk
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Volodymyr I Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
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Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis. Microb Cell Fact 2019; 18:192. [PMID: 31690314 PMCID: PMC6833178 DOI: 10.1186/s12934-019-1235-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Terpenoids are of high interest as chemical building blocks and pharmaceuticals. In microbes, terpenoids can be synthesized via the methylerythritol phosphate (MEP) or mevalonate (MVA) pathways. Although the MEP pathway has a higher theoretical yield, metabolic engineering has met with little success because the regulation of the pathway is poorly understood. RESULTS We applied metabolic control analysis to the MEP pathway in Escherichia coli expressing a heterologous isoprene synthase gene (ispS). The expression of ispS led to the accumulation of isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP) and severely impaired bacterial growth, but the coexpression of ispS and isopentenyl diphosphate isomerase (idi) restored normal growth and wild-type IPP/DMAPP levels. Targeted proteomics and metabolomics analysis provided a quantitative description of the pathway, which was perturbed by randomizing the ribosome binding site in the gene encoding 1-deoxyxylulose 5-phosphate synthase (Dxs). Dxs has a flux control coefficient of 0.35 (i.e., a 1% increase in Dxs activity resulted in a 0.35% increase in pathway flux) in the isoprene-producing strain and therefore exerted significant control over the flux though the MEP pathway. At higher dxs expression levels, the intracellular concentration of 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEcPP) increased substantially in contrast to the other MEP pathway intermediates, which were linearly dependent on the abundance of Dxs. This indicates that 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (IspG), which consumes MEcPP, became saturated and therefore limited the flux towards isoprene. The higher intracellular concentrations of MEcPP led to the efflux of this intermediate into the growth medium. DISCUSSION These findings show the importance of Dxs, Idi and IspG and metabolite export for metabolic engineering of the MEP pathway and will facilitate further approaches for the microbial production of valuable isoprenoids.
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Abstract
Abstract
Living organisms in analogy with chemical factories use simple molecules such as sugars to produce a variety of compounds which are necessary for sustaining life and some of which are also commercially valuable. The metabolisms of simple (such as bacteria) and higher organisms (such as plants) alike can be exploited to convert low value inputs into high value outputs. Unlike conventional chemical factories, microbial production chassis are not necessarily tuned for a single product overproduction. Despite the same end goal, metabolic and industrial engineers rely on different techniques for achieving productivity goals. Metabolic engineers cannot affect reaction rates by manipulating pressure and temperature, instead they have at their disposal a range of enzymes and transcriptional and translational processes to optimize accordingly. In this review, we first highlight how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed in systems and control engineering. Specifically, how algorithmic concepts derived in operations research can help explain the structure and organization of metabolic networks. Finally, we consider the future directions and challenges faced by the field of metabolic network modeling and the possible contributions of concepts drawn from the classical fields of chemical and control engineering. The aim of the review is to offer a current perspective of metabolic engineering and all that it entails without requiring specialized knowledge of bioinformatics or systems biology.
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Targeting pteridine reductase 1 and dihydrofolate reductase: the old is a new trend for leishmaniasis drug discovery. Future Med Chem 2019; 11:2107-2130. [DOI: 10.4155/fmc-2018-0512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Leishmaniasis is one of the major neglected tropical diseases in the world and it is considered endemic in 88 countries. This disease is transmitted by a Leishmania spp. infected sandfly and it may lead to cutaneous or systemic manifestations. The preconized treatment has low efficacy and there are cases of resistance to some drugs. Therefore, the search for new efficient molecular targets that can lead to the preparation of new drugs must be pursued. This review aims to evaluate both Leishmania enzymes PTR1 and DHFR-TS as potential drug targets, highlight their inhibitors and to discuss critically the use of chemoinformatics to elucidate interactions and propose new molecules against these enzymes.
