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flux balance analysis Reveals Potential Anti-HIV-1 Metabolic Targets

Infectious Diseases & Immunity 2024年第2期4卷 61-68页

作者： Runpeng Han Fei Luo Haisheng Yu Yajun Yan Yan Gong Conghua Xie Liang Cheng Department of Radiation and Medical Oncology Medical Research InstituteZhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan 430071China Frontier Science Center for Immunology and Metabolism Zhongnan Hospital of Wuhan UniversityState Key Laboratory of VirologyWuhan UniversityWuhan 430071China Guangzhou Eighth People's Hospital Guangzhou Medical UniversityGuangzhou 510440China Department of Infectious Diseases Zhongnan Hospital of Wuhan UniversityWuhan 430071China Department of Biological Repositories Zhongnan Hospital of Wuhan UniversityWuhan 430071China Wuhan Research Center for Infectious Diseases and Cancer Chinese Academy of Medical SciencesWuhan 430071China

Background:Human immunodeficiency virus type 1(HIV-1)remains a persistent global health ***,a continuous exploration of novel therapeutic strategies is essential.A comprehensive understanding of how HIV-1 utilizes the cellular metabolism machinery for replication can provide insights into new therapeutic ***:In this study,we performed a flux balance analysis using a genome-scale metabolic model(GEM)integrated with an HIV-1 viral biomass objective function to identify potential targets for anti–HIV-1 *** generated a GEM by integrating an HIV-1 production reaction into CD4+T cells and optimized for both host and virus optimal states as objective functions to depict metabolic profiles of cells in the status for optimal host biomass maintenance or for optimal HIV-1 virion *** analysis was used to predict biochemical reactions altered optimal for HIV-1 *** addition,we conducted in silico simulations involving gene and reaction knock-outs to identify potential anti–HIV-1 targets,which were subsequently validated by human phytohemagglutinin(PHA)blasts infected with ***:Differential analysis identified several altered biochemical reactions,including increased lysine uptake and oxidative phosphorylation(OXPHOS)activities in the virus optima compared with the host *** silico gene and reaction knock-out simulations revealed de novo pyrimidine synthesis,and OXPHOS could serve as potential anti–HIV-1 metabolic *** vitro assay confirmed that targeting OXPHOS using metformin could suppress the replication of HIV-1 by 56.6%(385.4±67.5 pg/mL in the metformintreated group vs.888.4±32.3 pg/mL in the control group,P<0.001).Conclusion:Our integrated host-virus genome-scale metabolic study provides insights on potential targets(OXPHOS)for anti-HIV therapies.

关键词： HIV-1 flux balance analysis Genome-scale metabolic models Viral biomass objective function Therapeutic target

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Noise effect in metabolic networks

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Chinese Physics B 2009年第12期18卷 5544-5551页

作者：李政言谢正伟陈同欧阳颀 Center for Theoretical Biology and State Key Laboratory for Mesoscopic PhysicsDepartment of PhysicsPeking University

Constraint-based models such as flux balance analysis （FBA） are a powerful tool to study biological metabolic networks. Under the hypothesis that cells operate at an optimal growth rate as the result of evolution and natural selection, this model successfully predicts most cellular behaviours in growth rate. However, the model ignores the fact that cells can change their cellular metabolic states during evolution, leaving optimal metabolic states unstable. Here, we consider all the cellular processes that change metabolic states into a single term‘noise＇, and assume that cells change metabolic states by randomly walking in feasible solution space. By simulating a state of a cell randomly walking in the constrained solution space of metabolic networks, we found that in a noisy environment cells in optimal states tend to travel away from these points. On considering the competition between the noise effect and the growth effect in cell evolution, we found that there exists a trade-off between these two effects. As a result, the population of the cells contains different cellular metabolic states, and the population growth rate is at suboptimal states.

