| Recently,the development and accumulation of the data of essential genes greatly accelerate the researching of minimal genome.As the hotspot fields of synthetic biology,they are necessary tools for scientists to explore the truth of life and decode the genetic information.Meanwhile they also have great significance for the fermentation and pharmaceutical industry.Based on the previous study of essential gene and minimal genome,we updated the CEG database and introduced some new methods including half-retaining,metabolic analysis and gene interaction to construct a more universal minimal genome.For prokaryote and eukaryote,we have two main parts of work.Firstly,we updated the CEG(Cluster of Essential Genes)database from 16 species to 29 species,then through the method of half-retaining,266 conservative essential clusters were screened out.After the re-annotation using the online tool RAST SEED,we adopted the MetaNetX to execute metabolic analysis.78 metabolic genes were supplemented to increase the survival rate of minimal genome.As for the chassis cell,we chose Escherichia coli,one of the model organisms,and based on the design of JCVI-syn3.0 to edit E.coli genome.During the design of minimal genome,we fully discussed the problems of genome structure,regulatory elements and so on,and 39 mDNA and 22 rDNA were kept.Meanwhile we found an interesting phenomenon of essential genes clustering,and simply explored its biological significance.On the aspect of eukaryotic minimal genome,eukaryote need far more essential genes than prokaryote because of the more elaborate cell structure and complex organelles.We focused on Saccharomyces cerevisiae chromosome XII-left arm and evaluated the essential level of the 65 genes through the analysis of functional multicopy,gene interaction,synthetic lethality based on the experimental data of its essential genes.We believe that our work will provide some referential ideas and experience for the future research on minimal genome. |
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