Optimizing multicopy chromosomal integration for stable high-performing strains.
Fei DuZijia LiXin LiDuoduo ZhangFeng ZhangZixu ZhangYingshuang XuJin TangYongqian LiXing-Xu HuangYang GuXiao-Man SunHe HuangPublished in: Nature chemical biology (2024)
The copy number of genes in chromosomes can be modified by chromosomal integration to construct efficient microbial cell factories but the resulting genetic systems are prone to failure or instability from triggering homologous recombination in repetitive DNA sequences. Finding the optimal copy number of each gene in a pathway is also time and labor intensive. To overcome these challenges, we applied a multiple nonrepetitive coding sequence calculator that generates sets of coding DNA sequence (CDS) variants. A machine learning method was developed to calculate the optimal copy number combination of genes in a pathway. We obtained an engineered Yarrowia lipolytica strain for eicosapentaenoic acid biosynthesis in 6 months, producing the highest titer of 27.5 g l -1 in a 50-liter bioreactor. Moreover, the lycopene production in Escherichia coli was also greatly improved. Importantly, all engineered strains of Y. lipolytica, E. coli and Saccharomyces cerevisiae constructed with nonrepetitive CDSs maintained genetic stability.
Keyphrases
- copy number
- escherichia coli
- genome wide
- saccharomyces cerevisiae
- mitochondrial dna
- dna methylation
- circulating tumor
- machine learning
- wastewater treatment
- dna damage
- cell free
- dna repair
- single molecule
- quantum dots
- genome wide identification
- klebsiella pneumoniae
- high frequency
- single cell
- biofilm formation
- artificial intelligence
- bioinformatics analysis
- nucleic acid
- big data
- genome wide analysis
- mesenchymal stem cells
- circulating tumor cells
- stem cells
- bone marrow