Transcriptional start site turnover in the evolution of bacterial paralogous genes - the pelE-pelD virulence genes in Dickeya

FEBS J. 2016 Nov;283(22):4192-4207. doi: 10.1111/febs.13921. Epub 2016 Oct 26.


After a gene duplication event, the resulting paralogous genes frequently acquire distinct expression profiles, roles, and/or functions but the underlying mechanisms are poorly understood. While transcription start site (TSS) turnover, i.e., the repositioning of the TSS during evolution, is widespread in eukaryotes, it is less documented in bacteria. Using pelD and pelE, two closely related paralogous genes encoding key virulence factors in Dickeya, a gamma proteobacterial genus of phytopathogens, we show that pelE has been selected as an initiator of bacterial aggression, while pelD acts at a later stage, thanks to modifications in the transcriptional regulation of these two genes. This expression change is linked to a few mutations that caused a shift in the position of the pelETSS and the rapid divergence in the regulation of these genes after their duplication. Genomic surveys detected additional examples of putative turnovers in other bacteria. This first report of TSS shifting in bacteria suggests that this mechanism could play a major role in paralogous genes fixation in prokaryotes.

Keywords: adaptation; gene duplication; pectate lyases; promoter; transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Base Sequence
  • Binding Sites / genetics
  • Evolution, Molecular
  • Gene Expression Regulation, Bacterial
  • Models, Genetic
  • Pectobacterium / classification
  • Pectobacterium / genetics*
  • Pectobacterium / pathogenicity
  • Phylogeny
  • Polysaccharide-Lyases / genetics*
  • Regulatory Sequences, Nucleic Acid / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Homology, Nucleic Acid
  • Species Specificity
  • Transcription Initiation Site*
  • Virulence / genetics


  • Bacterial Proteins
  • PelE protein, Erwinia chrysanthemi
  • Polysaccharide-Lyases
  • pectate lyase