Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models

	Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models
	Yuan, Qianqian 1,2,3; Huang, Teng 2; Li, Peishun 2; Hao, Tong 4; Li, Feiran 1,2,3; Ma, Hongwu 1,2,5; Wang, Zhiwen 1,3; Zhao, Xueming 1,3; Chen, Tao 1,3; Goryanin, Igor 2,5
刊名	PLOS ONE
	2017-01-13
卷号	12 期号:1
英文摘要	Over 100 genome-scale metabolic networks (GSMNs) have been published in recent years and widely used for phenotype prediction and pathway design. However, GSMNs for a specific organism reconstructed by different research groups usually produce inconsistent simulation results, which makes it difficult to use the GSMNs for precise optimal pathway design. Therefore, it is necessary to compare and identify the discrepancies among networks and build a consensus metabolic network for an organism. Here we proposed a process for systematic comparison of metabolic networks at pathway level. We compared four published GSMNs of Pseudomonas putida KT2440 and identified the discrepancies leading to inconsistent pathway calculation results. The mistakes in the models were corrected based on information from literature so that all the calculated synthesis and uptake pathways were the same. Subsequently we built a pathway-consensus model and then further updated it with the latest genome annotation information to obtain modelPpuQY1140 for P. putida KT2440, which includes 1140 genes, 1171 reactions and 1104 metabolites. We found that even small errors in a GSMN could have great impacts on the calculated optimal pathways and thus may lead to incorrect pathway design strategies. Careful investigation of the calculated pathways during the metabolic network reconstruction process is essential for building proper GSMNs for pathway design.
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	FLUX BALANCE ANALYSIS ; GLUCOSE CATABOLISM ; GENOTYPE ; ENZYMES ; YEAST
收录类别	SCI
语种	英语
WOS记录号	WOS:000391972600020
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/834782/2276]
专题	天津工业生物技术研究所_总体研究部_期刊论文
作者单位	1.Tianjin Univ, Sch Chem Engn & Technol, Minist Educ, Key Lab Syst Bioengn, Tianjin, Peoples R China 2.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin, Peoples R China 3.Tianjin Univ, Sch Chem Engn & Technol, Collaborat Innovat Ctr Chem Sci & Engn Tianjin, SynBio Res Platform, Tianjin, Peoples R China 4.Tianjin Normal Univ, Coll Life Sci, Tianjin, Peoples R China 5.Univ Edinburgh, Informat Forum, Sch Informat, Edinburgh, Midlothian, Scotland
推荐引用方式 GB/T 7714	Yuan, Qianqian,Huang, Teng,Li, Peishun,et al. Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models[J]. PLOS ONE,2017,12(1).
APA	Yuan, Qianqian.,Huang, Teng.,Li, Peishun.,Hao, Tong.,Li, Feiran.,...&Goryanin, Igor.(2017).Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models.PLOS ONE,12(1).
MLA	Yuan, Qianqian,et al."Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models".PLOS ONE 12.1(2017).