E. coli transcriptomic response to nitrogen limitation

Stochastic fluctuation in the levels of expression of a critical factor likely causes persister formation. For example, cells with high levels of expression of the HipA toxin are tolerant of antibiotics (S Hansen et al. PLoS One 2012), as are cells with low levels of expression of Krebs cycle enzymes (Manuse S et al., PLoS Biol, 2021, Conlon BP, et al. Nat Microbiol. 2016). We therefore sought to identify the critical components whose fluctuation in expression may determine formation of persisters in a N limited cell population. We reasoned that such persister genes are likely to be found among those whose expression is most affected by nitrogen starvation. We therefore performed a transcriptome analysis of E. coli responding to nitrogen starvation. Overall design: Transcriptomic profiling of MG1655 in minimal media containing high or low concentration of ammonia (as nitrogen source). The same number of bacteria were aliquoted from a early exponential phase culture (nitrogen rich) and a culture experiencing nitrogen starvation foor after 5 h.