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Gamma-glutamylcysteine synthetase and tryparedoxin 1 exert high control on the antioxidant system in Trypanosoma cruzi contributing to drug resistance and infectivity. Redox Biol 2019; 26:101231. [PMID: 31203195 PMCID: PMC6581782 DOI: 10.1016/j.redox.2019.101231] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/31/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022] Open
Abstract
Trypanothione (T(SH)2) is the main antioxidant metabolite for peroxide reduction in Trypanosoma cruzi; therefore, its metabolism has attracted attention for therapeutic intervention against Chagas disease. To validate drug targets within the T(SH)2 metabolism, the strategies and methods of Metabolic Control Analysis and kinetic modeling of the metabolic pathway were used here, to identify the steps that mainly control the pathway fluxes and which could be appropriate sites for therapeutic intervention. For that purpose, gamma-glutamylcysteine synthetase (γECS), trypanothione synthetase (TryS), trypanothione reductase (TryR) and the tryparedoxin cytosolic isoform 1 (TXN1) were separately overexpressed to different levels in T. cruzi epimastigotes and their degrees of control on the pathway flux as well as their effect on drug resistance and infectivity determined. Both experimental in vivo as well as in silico analyses indicated that γECS and TryS control T(SH)2 synthesis by 60–74% and 15–31%, respectively. γECS overexpression prompted up to a 3.5-fold increase in T(SH)2 concentration, whereas TryS overexpression did not render an increase in T(SH)2 levels as a consequence of high T(SH)2 degradation. The peroxide reduction flux was controlled for 64–73% by TXN1, 17–20% by TXNPx and 11–16% by TryR. TXN1 and TryR overexpression increased H2O2 resistance, whereas TXN1 overexpression increased resistance to the benznidazole plus buthionine sulfoximine combination. γECS overexpression led to an increase in infectivity capacity whereas that of TXN increased trypomastigote bursting. The present data suggested that inhibition of high controlling enzymes such as γECS and TXN1 in the T(SH)2 antioxidant pathway may compromise the parasite's viability and infectivity. The trypanothione synthesis flux is primarily but not exclusively controlled by γECS. Tryparedoxin exerts high control on the peroxide reduction flux. Kinetic metabolic modeling may reliably predict the in vivo pathway behavior. TXN1 overexpression provides benznidazole resistance. γECS and TXN contribute to parasite infectivity.
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Rozendaal YJW, Wang Y, Hilbers PAJ, van Riel NAW. Computational modelling of energy balance in individuals with Metabolic Syndrome. BMC SYSTEMS BIOLOGY 2019; 13:24. [PMID: 30808366 PMCID: PMC6390597 DOI: 10.1186/s12918-019-0705-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/14/2019] [Indexed: 02/07/2023]
Abstract
Background A positive energy balance is considered to be the primary cause of the development of obesity-related diseases. Treatment often consists of a combination of reducing energy intake and increasing energy expenditure. Here we use an existing computational modelling framework describing the long-term development of Metabolic Syndrome (MetS) in APOE3L.CETP mice fed a high-fat diet containing cholesterol with a human-like metabolic system. This model was used to analyze energy expenditure and energy balance in a large set of individual model realizations. Results We developed and applied a strategy to select specific individual models for a detailed analysis of heterogeneity in energy metabolism. Models were stratified based on energy expenditure. A substantial surplus of energy was found to be present during MetS development, which explains the weight gain during MetS development. In the majority of the models, energy was mainly expended in the peripheral tissues, but also distinctly different subgroups were identified. In silico perturbation of the system to induce increased peripheral energy expenditure implied changes in lipid metabolism, but not in carbohydrate metabolism. In silico analysis provided predictions for which individual models increase of peripheral energy expenditure would be an effective treatment. Conclusion The computational analysis confirmed that the energy imbalance plays an important role in the development of obesity. Furthermore, the model is capable to predict whether an increase in peripheral energy expenditure – for instance by cold exposure to activate brown adipose tissue (BAT) – could resolve MetS symptoms. Electronic supplementary material The online version of this article (10.1186/s12918-019-0705-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yvonne J W Rozendaal
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Yanan Wang
- Department of Pediatrics, Section Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A J Hilbers
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Natal A W van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands. .,Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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Control and regulation of the pyrophosphate-dependent glucose metabolism in Entamoeba histolytica. Mol Biochem Parasitol 2019; 229:75-87. [PMID: 30772421 DOI: 10.1016/j.molbiopara.2019.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 02/09/2019] [Indexed: 01/10/2023]
Abstract
