Early fate of exogenous promoters in E. coli

Nucleic Acids Res. 2020 Mar 18;48(5):2348-2356. doi: 10.1093/nar/gkz1196.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / chemistry
  • Chromatin / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Fimbriae Proteins / genetics*
  • Fimbriae Proteins / metabolism
  • Gene Dosage
  • Gene Expression Regulation, Bacterial*
  • Gene Silencing
  • Gene Transfer, Horizontal
  • Genes, Reporter
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • Mutagenesis, Insertional*
  • Promoter Regions, Genetic*
  • Protein Binding
  • Protein Biosynthesis
  • Transgenes


  • Chromatin
  • Escherichia coli Proteins
  • FimG protein, E coli
  • Green Fluorescent Proteins
  • Fimbriae Proteins