Mechanical Genomics Identifies Diverse Modulators of Bacterial Cell Stiffness

• Published in: Cell systems Vol. 2; no. 6; pp. 402 - 411
• Main Authors: Auer, George K., Lee, Timothy K., Rajendram, Manohary, Cesar, Spencer, Miguel, Amanda, Huang, Kerwyn Casey, Weibel, Douglas B.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 22.06.2016
• Subjects: Anti-Bacterial Agents; Bacterial Proteins; Cell Membrane; Cell Wall; DNA Replication; Escherichia coli; Genomics; Mechanical Phenomena; Spores, Bacterial; Stress, Mechanical
• ISSN: 2405-4712; 2405-4720
• DOI: 10.1016/j.cels.2016.05.006

Bacteria must maintain mechanical integrity to withstand the large osmotic pressure differential across the cell membrane and wall. Although maintaining mechanical integrity is critical for proper cellular function, a fact exploited by prominent cell-wall-targeting antibiotics, the proteins that contribute to cellular mechanics remain unidentified. Here, we describe a high-throughput optical method for quantifying cell stiffness and apply this technique to a genome-wide collection of ∼4,000 Escherichia coli mutants. We identify genes with roles in diverse functional processes spanning cell-wall synthesis, energy production, and DNA replication and repair that significantly change cell stiffness when deleted. We observe that proteins with biochemically redundant roles in cell-wall synthesis exhibit different stiffness defects when deleted. Correlating our data with chemical screens reveals that reducing membrane potential generally increases cell stiffness. In total, our work demonstrates that bacterial cell stiffness is a property of both the cell wall and broader cell physiology and lays the groundwork for future systematic studies of mechanoregulation. [Display omitted] •A straightforward assay reveals cell-stiffness modulators across a bacterial proteome•Bacterial cell stiffness is connected to many biochemical pathways•PBP1b and its associated protein LpoB are both major contributors to cell stiffness•The proton ionophore CCCP generally increases bacterial cell stiffness Auer et al. present a mechanical genomics assay that can be applied in high throughput to estimate bacterial cell stiffness. From a collection of 3,844 E. coli single non-essential gene deletion mutants, 46 genes were identified that significantly altered cell stiffness; these genes represent a diverse set of intracellular functions. Correlating these high-throughput measurements with previous chemical genomics data also identified chemical and environmental conditions that alter bacterial cell stiffness.