title: Reconstruction of a genome-scale metabolic model and in silico analysis of the polymalic acid producer Aureobasidium pullulans CCTCC M2012223.
abstract: Aureobasidium pullulans is a yeast-like fungus used for producing biopolymers e.g. polymalic acid (PMA) and pullulan. A high PMA producing strain, A. pullulans CCTCC M2012223, was isolated and sequenced in our previous study. To understand its metabolic performance, a genome-scale metabolic model, iZX637, consisting of 637 genes, 1347 reactions and 1133 metabolites, was reconstructed based on genome annotation and literature mining studies. The iZX637 model was validated by simulating cell growth, utilization of carbon and nitrogen sources, and gene essentiality analysis in A. pullulans. We further validated our model, designed a simulation program for the prediction of PMA production using experimental data, and further analyzed the carbon flux distribution and change with increasing PMA synthesis rates. Through the calculated flux distribution, NADPH- and NADH-dependent methylenetetrahydrofolate dehydrogenase (MTHFD) were found to be associated with the transfer of reducing equivalents from NADPH to NADH for supplementing NADH in the metabolic network. Furthermore, under the high PMA synthesis rate, a large amount of carbon flux was through pyruvate into malic acid via the reductive TCA cycle. Thus, pyruvate carboxylase, which can convert pyruvate to oxaloacetate with CO2fixation, may also be an important target for PMA synthesis. These results illustrated that the model iZX637 was a powerful tool for optimization of A. pullulans metabolism and identification of targets for guiding metabolic engineering.
authors.affiliation: College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing 400715, PR China.
authors.forename: Jun
authors.initials: J
authors.lastname: Feng
authors.affiliation: College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing 400715, PR China.
authors.forename: Jing
authors.initials: J
authors.lastname: Yang
authors.affiliation: College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing 400715, PR China.
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, PR China.
authors.forename: Meijin
authors.initials: M
authors.lastname: Guo
authors.affiliation: Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Chongqing 400044, PR China.
authors.forename: Bochu
authors.initials: B
authors.lastname: Wang
authors.affiliation: William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Shang-Tian
authors.initials: ST
authors.lastname: Yang
authors.affiliation: College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing 400715, PR China; Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Chongqing 400044, PR China. Electronic address: zhx1030@swu.edu.cn.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zou
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D003198:Computer Simulation; D005800:Genes, Fungal; D016681:Genome, Fungal; D008293:Malates / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D009249:NADP / Q000378:metabolism; D011108:Polymers / Q000378:metabolism*; D011766:Pyruvate Carboxylase / Q000235:genetics / Q000378:metabolism
chemical_list: D008293:Malates; D011108:Polymers; C121060:poly(malic acid); D009249:NADP; D002244:Carbon; D011766:Pyruvate Carboxylase
keywords: Biopolymers; Metabolic engineering; Pyruvate carboxylase; Reducing equivalents