Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements

Abstract

Transcription kinetics is limited by its initiation steps, which differ between promoters and with intra- and extracellular conditions. Regulation of these steps allows tuning both the rate and stochasticity of RNA production. We used time-lapse, single-RNA microscopy measurements in live Escherichia coli to study how the rate-limiting steps in initiation of the Plac/ara-1 promoter change with temperature and induction scheme. For this, we compared detailed stochastic models fit to the empirical data in maximum likelihood sense using statistical methods. Using this analysis, we found that temperature affects the rate limiting steps unequally, as nonlinear changes in the closed complex formation suffice to explain the differences in transcription dynamics between conditions. Meanwhile, a similar analysis of the PtetA promoter revealed that it has a different rate limiting step configuration, with temperature regulating different steps. Finally, we used the derived models to explore a possible cause for why the identified steps are preferred as the main cause for behavior modifications with temperature: we find that transcription dynamics is either insensitive or responds reciprocally to changes in the other steps. Our results suggests that different promoters employ different rate limiting step patterns that control not only their rate and variability, but also their sensitivity to environmental changes.

Metagenomic and metatranscriptomic responses of natural oil degrading bacteria in the presence of dispersants

“…4 may be limited to the selected oil degradation genes investigated in this study. Temperature is known to modulate specific gene expression patterns in E. coli (Oliveira et al, 2016), and our results suggest that low temperature could also be a trigger for the following genes: K00496/AlkB, K00529/ Rubredoxin, K02660/PilJ, K00114/PQQ and K00154. The results also suggest that Oleispira shifts to distinct expression patterns, were associated with increasing transcription of these specific genes in the presence of oil and dispersant at low temperatures.…”

Non-transcriptional processes in circadian rhythm generation

“…However, the period of circadian rhythms in mammalian cells is surprisingly resilient against inhibition of RNA polymerase II [ 194 ] and, under these conditions, remains compensated against changes in temperature. Moreover, both transcription and translation are temperature-dependent processes [ 195 , 196 , 197 , 198 ], whereas circadian period determination is not. A potential solution to this quandary is vested in some recent work where the activity of CK1 against its clock protein substrates was shown to be intrinsically temperature-compensated [ 199 , 200 • ], suggesting that since temperature compensation of circadian period occurs post-translationally, then perhaps so too does period determination.…”

Multiscale effects of heating and cooling on genes and gene networks

“…This twofold involvement as both the subject and agent of cellular protection makes it difficult to understand what happens with gene networks at nonoptimal temperatures. Additional complexity stems from nontrivial effects of temperature on transcription ( 10 ), translation ( 11 ), and their regulation ( 12 , 13 ). Previous transcriptome expression measurements in heat and cold shock revealed broad responses ( 14 ), but it is hard to discern the degree to which these changes are individual gene-level ( 15 ) or network-level effects, or cellular attempts to restore homeostasis.…”