Rhs elements comprise three subfamilies which diverged prior to acquisition by Escherichia coli

Area of Science:

• Microbiology
• Genetics
• Bacterial Evolution

Background:

• Rhs elements are widespread, complex genetic composites found in Escherichia coli isolates.
• These elements consist of a conserved GC-rich core and variable AT-rich extensions.
• Rhs core homology contrasts with significant divergence in their extension regions.

Purpose of the Study:

• To characterize two novel Rhs elements, RhsG and RhsH, from the ECOR reference collection.
• To investigate the evolutionary relationships and subfamily diversification of Rhs cores.
• To explore the mechanisms of genetic exchange and the origins of Rhs element components.

Main Methods:

• Characterization of RhsG and RhsH elements from specific E. coli strains (ECOR-11 and ECOR-45).
• Phylogenetic analysis of known Rhs core sequences to determine subfamily relationships.
• Comparative analysis of sequence substitutions to infer evolutionary history and background.
• Identification and characterization of the novel vgr component in RhsE and RhsG.

Main Results:

• RhsG (ECOR-11) and RhsH (ECOR-45) were identified and mapped.
• Phylogenetic analysis delineated three distinct Rhs core subfamilies (RhsA-B-C-F, RhsD-E, RhsG-H) with 22-29% divergence.
• Evidence suggests ancestral cores originated in a GC-rich environment, with independent transitions to E. coli's less GC-rich background.
• A novel instance of core-extension shuffling between different subfamilies was observed.
• The vgr component, encoding a repetitive Val-Gly peptide protein, was identified in RhsE and RhsG.

Conclusions:

• Rhs elements exhibit significant evolutionary complexity, with distinct subfamilies arising from a common GC-rich ancestor.
• Independent horizontal gene transfer and recombination events shape Rhs element diversity in E. coli.
• The vgr component represents a novel functional domain within specific Rhs elements.