Chromosome-segment scanning for gain- or loss-of-function screening (CHASING).

Area of Science:

• Genomics
• Synthetic Biology
• Functional Genomics

Background:

• Identifying beneficial mutations typically requires extensive single-gene knockout libraries.
• This process is labor-intensive and time-consuming for researchers.

Purpose of the Study:

• To develop a more efficient method for identifying functional mutations using genome-scale libraries.
• To enable rapid screening and identification of genes responsible for specific phenotypes.

Main Methods:

• Construction of a genome-scale library with large fragment deletion strains designed by AutoGSL.
• Application of chromosome-segment scanning for loss-of- and gain-of-function screening (CHASING).
• Utilizing a computer-aided gene-annotation web tool for gene identification and visualization.
• Employing Clusters of Orthologous Gene Transformer for phenotype prediction.

Main Results:

• Successfully screened for loss-of- and gain-of-function phenotypes.
• Identified specific genes associated with observed phenotypes efficiently.
• Developed acetoin- and lycopene-overproducing hosts using the CHASING strategy.
• Demonstrated the predictive power of the gene transformer model for growth phenotypes.

Conclusions:

• The developed genome-scale library and CHASING strategy significantly improve functional genomics investigations.
• This method offers a robust platform for chassis engineering and optimizing chemical overproduction.
• Highlights the potential of large fragment deletion libraries for rapid functional gene discovery.