Design And Assembly Of Yeast Large Fragment DNA Based On Natural Product Biosynthesis Pathway

Biosynthesis is changing the pattern of world industry in different fields such as medicine,chemicals,food,and biofuels,and is creating a new era of economic green growth.As one of the most important microbial biocatalytic synthetic chassis cells,yeast cells are the key site for biosynthesis and the focus of biotechnology revolution and industry attention and competition.Yeast cells could use a variety of substrate materials to produce different types of target compounds,such as biofuels,food,pharmaceuticals and feed,using metabolic engineering and fermentation.The main attraction of metabolic engineering over traditional methods is that many compounds of commercial value and interest can be produced in a more environmentally friendly,cost-effective and sustainable manner through biological pathways.Metabolic engineering methods can be used to engineer the original metabolic processes of yeast cells,enhance the production of certain metabolites,or confer the ability of yeast cells to produce new metabolites.In this study,in order to fully explore the biosynthesis ability of Saccharomyces cerevisiae as a cell factory,GenomeDesigner,a design and assembly platform for yeast large fragment DNA based on natural product biosynthesis pathway,was established.This system uses the native reactions of the two metabolic network models iMM904 and iND750 of wild-type Saccharomyces cerevisiae S288C and integrates reactions in KEGG reaction database and Rhea database as the source of heterologous reactions data.The Probabilistic Pathway Construction algorithm was used to calculate the synthetic route to obtain the target compound for yeast cell synthesis under specific conditions.The designed synthetic pathways were evaluated using the Flux Balance Analysis method.Based on the results of the evaluation,all the gene sequence fragments required for the activated native reactions are assembled online and presented by a visualization tool.GenomeDesigner uses computer method to comprehensively and systematically provide and display information on the metabolism of the whole cell of the strain,the synthetic route of the target product,the quantification for the pathway,and the endogenous gene sequence under the specified culture conditions.These information based on rational computational analysis can provide some valuable suggestions for the researcher's cell factory experimental design.