Genome wide functional screen for calcium transients in E. coli identifies decreased membrane potential adaptation to persistent DNA damage

Abstract

1.Calcium plays numerous critical roles in signaling and homeostasis in eukaryotic cells. Unlike eukaryotic cells, far less is known about calcium signaling in bacteria, and few genes controlling influx and efflux have been identified. Previous work in Escherichia coli showed calcium influx is induced by voltage depolarization, which were enhanced by mechanical stimulation, suggesting a role in bacterial mechanosensation. To identify proteins and pathways affecting calcium handling in bacteria, we designed a live cell screen to monitor calcium dynamics in single cells across a genome wide knockout panel in E. coli. The screen measured cells from the Keio collection of knockouts and quantified calcium transients across the population. Overall, we found 143 gene knockouts that decreased calcium transients, and 32 genes knockouts that increased transients. Knockouts involved in energy production and regulation appeared, as expected, as well as knockouts of the voltage sink, the F1Fo-ATPase. Knockouts in exopolysaccharide and outer membrane synthesis showed reduced transients and refined our model of electrophysiology mediated mechanosensation in E. coli. Additionally, knockouts annotated in DNA repair had reduced calcium transients and voltage. However, acute DNA damage did not affect voltage, and suggested that only long term adaptation to DNA damage decreased membrane potential and calcium transients. Our work showed a distinct separation between the acute and long term DNA damage responses in bacteria, which has implications for mitochondrial DNA damage in eukaryotes. ImportanceAll eukaryotic cells use calcium as a critical signaling molecule. There is tantalizing evidence that bacteria also use calcium for cellular signaling, but much less is known about the molecular actors and physiological roles. To identify genes regulating cytoplasmic calcium in Escherichia coli, we created a single cell screen for modulators of calcium dynamics. The genes uncovered in this screen helped refine a model for voltage mediated bacterial mechanosensation. Additionally, we were able to more carefully dissect the mechanisms of adaptation to long term DNA damage, which has implications for both bacteria and mitochondria in the face of unrepaired DNA.