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Acevedo A, Torres F, Kiwi M, Baeza-Lehnert F, Barros LF, Lee-Liu D, González-Billault C. Metabolic switch in the aging astrocyte supported via integrative approach comprising network and transcriptome analyses. Aging (Albany NY) 2023; 15:9896-9912. [PMID: 37074814 PMCID: PMC10599759 DOI: 10.18632/aging.204663] [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: 12/22/2022] [Accepted: 03/20/2023] [Indexed: 04/20/2023]
Abstract
Dysregulated central-energy metabolism is a hallmark of brain aging. Supplying enough energy for neurotransmission relies on the neuron-astrocyte metabolic network. To identify genes contributing to age-associated brain functional decline, we formulated an approach to analyze the metabolic network by integrating flux, network structure and transcriptomic databases of neurotransmission and aging. Our findings support that during brain aging: (1) The astrocyte undergoes a metabolic switch from aerobic glycolysis to oxidative phosphorylation, decreasing lactate supply to the neuron, while the neuron suffers intrinsic energetic deficit by downregulation of Krebs cycle genes, including mdh1 and mdh2 (Malate-Aspartate Shuttle); (2) Branched-chain amino acid degradation genes were downregulated, identifying dld as a central regulator; (3) Ketone body synthesis increases in the neuron, while the astrocyte increases their utilization, in line with neuronal energy deficit in favor of astrocytes. We identified candidates for preclinical studies targeting energy metabolism to prevent age-associated cognitive decline.
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Affiliation(s)
- Alejandro Acevedo
- Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, Santiago, Región Metropolitana 7800003, Chile
| | - Felipe Torres
- Department of Physics, Universidad de Chile, Santiago, Región Metropolitana 7800003, Chile
- Center for the Development of Nanoscience and Nanotechnology, CEDENNA, Santiago, Región Metropolitana 7800003, Chile
- Department of Physics, Center for Advanced Nanoscience, University of California, San Diego, CA 92093, USA
| | - Miguel Kiwi
- Department of Physics, Universidad de Chile, Santiago, Región Metropolitana 7800003, Chile
- Center for the Development of Nanoscience and Nanotechnology, CEDENNA, Santiago, Región Metropolitana 7800003, Chile
| | | | - L. Felipe Barros
- Centro de Estudios Científicos (CECs), Valdivia 5110466, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Región de Los Ríos 5110773, Chile
| | - Dasfne Lee-Liu
- Department of Biology, Laboratory of Cellular and Neuronal Dynamics, Faculty of Sciences, Universidad de Chile, Santiago, Región Metropolitana 7800003, Chile
- Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Región Metropolitana 7800003, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Región Metropolitana 7510157, Chile
| | - Christian González-Billault
- Department of Biology, Laboratory of Cellular and Neuronal Dynamics, Faculty of Sciences, Universidad de Chile, Santiago, Región Metropolitana 7800003, Chile
- Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Región Metropolitana 7800003, Chile
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
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Immanuel SRC, Banerjee D, Rajankar MP, Raghunathan A. Integrated constraints based analysis of an engineered violacein pathway in Escherichia coli. Biosystems 2018; 171:10-19. [PMID: 30008425 DOI: 10.1016/j.biosystems.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/05/2018] [Accepted: 06/15/2018] [Indexed: 12/20/2022]
Abstract
Strategies towards optimal violacein biosynthesis, a potential drug molecule, need systems level coordination of enzymatic activities of individual genes in a multigene operon vioABCDE. Constraints-based flux balance analysis of an extended iAF1260 model (iAF1260vio) with a reconstructed violacein module predicted growth and violacein yields in Escherichia coli accurately. Shadow price (SP) analysis identified tryptophan metabolism and NADPH as limiting. Increased tryptophan levels in Δpgi & ΔpheA were validated using in silico gene deletion analysis. Phenotypic phase plane (PhPP) analysis highlighted sensitivity between tryptophan and NADPH for violacein synthesis at molar growth yields. A synthetic VioABCDE operon (SYNO) sequence was designed to maximize Codon Adaptive Index (CAI: 0.9) and tune translation initiation rates (TIR: 2-50 fold higher) in E. coli. All pSYN E. coli transformants produced higher violacein, with a maximum six-fold increase in yields. The rational design E. coli: ΔpheA SYN: gave the highest violacein titers (33.8 mg/l). Such integrated approaches targeting multiple molecular hierarchies in the cell can be extended further to increase violacein yields.
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Affiliation(s)
| | - Deepanwita Banerjee
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Mayooreshwar P Rajankar
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Anu Raghunathan
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
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Xu N, Ye C, Liu L. Genome-scale biological models for industrial microbial systems. Appl Microbiol Biotechnol 2018; 102:3439-3451. [PMID: 29497793 DOI: 10.1007/s00253-018-8803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 01/08/2023]
Abstract
The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China. .,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China.
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Acevedo A, Conejeros R, Aroca G. Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis. PLoS One 2017; 12:e0180074. [PMID: 28658270 PMCID: PMC5489217 DOI: 10.1371/journal.pone.0180074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/11/2017] [Indexed: 11/18/2022] Open
Abstract
The yeast Scheffersomyces stipitis naturally produces ethanol from xylose, however reaching high ethanol yields is strongly dependent on aeration conditions. It has been reported that changes in the availability of NAD(H/+) cofactors can improve fermentation in some microorganisms. In this work genome-scale metabolic modeling and phenotypic phase plane analysis were used to characterize metabolic response on a range of uptake rates. Sensitivity analysis was used to assess the effect of ARC on ethanol production indicating that modifying ARC by inhibiting the respiratory chain ethanol production can be improved. It was shown experimentally in batch culture using Rotenone as an inhibitor of the mitochondrial NADH dehydrogenase complex I (CINADH), increasing ethanol yield by 18%. Furthermore, trajectories for uptakes rates, specific productivity and specific growth rate were determined by modeling the batch culture, to calculate ARC associated to the addition of CINADH inhibitor. Results showed that the increment in ethanol production via respiratory inhibition is due to excess in ARC, which generates an increase in ethanol production. Thus ethanol production improvement could be predicted by a change in ARC.
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Affiliation(s)
- Alejandro Acevedo
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Raúl Conejeros
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
- * E-mail:
| | - Germán Aroca
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
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Banerjee D, Parmar D, Bhattacharya N, Ghanate AD, Panchagnula V, Raghunathan A. A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD +/NADH + imbalance. BMC SYSTEMS BIOLOGY 2017; 11:51. [PMID: 28446174 PMCID: PMC5405553 DOI: 10.1186/s12918-017-0427-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/21/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic. Growth and viability testing identified malate, maleate, succinate, pyruvate and oxoadipate as resensitising agents for antibiotic therapy. Resistant genes were catalogued through whole genome sequencing. Intracellular metabolomic profiling identified violacein as a potential biomarker for resistance. The temporal variance of metabolites captured the linearized dynamics around the steady state and correlated to growth rate. A constraints-based flux balance model of the core metabolism was used to predict the metabolic basis of antibiotic susceptibility and resistance. CONCLUSIONS The model predicts electron imbalance and skewed NAD/NADH ratios as a result of antibiotics - chloramphenicol and streptomycin. The resistant pathogen rewired its metabolic networks to compensate for disruption of redox homeostasis. We foresee the utility of such scalable workflows in identifying metabolites for clinical isolates as inevitable solutions to mitigate antibiotic resistance.
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Affiliation(s)
- Deepanwita Banerjee
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
| | | | | | - Avinash D. Ghanate
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
| | | | - Anu Raghunathan
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
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