Rinat Arbel-Goren

Weizmann Institute of Science, Israel

Post-transcriptional regulatory processes may change transcript levels and affect cell-to-cell variability or noise. We study small-RNA regulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli. In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of several target genes, as well as upregulates the translation of other target genes, in response to iron stress. Using single-molecule fluorescence in situ hybridization (smFISH), we measured transcript numbers of RyhB-regulated genes in individual cells, as a function of iron deprivation. We observed a monotonic increase of noise with iron stress, but no evidence of theoretically predicted, enhanced stoichiometric fluctuations in transcript numbers, nor of bistable behavior in transcript distributions. Direct detection of RyhB in individual cells shows that its noise is much smaller than that of these two targets, when RyhB production is significant. A generalized stochastic, two-state model of bursty transcription that neglects RyhB fluctuations describes quantitatively the dependence of noise and transcript distributions on iron deprivation, enabling extraction of in vivo parameters such as RyhB-mediated transcript degradation rates. The transcripts’ threshold-linear behavior indicates that the effective in vivo interaction strength between RyhB and its two target transcripts is comparable. Visualization of various transcripts by smFISH and super-resolution microscopy indicates that their subcellular localization is not significantly affected by iron stress. The results do not support predictions of a theoretical model that claims that excluded volume effects favor transcript localization at the cellular poles.