phnE frameshift reversion frequency: beyond density effects to genomic prevalence.

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• Phosphonates serve as alternative phosphorus sources.
• The phn operon in Escherichia coli mediates phosphonate uptake.
• Previous studies reported high frequencies of phn revertants in E. coli K-12.

Purpose of the Study:

• Reexamine phn revertant frequencies in E. coli K-12.
• Investigate the effect of phosphate contamination and cell density on reversion.
• Assess the fitness advantage of functional phnE under phosphate limitation.
• Determine the prevalence of non-functional phn genes in natural E. coli isolates.

Main Methods:

• Culturing E. coli K-12 under strictly phosphate-limited conditions.
• Eliminating phosphate impurities from growth media.
• Assessing revertant frequencies at varying bacterial densities.
• Evaluating bacterial fitness with functional vs. non-functional phnE.
• Conducting an in silico survey of phn gene functionality in E. coli genomes.

Main Results:

• Phosphate-free conditions drastically reduced estimated revertant frequencies.
• Bacterial density did not significantly affect revertant frequency.
• Functional phnE provided no measurable fitness advantage under phosphate limitation.
• Approximately 15% of natural E. coli strains lack functional phn genes.

Conclusions:

• Reported high frequencies of phn revertants were likely artifacts of phosphate contamination.
• Loss of phosphonate utilization does not impose a fitness cost under phosphate limitation.
• Loss of phn gene function may be an adaptive strategy in natural E. coli populations.