Growth influences the single cell variability of the DNA damage response in Escherichia coli

Abstract

The resilience of bacteria depends upon their capacity to proliferate and survive under different conditions, including in the human body where some bacterial infections can be fatal. Many antibiotics used to treat infections cause direct and indirect DNA damage, in particular DNA double-strand breaks, which can lead to bacterial cell death. Bacteria respond to DNA damage by inducing the SOS response, which is an important process in the repair and tolerance of DNA damage. Additional consequences of SOS induction by antibiotic exposure, is the potential increase of mutagenesis, horizontal gene transfer, and tolerance to other antibiotics. Therefore, identifying the factors involved in SOS induction is essential to understanding the dynamics of bacterial infections.

Previous studies have indicated that bacterial susceptibility to DNA damaging agents is dependent on growth conditions, but the mechanisms involved are not well understood. Many physiological changes are associated with growth rate, including DNA replication (a major mechanismleading to DNA damage), and reallocation of resources towards growth-limiting processes, which could impair the capacity of cells to induce the SOS response. In addition, previous reports indicate that SOS expression is variable in single cells, and the effect of growth conditions in variability has not been evaluated.

In order to evaluate how changes in growth conditions influence the SOS response, we have quantified the levels of SOS induction by DNA damage in single cells using E. coli as a model organism. Our results show that cells with very high levels of SOS expression are more abundant in slow-growing conditions, that is under spontaneous DNA damage, under damage induced by the antibiotic ciprofloxacin, and under replication-dependent chronic double-strand breaks. We explain these observations as a combination of population dynamics, that contributes to enriching for slow dividing cells (high SOS) in slow-growing populations, and an influence of growth conditions in the variability of SOS induction, possibly because of influences in the DNA-repair process via an unknown mechanism. The population dynamics arguments presented here may be relevant to other antibiotics, and argue to the significance of studying the response to antibiotics in single cells. We believe the observations on variability in SOS-expression may open new avenues for understanding the limiting factors for DNA repair.