关键词： noise metabolic networks flux balance analysis

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High production of butyric acid by Clostridium tyrobutyricum mutant

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Frontiers of Chemical Science and Engineering 2015年第3期9卷 369-375页

作者： Chao Ma Jianfa Ou Matthew Miller Sarah McFann Xiaoguang (Margaret) Liu Department of Chemical and Biological Engineering The University of Alabama 245 7th Avenue Tuscaloosa AL 35401 USA

The objective of this study was to improve the production of butyric acid by process optimization using the metabolically engineered mutant of Clostridium tyrobutyricum （PAK-Em）. First, the free-cell fermentation at pH 6.0 produced butyric acid with concentration of 38.44 g/L and yield of 0.42 g/g. Second, the immobilized- cell fermentations using fibrous-bed bioreactor （FBB） were run at pHs of 5.0, 5.5, 6.0, 6.5 and 7.0 to optimize fermentation process and improve the butyric acid production. It was found that the highest titer of butyric acid, 63.02g/L, was achieved at pH 6.5. Finally, the metabolic flux balance analysis was performed to inves- tigate the carbon rebalance in C. tyrobutyricum. The results show both gene manipulation and fermentation pH change redistribute carbon between biomass, acetic acid and butyric acid. This study demonstrated that high butyric acid production could be obtained by integrating metabolic engineering and fermentation process optimization.

关键词： Clostridium tyrobutyricum butyric acid production fermentation mutant pH flux balance analysis

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Using high-throughput data and dynamic flux balance modeling techniques to identify points of constraint in xylose utilization in Saccharomyces cerevisiae

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Systems Microbiology and Biomanufacturing 2021年第1期1卷 58-75页

作者： William Hohenschuh Ronald E.Hector Frank Chaplen Ganti S.Murthy Oregon State University CorvallisUSA USDA ARSNCAURPeoriaUSA Present Address:EMD Serono Inc. RocklandUSA Present Address:Indian Institute of Technology-Indore IndoreIndia

Background Several enzymes and cofactors have been identified as contributing to the slow utilization of xylose by xylose-fermenting strains of Saccharomyces ***,there has been no consensus on which of these possible bottle-necks are the most important to address.A previous strain characterization study from our lab suggested that insufficient NAD+limits fermentation and may be the most important bottleneck affecting utilization of xylose for the production of *** development and validation of a genome scale dynamic flux balance model would help to verify the existence and extent of this and other metabolic bottlenecks and suggest solutions to guide future strain development thereby minimiz-ing bottleneck impact on process *** A dynamic flux balance model was developed to identify bottlenecks in several strains of ***,both with wild-type pentose phosphate pathway expression and with the pathway over ***1 was found to be limiting in the oxidative portion of the pentose phosphate pathway under oxygen replete *** pathway is used to regenerate *** oxygen limiting conditions,respiration of xylose was limited by the lack of oxygen as a terminal electron *** production was also limited under these conditions due to the inability to balance NAD+/*** model suggests the use of the anaplerotic glyoxylate pathway to improve NAD+/NADH balance,increasing ethanol produc-tion by 50%while producing succinate as a coproduct at upwards of 20 g/*** In the production of high value chemicals from biomass,the use of the respiratory metabolism is a waste of feedstock *** previously identified in the oxidative pentose phosphate pathway are currently only relevant under oxygen-replete conditions and cannot impact the partitioning of carbon between the respiratory and fermentative *** future efforts on the non-respiratory balancing of NAD+/NADH,perhaps through th

关键词： Xylose Ethanol Biofuel Lignocellulose Metabolic bottlenecks flux balance analysis Modeling Cofactor imbalance Glyoxylate pathway NAD+ NADH

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Genome-scale metabolic modeling in antimicrobial pharmacology

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Engineering Microbiology 2022年第2期2卷 21-28页

作者： Yan Zhu Jinxin Zhao Jian Li Infection Program and Department of Microbiology Biomedicine Discovery InstituteMonash University19 Innovation WalkMelbourneVictoria 3800Australia

