Genome-wide analysis of E. coli cell-gene interactions

Area of Science:

• Synthetic biology
• Systems biology
• Microbiology

Background:

• Synthetic biology aims for predictable genetic circuits, but interactions with cellular systems remain challenging.
• Existing models and screening methods cannot fully predict synthetic gene behavior within host cells.
• This study investigates how cellular function perturbations affect synthetic gene expression genome-wide.

Purpose of the Study:

• To perform a genome-wide analysis of synthetic gene expression modulation by cellular function perturbations.
• To identify and characterize the Size-Expression interaction in Escherichia coli.
• To understand the feedback mechanisms between genetic and physiological systems.

Main Methods:

• A dual fluorescent reporter gene construct was integrated into 3822 single-gene deletion strains (KEIO collection).
• Single-cell size was measured using flow cytometry.
• Regression analyses differentiated expression-specific from gene-specific effects.

Main Results:

• Most perturbations affected synthetic gene expression indirectly via cell size changes, indicating a Size-Expression interaction.
• Gene deletions mapped to three systems: Division and Biosynthesis (DB) linked to large cells/high expression; Membrane and Motility (MM) to small cells/low expression; Energy, Protein synthesis and Ribosome (EPR) to small cells/ribosome feedback.
• Cellular systems exhibit feedback between growth (cell size) and gene expression.

Conclusions:

• Widespread feedback exists between cell growth and gene expression across cellular systems.
• Gene disruptions impact both cell size and gene expression, with effects propagating through the Size-Expression interaction.
• Cell division and ribosomal content mediate the dual impact of growth on cell size and gene expression, offering insights into genetic and physiological system feedbacks.