Single cell, over-time protein numbers of cold shock repressed genes in Escherichia coli

Adaptation to temperature shifts is essential for cell survival. The effects of such shifts are still relatively uncharacterized at the single-gene, single-cell levels, but are expected to be complex [1] and heterogeneous [2]. To study this phenomenon in the prokaryote E. coli, first, we performed RNA-seq to identify the 30 most repressed genes following a temperature downshift from 30 to 15 ⁰C. Next, we performed over-time flow-cytometry of those genes, using a strain library with proteins tagged with YFP [3], to characterize changes in the single-cell statistics of their protein numbers. We found that their responses can be explained by an analytical model of gene expression, where the squared coefficient of variation (CV2) of single cell expression levels equals the inverse of the mean, times a constant C [4]. Notably, the relationship between the mean and the CV2 is temperature dependent, with C increasing by 30% with the temperature downshift. Also, C differs significantly between the genes. Moreover, the skewness of the distribution of single-cell protein numbers has a complex, yet to explain, temperature dependence. Finally, we analyze which kinetic parameters of the model are more likely to be temperature dependent, based on the observations. Our results provide the most detailed characterization of the changes in the single cell statistics of protein numbers following a cold shock, and thus should assist in better understanding how E. coli cells rapidly recover homeostasis following this stress.
References :
[1] Oliveira, S.M.D. et al. (2019). doi: 10.1038/s41598-019-39618-z
[2] Häkkinen, A. et al. (2016). doi: 10.1371/journal.pcbi.1005174
[3] Taniguchi, Y. et al. (2020). doi: 10.1126/science.1188308
[4] Bar-Even, A. et al. (2006). doi: 10.1038/ng1807