Open AccessA novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
Author(s) -
Yuan g Ye,
Bin Guang,
Chuan Dong,
Hong Zhang,
Ling Ling Chen,
FengBiao Guo
Publication year - 2016
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/srep35082
Subject(s) - gene , computational biology , computer science , metabolic network , set (abstract data type) , gene regulatory network , synthetic biology , replication (statistics) , biology , genetics , gene expression , virology , programming language
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.