Entamoeba histolytica has neither Krebs cycle nor oxidative phosphorylation activities; therefore, glycolysis is the main pathway for ATP supply and provision of carbon skeleton precursors for the synthesis of macromolecules. Glucose is metabolized through fermentative glycolysis, producing ethanol as its main end-product as well as some acetate. Amoebal glycolysis markedly differs from the typical Embden-Meyerhof-Parnas pathway present in human cells: (i) by the use of inorganic pyrophosphate, instead of ATP, as the high-energy phospho group donor; (ii) with one exception, the pathway enzymes can catalyze reversible reactions under physiological conditions; (iii) there is no allosteric regulation and sigmoidal kinetic behavior of key enzymes; and (iv) the presence of some glycolytic and fermentation enzymes similar to those of anaerobic bacteria. These peculiarities bring about alternative mechanisms of control and regulation of the PPi-dependent fermentative glycolysis in the parasite in comparison to the ATP-dependent and allosterically regulated glycolysis in many other eukaryotic cells. In this review, the current knowledge of the carbohydrate metabolism enzymes in E. histolytica is analyzed. Thermodynamics and stoichiometric analyses indicate 2 to 3.5 ATP yield per glucose metabolized, instead of the often presumed 5 ATP/glucose ratio. PPi derived from anabolism seems insufficient for PPi-glycolysis; hence, alternative ways of PPi supply are also discussed. Furthermore, the underlying mechanisms of control and regulation of the E. histolytica carbohydrate metabolism, analyzed by applying integral and systemic approaches such as Metabolic Control Analysis and kinetic modeling, contribute to unveiling alternative and promising drug targets.
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Koeman M, Engel J, Jansen J, Buydens L. Critical comparison of methods for fault diagnosis in metabolomics data. Sci Rep 2019; 9:1123. [PMID: 30718783 PMCID: PMC6362212 DOI: 10.1038/s41598-018-37494-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/20/2018] [Indexed: 11/09/2022] Open
Abstract
Platforms like metabolomics provide an unprecedented view on the chemical versatility in biomedical samples. Many diseases reflect themselves as perturbations in specific metabolite combinations. Multivariate analyses are essential to detect such combinations and associate them to specific diseases. For this, usually targeted discriminations of samples associated to a specific disease from non-diseased control samples are used. Such targeted data interpretation may not respect the heterogeneity of metabolic responses, both between diseases and within diseases. Here we show that multivariate methods that find any set of perturbed metabolites in a single patient, may be employed in combination with data collected with a single metabolomics technology to simultaneously investigate a large array of diseases. Several such untargeted data analysis approaches have been already proposed in other fields to find both expected and unexpected perturbations, e.g. in Statistical Process Control. We have critically compared several of these approaches for their sensitivity and their correct identification of the specifically perturbed metabolites. Also a new approach is introduced for this purpose. The newly introduced Sparse Mean approach, which we find here as most sensitive and best able to identify the specifically perturbed metabolites, turns metabolomics into an untargeted diagnostic platform. Aside from metabolomics, the proposed approach may greatly benefit fault diagnosis with untargeted analyses in many other fields, such as Industrial Process Control, food Adulteration Detection, and Intrusion Detection.
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Affiliation(s)
- M Koeman
- Radboud University, Institute for Molecules and Materials (IMM) Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - J Engel
- Radboud University, Institute for Molecules and Materials (IMM) Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands.,Biometris, Wageningen UR, Droevendaalsesteeg 1, 6708, PB Wageningen, The Netherlands
| | - J Jansen
- Radboud University, Institute for Molecules and Materials (IMM) Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands.
| | - L Buydens
- Radboud University, Institute for Molecules and Materials (IMM) Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
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48
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Dai Z, Locasale JW. Thermodynamic constraints on the regulation of metabolic fluxes. J Biol Chem 2018; 293:19725-19739. [PMID: 30361440 PMCID: PMC6314121 DOI: 10.1074/jbc.ra118.004372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/17/2018] [Indexed: 12/20/2022] Open
Abstract
Nutrition and metabolism are fundamental to cellular function. Metabolic activity (i.e. rates of flow, most commonly referred to as flux) is constrained by thermodynamics and regulated by the activity of enzymes. The general principles that relate biological and physical variables to metabolic control are incompletely understood. Using metabolic control analysis and computer simulations in several models of simplified metabolic pathways, we derive analytical expressions that define relationships between thermodynamics, enzyme activity, and flux control. The relationships are further analyzed in a mathematical model of glycolysis as an example of a complex biochemical pathway. We show that metabolic pathways that are very far from equilibrium are controlled by the activity of upstream enzymes. However, in general, regulation of metabolic fluxes by an enzyme has a more adaptable pattern, which relies more on distribution of free energy among reaction steps in the pathway than on the thermodynamic properties of the given enzyme. These findings show how the control of metabolic pathways is shaped by thermodynamic constraints of the given pathway.
