title: A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network.
abstract: A minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. Second, we introduced a half-retaining strategy to extract persistent essential genes to ensure stability. Third, we constructed a viable metabolic network to supplement SBGS. The proposed SBGS includes 327 genes and required 431 reactions. This report describes an SBGS that preserves both self-replication and self-maintenance systems. In the minimized metabolic network, we identified five novel hub metabolites and confirmed 20 known hubs. Highly essential genes were found to distribute the connecting metabolites into more reactions. Based on our SBGS, we expanded the pool of targets for designing broad-spectrum antibacterial drugs to reduce pathogen resistance. We also suggested a rough semi-de novo strategy to synthesize an artificial cell, with potential applications in industry.
authors.affiliation: Center of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.|School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, China.
authors.forename: Yuan-Nong
authors.initials: YN
authors.lastname: Ye
authors.affiliation: College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Bin-Guang
authors.initials: BG
authors.lastname: Ma
authors.affiliation: Center of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Chuan
authors.initials: C
authors.lastname: Dong
authors.affiliation: College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
authors.affiliation: Center of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
mesh_terms: D058045:Artificial Cells / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics*; D020043:Genes, Essential / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006193:Haemophilus influenzae / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D045704:Mycoplasma genitalium / Q000235:genetics
chemical_list: D001426:Bacterial Proteins