A Comprehensive, CRISPR-based Approach to Functional Analysis of Essential Genes in Bacteria. Bacillus subtilis

Essential gene products underpin the core reactions required for cell viability, but are poorly studied in vivo due to a shortage of appropriate technologies. Using CRISPR interference, we created knockdowns of every essential gene in Bacillus subtilis and probed their phenotypes. Our high-confidence essential gene network, established using chemical genomics, showed extensive interconnections among distantly related processes and identified the modes of action for uncharacterized antibiotics. Importantly, mild knockdown of essential gene functions significantly reduced stationary-phase survival without affecting maximal growth rate, suggesting that essential protein levels are set to maximize viability of cells during stress. Finally, high-throughput microscopy indicated that cell morphology is relatively insensitive to mild knockdown but profoundly affected by depletion of gene function, revealing intimate connections between cell growth and shape. Our results provide a framework for systematic investigation of essential gene functions in vivo that is broadly applicable to diverse microorganisms and amenable to comparative analysis. Overall design: 2 samples of B. subtilis NET-seq and 7 samples of B. subtilis mRNA-seq.