The increasing antimicrobial resistance has seriously threatened human health worldwide over the last three *** severe medical crisis and the dwindling antibiotic discovery pipeline require the development of novel antimicrobial treatments to combat life-threatening infections caused by multidrug-resistant micro-bial ***,the detailed mechanisms of action,resistance,and toxicity of many antimicrobials remain uncertain,significantly hampering the development of novel ***-scale metabolic model(GSMM)has been increasingly employed to investigate microbial *** this review,we discuss the latest progress of GSMM in antimicrobial pharmacology,particularly in elucidating the complex interplays of multiple metabolic pathways involved in antimicrobial activity,resistance,and *** also highlight the emerging areas of GSMM applications in modeling non-metabolic cellular activities(e.g.,gene expression),identi-fication of potential drug targets,and integration with machine learning and pharmacokinetic/pharmacodynamic ***,GSMM has significant potential in elucidating the critical role of metabolic changes in antimi-crobial pharmacology,providing mechanistic insights that will guide the optimization of dosing regimens for the treatment of antimicrobial-resistant infections.

关键词： Genome-scale metabolic model flux balance analysis Antimicrobial pharmacology Antimicrobial resistance Toxicity Pharmacokinetic/pharmacodynamic model

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SupraBiology 2014： Promoting UK-China collaboration on Systems Biology and High Performance Computing

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Frontiers of Electrical and Electronic Engineering in China 2015年第1期10卷 46-53页

作者： Ettore Murabito Riccardo Colombo Chengkun Wu Malkhey Verma Samrina Rehman Jacky Snoep Shao-Liang Peng Naiyang Guan Xiangke Liao Hans V. Westerhoff Manchester Institute of Biotechnology School of Computer Science Faculty of Engineering and Physical Sciences Manchester Centre for Integrative Systems Biology The University of Manchester Manchester M139PL United Kingdom. Department of Informatics Systems and Communication University of Milan-Bicocca Milan 20126 Italy. SYSBIO - Centre of Systems Biology Milan 20126 Italy. Manchester Institute of Biotechnology School of Chemical Engineering and Analytical Sciences Manchester Centre forIntegrative Systems Biology The University of Manchester Manchester M139PL United Kingdom. School of Computer Science National University of Defence Technology Changsha 410073China

In the second half of 2014 the Manchester Institute of Biotechnology, based in Manchester （UK）, hosted the first SupraBiology congress, an event attended by representa- tives of different academic institutions and industry based in both the UK and China. The congress was aimed to serve as a platform to discuss and promote potential collaborations between the UK and China on the subject of Systems Biology and High Performance Computing. The event, sponsored by the ＂BBSRC China Partnering Awards＂ and ISBE, was organised as a sequence of talks addressing the different aspects of Systems Biology that can benefit from High Performance Computing. A general discussion session followed where the scientific, techni- cal, and logistic aspects of the prospected UK-China collaborations were examined.

关键词： System Biology High Performance Computing flux balance analysis Nonnegative Matrix Factorization Biochemical Network

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Optimization and Control of Metabolic Networks

Optimization and Control of Metabolic Networks

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第二十九届中国控制会议

作者： WANG Rui-Sheng1,LI Zhenping2,ZHANG Xiang-Sun3,CHEN Luonan4 1.Department of Physics,Pennsylvania State University,University Park,PA 16802,USA2.School of Information,Beijing Wuzi University,Beijing 101149,P.R.China3.Academy of Mathematics and Systems Science,Chinese Academy of Sciences,Beijing 100190,P.R.China4.Key Laboratory of Systems Biology,SIBS-Novo Nordisk Translational Research Centre for PreDiabetes,Chinese Academy of Sciences,Shanghai 200031,P.R.China

Metabolism,which comprises the complete set of biochemical reactions in a living cell,is one of the most complex cellular *** networks connect biochemical reactions via substrate and product substances called *** of metabolic networks via network theory,stoichiometry,optimization and control tools is one of central topics in systems biology and allows for in depth comprehending the complex molecular mechanisms of an *** this paper,we first introduce metabolic flux balance analysis and its application in prediction of gene essentiality,synthetic lethality,and disease *** we review metabolic control models including strain optimization models,drug target discovery models and other metabolic intervention ***,we look at new progresses in this area and present our work in these aspects including a metabolite-centric mass flow *** overview gives a general framework for metabolic network analysis and its application in diverse areas.

