A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

• CRISPRi knockdown of essential genes enables discovery of direct antibiotic targets
• An essential gene network reveals functional connections between core processes
• A cell morphology screen identifies essential genes intimately tied to cell shape
• A majority of essential genes show morphological defects as a terminal phenotype

SummaryEssential gene functions underpin the core reactions required for cell viability, but their contributions and relationships are poorly studied in vivo. 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 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 outgrowth from stationary phase. 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 broadly applicable to diverse microorganisms and amenable to comparative analysis.

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