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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.
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Malikmohamed Yousuf, Ilaria Iuliani, Reshma Veetil, Aswin Sai Narain Seshasayee, Bianca Sclavi, et al.. Early fate of exogenous promoters in E. coli. Nucleic Acids Research, Oxford University Press, 2020, 48 (5), pp.2348-2356. ⟨10.1093/nar/gkz1196⟩. ⟨hal-02557129⟩

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