关键词： Metabolic Networks flux balance analysis Optimization Control Gene Essentiality Intervention

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Genome-scale metabolic network analysis of the opportunistic pathogen Burkholderia cenocepacia J2315

Genome-scale metabolic network analysis of the opportunistic...

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第四届全国生物信息学与系统生物学学术大会

作者：房柯池赵韩生孙常悦王晶中国科学院心理研究所心理健康院重点实验室

Burkholderia cenocepacia is an emerging gram-negative opportunistic pathogen that commonly infects patients with cystic fibrosis (CF) and immunocompromised individuals. This bacterium is notorious for its high levels of antibiotic resistance,yet the mechanisms of host infection and drug resistance remain mostly *** genome of B. cenocepacia J2315 has been sequenced and

关键词： Genome-scale metabolic network reconstruction B.cenocepacia flux balance analysis

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Comparative analysis of C3 and C4 Plants using Constraint-based Model

Comparative Analysis of C3 and C4 Plants using Constraint-ba...

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2012 IEEE 4th International Symposium on Plant Growth Modeling,Simulation,Visualization and Applications(PMA 2012)

作者： Chuanli Wang Longyun Guo Zhuo Wang Department of Bioinformatics and Biostatistics Shanghai Jiao Tong University

To realize the transition from C3 to C4 plants,the systematic comparison of C3 and C4 metabolism is *** this study,we detected their differences using the improved constraint-based models by setting the ratio between carboxylation and oxygenation by *** found the C3 model exhibit more dense topology structure than *** simulation of enzyme knockouts demonstrated that both C3 and C4 models are very robust,especially when optimizing CO2 ***,C4 plant has better robustness no matter the objective function is biomass or CO2 *** addition,all the essential reactions in C3 model are also essential for C4,while there are some other reactions specifically essential for C4,which validated that the basic metabolism of C4 plant is similar to C3,but C4 is more *** also identified more correlated reaction sets in C4,and demonstrated C4 plants have better modularity with complex mechanism coordinates the reactions and pathways than that of C3 ***,the increase of both biomass and CO2 fixation with light intensity and CO2 concentration in C4 is faster than that in C3,which reflect more efficient use of light and CO2 in C4 *** results are consistent with the actual situation,which indicate that constraint-based modeling is a powerful method to study plant metabolism at systems level.

关键词： C3photosynthesis C4 photosynthesis constraint-based model flux balance analysis sampling

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A novel hyper-cube shrink algorithm to predict metabolic fluxes based on enzyme activity only

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中国药理学与毒理学杂志 2016年第10期30卷 1085-1085页

作者： XIE Zheng-wei ZHANG Tian-yu OUYANG Qi Department of Pharmacology School of Basic Medical SciencesPeking University Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences Peking University School of Life Science Peking University Condensed Matter Physics School of PhysicsPeking University

OBJECTIVE One of the long-expected goals of genome-scale metabolic modeling is to evaluate the influence of the perturbed enzymes to the yield of an expected end *** Metabolic control analysis(MCA)performs such role to calculate the sensitivity of flux change upon that of enzymes under the framework of ordinary differential equation(ODE)models,which are restricted in small-scale networks and require explicit kinetic *** constraint-based models,like flux balance analysis(FBA),lack of the room of performing MCA because they are *** this study,we developed a hyper-cube shrink algorithm(HCSA)to incorporate the enzymatic properties to the FBA model by introducing a pair of parameters for each *** algorithm was able to handle not only prediction of knockout strains but also strains with an adjustment of expression level of certain *** We first showed the concept by applying HCSA to a simplest three-nodes *** we show the HCSA possesses Michaelis-Menten like behaviors characterized by steady state of *** obtained good prediction of a synthetic network in Saccharomyces cerevisiae producing voilacein and *** we showed its capability of predicting the flux distribution in genome-scale networks by applying it to sporulation in *** We have developed an algorithm the impact on fluxes when certain enzymes were inhibited or *** provides us a powerful tool to evaluate the consequences of enzyme inhibitor or activator.

关键词： metabolic network linear programming flux balance analysis

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