High-Throughput Exploration of Sequence Space at Gene and Genome Scales
Understanding bacterial adaptation is key to both fundamental biology and strain engineering. In this talk, I will present my work on deep mutational scanning (DMS) to explore adaptation mediated by mutations in essential genes—critical yet underexplored drivers of bacterial evolution. To overcome limitations in mutational library diversity and editing efficiency, I developed CRISPR/Cas9-mediated error-prone editing (CREPE), achieving mutation efficiencies of 70–80%. Using CREPE, I mapped the adaptive landscape of RNA polymerase, uncovering modular domains that control global traits of growth and maintenance, with implications for optimizing engineered strains. Beyond individual gene adaptations, tracking beneficial mutations in evolving bacterial populations remains a major challenge due to low detection limits in conventional sequencing. To address this, I developed a CRISPR/Cas9-based molecular barcoding system capable of tracking over 100,000 bacterial lineages at ultra-low frequencies (10⁻⁵). Applying this system to a 20,000-generation evolution experiment, I identified 250 fitness-enhancing mutations in ~30 genes—dramatically improving upon traditional approaches. These insights demonstrate how a priori knowledge of adaptation mechanisms can enable knowledge-driven microbial engineering, accelerating the development of robust industrial strains.
Short bio
I am a researcher specializing in high-throughput genome engineering to study bacterial adaptation and optimize microbial strains for sustainable bioconversion. My work focuses on the molecular processes that regulate proteome composition and cell physiology, which often pose challenges for industrial bioproduction. By developing CRISPR/Cas9-based technologies, including deep mutational scanning (DMS) and molecular barcoding systems, I enable precise functional characterization of regulatory proteins and track bacterial evolutionary dynamics. Integrating synthetic biology, systems biology, and directed evolution, I aim to create standardized platforms for engineering microbial strains tailored for industrial applications.
Laboratory of the speaker
CEA-Genoscope
Invited by
Anne-Gaëlle Planson
