L-lysine. as an important amino acid for livestock has been increasing in demand, all traditional lysine producers have been created over many years by multiple rounds of random mutagenesis and selection. In recent decades, the development of recombinant DNA techniques and increased understanding of the biochemistry of metabolic reactions has enabled the identification of genetic targets for improved lysine production,and the successful optimization of a wild-type strain into a high-producing cell factory may serve as foundation to combine rational design of metabolic blueprints with targeted genetic engineering and integrated omics analysis for engineering microbial metabolism. Here, we describe the development of a genetically defined process of L-lysine hyperproducing by systems metabolic engineering of the wildtype and the method combining with high throughput screening (HTS) permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones.