Biosensor-Coupled In Vivo Mutagenesis and Omics Analysis Reveals Reduced Lysine and Arginine Synthesis To Improve Malonyl-Coenzyme A Flux in Saccharomyces cerevisiae.

Malonyl-coenzyme A (malonyl-CoA) is an important precursor for producing various chemicals, but its low availability limits the synthesis of downstream products in Saccharomyces cerevisiae. Owing to the complexity of metabolism, evolutionary engineering is required for developing strains with improved malonyl-CoA synthesis. Here, using the biosensor we constructed previously, a growth-based screening system that links the availability of malonyl-CoA with cell growth is developed. Coupling this system with in vivo continuous mutagenesis enabled rapid generation of genome-scale mutation library and screening strains with improved malonyl-CoA availability. The mutant strains are analyzed by whole-genome sequencing and transcriptome analysis. The omics analysis revealed that the carbon flux rearrangement to storage carbohydrate and amino acids synthesis affected malonyl-CoA metabolism. Through reverse engineering, new processes especially reduced lysine and arginine synthesis were found to improve malonyl-CoA synthesis. Our study provides a valuable complementary tool to other high-throughput screening method for mutant strains with improved metabolite synthesis and improves our understanding of the metabolic regulation of malonyl-CoA synthesis. IMPORTANCE Malonyl-CoA is a key precursor for the production a variety of value-added chemicals. Although rational engineering has been performed to improve the synthesis of malonyl-CoA in S. cerevisiae, due to the complexity of the metabolism there is a need for evolving strains and analyzing new mechanism to improve malonyl-CoA flux. Here, we developed a growth-based screening system that linked the availability of malonyl-CoA with cell growth and manipulated DNA replication for rapid in vivo mutagenesis. The combination of growth-based screening with in vivo mutagenesis enabled quick evolution of strains with improved malonyl-CoA availability. The whole-genome sequencing, transcriptome analysis of the mutated strains, together with reverse engineering, demonstrated weakening carbon flux to lysine and arginine synthesis and storage carbohydrate can contribute to malonyl-CoA synthesis. Our work provides a guideline in simultaneous strain screening and continuous evolution for improved metabolic intermediates and identified new targets for improving malonyl-CoA downstream product synthesis.

Characterization and evolution of xylose isomerase screened from the bovine rumen metagenome in Saccharomyces cerevisiae.

The conversion of abundant levels of xylose in lignocellulosic materials into viable products would generate economic benefits. The heterologous expression of the xylose isomerase (XI) gene is considered a direct and effective strategy for establishing the xylose metabolic pathway in Saccharomyces cerevisiae. However, only limited sources of xylA are functionally expressed in S. cerevisiae and are capable of driving effective xylose consumption. In this study, Ru-xylA (where Ru represents the rumen), which was screened from the contents of the bovine rumen metagenomic library, was functionally expressed in S. cerevisiae, and the enzyme activity was 1.31 U mg(-1) protein. This is a new source of XI that can exhibit high activity levels in S. cerevisiae. The activity of this enzyme is comparable to those of the Piromyces sp. XI. Then, the Ru-XI activity was further improved through mutagenesis and growth-based screening in a centromeric plasmid. A variant containing two mutations (K11T/D220V) that exhibited a 68% increase in enzyme activity was isolated. Our work identified a new xylose isomerase that can be functionally expressed in S. cerevisiae and results in a higher XI enzyme activity through mutagenesis.