SRA

The investigation of gene essentiality is key to many aspects of bacterial genetics. In E. coli, most functional genomic studies have been limited to the laboratory-evolved model strain K12 which is not representative of the broad diversity of the E. coli species. Indeed, E. coli is characterized by an open pangenome with high rates of recombination and horizontal gene transfer. While gene essentiality is known to be evolutionary conserved, it remains to be investigated to what extent this holds true in a species with such a genetic diversity. Here, we used CRISPRi screening to evaluate how the genetic background affects gene essentiality in E. coli. We designed a sgRNA library targeting ~3,300 conserved genes and used it in 18 E. coli isolates to evaluate the fitness of each knockdown in 3 different growth conditions. As expected, most gene essentiality was conserved across all tested strains but the screens highlighted strain-specific effects showing that gene essentiality can vary at the strain level. In particular, these differences involve some highly-studied genes such as the sigma factor E and the Lon and ClpXP proteases. We further showed that mobile genetic elements can modify the essentiality of conserved genes and that a significant part of the core genome is susceptible to become essential under certain genetic backgrounds.