Early fate of exogenous promoters in E. coli

Abstract

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.

Threshold accumulation of a constitutive protein explainsE. colicell division behavior in nutrient upshifts

“…Solving for N , under steady growth, one obtains and, as a consequence Our strains carried fluorescent reporters for ribosomal and constitutive promoters inserted in the chromosome close to either the origin or the terminus of replication (see methods and ref. [54, 55]), and we used their experimentally measured dynamics to define the putative production rate of the putative “adder protein”. The constitutive reporter “P5” is based on a strong exogenous promoter with consensus −10 and −35 sequences lacking any transcription factor regulation, as well as lacking a GC-rich ppGpp discriminator region at the transcirption initiation site that would render it sensitive to inhibition by ppGpp.…”

“…Our strains had fluorescent reporters for ribosomal and constitutive promoters inserted in the chromosome close to both the origin and the terminus of replication (see methods and ref. [53,54]), and we used their experimentally measured dynamics to define the putative production rate of the putative "adder protein". Following the literature, we agnostically assumed that an effector molecule that is produced at a rate proportional to volume triggers division once a critical amount is reached ("initiator accumulation" hypothesis [1]).…”

Genetic context effects can override canonicalcisregulatory elements inEscherichia coli

“…For example, H-NS binding sites are apparent as troughs on the transcriptional propensity map (i.e., low transcriptional propensity). Subsequent high-throughput assessment of fluorescent protein expression from transposon integrations largely confirmed these results, and also linked H-NS binding sites to low reporter expression (16). H-NS binds to and reduces expression of genes with AT rich sequences (17–20).…”

The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

“…6C ; Pearson’ rho is 0.81 and 0.61 for free-living and bacteroid ChIP-seq data, respectively; P values < 0.01). The importance of cis element variation is supported by a recent study on H-NS, in which with or without binding signals of xenogeneic silencer H-NS can partially explain a wild range of expression variability of a foreign gene that was randomly inserted into genomes of a population of E. coli [ 79 ]. In line with this scenario, a great variation in MucR1 recruitment levels was observed within individual replicons or pangenome subsets of S. fredii (Supplementary Fig.…”