The concept of minimal genome plays a pivotal role in studying the origin and evolutionof cellular organisms, microbial adaptation to the living environment, and the robustness of genetic networks. Meanwhile, minimal genome is an important branch of synthetic biology, which can help understand the necessary components of complex system and offer ideal "chassis" for synthetic biology. The 'dry' method to study a minimal genome is computer based bioinformatics analysis, while the 'wet' method is based on techniques of large scale gene inactivation or genomic synthesis. Our project used an integrated method to predict the essential gene sets maintaining the core functionality of a cellular life. We first chose Pseudomonas putida KT2440 as the initial genome for genome reduction study. Through a systematic method, which integrated comparative analysis, experimental essential genes, simulation of gene deletion based on the metabolic network, as well as extensive manual efforts, we get the minimal gene set of KT2440. Based on the gene set and genome-scale metabolic network, a minimal metabolic network was further constructed to validate the metabolism activities of the minimal gene set. Finally, candidate segments for genome reduction were provided as a reference for experimental practice. This project will not only
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