文献类型：期刊文献

英文题名：Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs

作者：Lu, Hongzhong[1];Cao, Weiqiang[1];Ouyang, Liming[1];Xia, Jianye[1];Huang, Mingzhi[1];Chu, Ju[1];Zhuang, Yingping[1];Zhang, Siliang[1];Noorman, Henk[2]

机构：[1]East China Univ Sci & Technol, State Key Lab Bioreactor Engn, Shanghai 200237, Peoples R China;[2]DSM Biotechnol Ctr, Delft, Netherlands

年份：2017

卷号：114

期号：3

起止页码：685

外文期刊名：BIOTECHNOLOGY AND BIOENGINEERING

收录：;EI(收录号：20164302932901);WOS:【SCI-EXPANDED(收录号:WOS:000394606000020)】；

基金：Contract grant sponsor: Royal DSM (Delft, the Netherlands) Contract grant sponsor: National Basic Research Program Contract grant number: 2013CB733600 Contract grant sponsor: NWO-MoST Joint Program Contract grant number: 2013DFG32630 Contract grant sponsor: Open Funding Project of the State Key Laboratory of Bioreactor Engineering

语种：英文

外文关键词：Aspergillus niger; genome-scale metabolic model; multi-omics; glucoamylase

摘要：Aspergillus niger is one of the most important cell factories for industrial enzymes and organic acids production. A comprehensive genome-scale metabolic network model (GSMM) with high quality is crucial for efficient strain improvement and process optimization. The lack of accurate reaction equations and gene-protein-reaction associations (GPRs) in the current best model of A. niger named GSMM iMA871, however, limits its application scope. To overcome these limitations, we updated the A. niger GSMM by combining the latest genome annotation and literature mining technology. Compared with iMA871, the number of reactions in iHL1210 was increased from 1,380 to 1,764, and the number of unique ORFs from 871 to 1,210. With the aid of our transcriptomics analysis, the existence of 63% ORFs and 68% reactions in iHL1210 can be verified when glucose was used as the only carbon source. Physiological data from chemostat cultivations, C-13-labeled and molecular experiments from the published literature were further used to check the performance of iHL1210. The average correlation coefficients between the predicted fluxes and estimated fluxes from C-13-labeling data were sufficiently high (above 0.89) and the prediction of cell growth on most of the reported carbon and nitrogen sources was consistent. Using the updated genome-scale model, we evaluated gene essentiality on synthetic and yeast extract medium, as well as the effects of NADPH supply on glucoamylase production in A. niger. In summary, the new A. niger GSMM iHL1210 contains significant improvements with respect to the metabolic coverage and prediction performance, which paves the way for systematic metabolic engineering of A. niger. Biotechnol. Bioeng. 2017;114: 685-695. (c) 2016 Wiley Periodicals, Inc.