Escherichia coli non-coding regulatory regions are highly conserved

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Microbial genome sequencing is advancing rapidly, enabling large-scale variation studies.
• Current research predominantly examines coding regions, overlooking non-coding regulatory elements' role in physiological responses.

Purpose of the Study:

• To conduct a large-scale investigation of intergenic sequence variation in non-coding regulatory regions of Escherichia coli.
• To create a comprehensive 'alleleome' of these regulatory regions for detailed analysis.

Main Methods:

• Identified non-coding regulatory region alleles across 2350 Escherichia coli strains at single base-pair resolution.
• Analyzed the conservation patterns of core promoter elements and transcription factor binding sites.
• Contrasted wild-type variation with mutations from adaptive laboratory evolution.

Main Results:

• The 'alleleome' comprises 117,781 unique alleles for 1169 reference regulatory regions.
• 64% of nucleotide positions were invariant; variants appeared in a median of 0.6% of strains.
• Non-coding alleles successfully recovered E. coli phylogroups, with conserved promoter and binding sites, especially near essential genes.
• Adaptive laboratory evolution mutations targeted conserved sites, differing from wild-type variation patterns.

Conclusions:

• Non-coding sequence variation in Escherichia coli is substantial and informative.
• This variation is sufficient for robust phylogroup recovery and offers insights into regulatory evolution.
• The study expands pangenomic analyses to non-coding regulatory regions at single-nucleotide resolution.