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Affiliation(s)
- Ziwei Dai
- From the Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Jason W Locasale
- From the Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
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Christensen CD, Hofmeyr JHS, Rohwer JM. Delving deeper: Relating the behaviour of a metabolic system to the properties of its components using symbolic metabolic control analysis. PLoS One 2018; 13:e0207983. [PMID: 30485345 PMCID: PMC6261606 DOI: 10.1371/journal.pone.0207983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/11/2018] [Indexed: 11/22/2022] Open
Abstract
High-level behaviour of metabolic systems results from the properties of, and interactions between, numerous molecular components. Reaching a complete understanding of metabolic behaviour based on the system’s components is therefore a difficult task. This problem can be tackled by constructing and subsequently analysing kinetic models of metabolic pathways since such models aim to capture all the relevant properties of the system components and their interactions. Symbolic control analysis is a framework for analysing pathway models in order to reach a mechanistic understanding of their behaviour. By providing algebraic expressions for the sensitivities of system properties, such as metabolic flux or steady-state concentrations, in terms of the properties of individual reactions it allows one to trace the high level behaviour back to these low level components. Here we apply this method to a model of pyruvate branch metabolism in Lactococcus lactis in order to explain a previously observed negative flux response towards an increase in substrate concentration. With this method we are able to show, first, that the sensitivity of flux towards changes in reaction rates (represented by flux control coefficients) is determined by the individual metabolic branches of the pathway, and second, how the sensitivities of individual reaction rates towards their substrates (represented by elasticity coefficients) contribute to this flux control. We also quantify the contributions of enzyme binding and mass-action to enzyme elasticity separately, which allows for an even finer-grained understanding of flux control. These analytical tools allow us to analyse the control properties of a metabolic model and to arrive at a mechanistic understanding of the quantitative contributions of each of the enzymes to this control. Our analysis provides an example of the descriptive power of the general principles of symbolic control analysis.
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Affiliation(s)
- Carl D. Christensen
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Jan-Hendrik S. Hofmeyr
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- Centre for Complex Systems in Transition, Stellenbosch University, Stellenbosch, South Africa
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
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50
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Kleijn IT, Krah LHJ, Hermsen R. Noise propagation in an integrated model of bacterial gene expression and growth. PLoS Comput Biol 2018; 14:e1006386. [PMID: 30289879 PMCID: PMC6192656 DOI: 10.1371/journal.pcbi.1006386] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/17/2018] [Accepted: 07/20/2018] [Indexed: 12/17/2022] Open
Abstract
In bacterial cells, gene expression, metabolism, and growth are highly interdependent and tightly coordinated. As a result, stochastic fluctuations in expression levels and instantaneous growth rate show intricate cross-correlations. These correlations are shaped by feedback loops, trade-offs and constraints acting at the cellular level; therefore a quantitative understanding requires an integrated approach. To that end, we here present a mathematical model describing a cell that contains multiple proteins that are each expressed stochastically and jointly limit the growth rate. Conversely, metabolism and growth affect protein synthesis and dilution. Thus, expression noise originating in one gene propagates to metabolism, growth, and the expression of all other genes. Nevertheless, under a small-noise approximation many statistical quantities can be calculated analytically. We identify several routes of noise propagation, illustrate their origins and scaling, and establish important connections between noise propagation and the field of metabolic control analysis. We then present a many-protein model containing >1000 proteins parameterized by previously measured abundance data and demonstrate that the predicted cross-correlations between gene expression and growth rate are in broad agreement with published measurements.
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Affiliation(s)
- Istvan T. Kleijn
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Laurens H. J. Krah
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Rutger Hermsen
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
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