title: Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species.
abstract: We present a novel genome-scale metabolic model iWV1213 of Mucor circinelloides, which is an oleaginous fungus for industrial applications. The model contains 1213 genes, 1413 metabolites and 1326 metabolic reactions across different compartments. We demonstrate that iWV1213 is able to accurately predict the growth rates of M. circinelloides on various nutrient sources and culture conditions using Flux Balance Analysis and Phenotypic Phase Plane analysis. Comparative analysis of three oleaginous genome-scale models, including M. circinelloides (iWV1213), Mortierella alpina (iCY1106) and Yarrowia lipolytica (iYL619_PCP) revealed that iWV1213 possesses a higher number of genes involved in carbohydrate, amino acid, and lipid metabolisms that might contribute to its versatility in nutrient utilization. Moreover, the identification of unique and common active reactions among the Zygomycetes oleaginous models using Flux Variability Analysis unveiled a set of gene/enzyme candidates as metabolic engineering targets for cellular improvement. Thus, iWV1213 offers a powerful metabolic engineering tool for multi-level omics analysis, enabling strain optimization as a cell factory platform of lipid-based production.
authors.affiliation: Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Center for Systems Biology, Soochow University, Suzhou 215006, China; Computational Biomodelling Laboratory for Agricultural Science and Technology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
authors.forename: Wanwipa
authors.initials: W
authors.lastname: Vongsangnak
authors.affiliation: Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, 126 Pracha Uthit Rd, Thung Khru, Bangkok 10140, Thailand.
authors.forename: Amornpan
authors.initials: A
authors.lastname: Klanchui
authors.affiliation: Systems Biology Research Group, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand.
authors.forename: Iyarest
authors.initials: I
authors.lastname: Tawornsamretkit
authors.affiliation: Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand.
authors.forename: Witthawin
authors.initials: W
authors.lastname: Tatiyaborwornchai
authors.affiliation: Bioprocess Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency, Khong Luang, Pathum Thani 12120, Thailand. Electronic address: kobkul@biotec.or.th.
authors.forename: Kobkul
authors.initials: K
authors.lastname: Laoteng
authors.affiliation: Systems Biology Research Group, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand; Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand. Electronic address: asawin.mee@kmutt.ac.th.
authors.forename: Asawin
authors.initials: A
authors.lastname: Meechai
mesh_terms: D016681:Genome, Fungal; D050356:Lipid Metabolism / Q000235:genetics*; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008957:Models, Genetic; D020094:Mortierella / Q000235:genetics* / Q000378:metabolism; D009089:Mucor / Q000235:genetics* / Q000378:metabolism; D025062:Yarrowia / Q000235:genetics* / Q000378:metabolism
keywords: Genome-scale metabolic modeling; Lipid; Metabolic engineering; Mucor circinelloides; Oleaginous species