DNA sequence repeats identify numerous Type I restriction-modification systems that are potential epigenetic...

Area of Science:

• Microbiology
• Epigenetics
• Bacterial Genetics

Background:

• Pathogenic bacteria utilize randomly switching methyltransferases in Type III restriction-modification (R-M) systems.
• These systems, known as phasevarions, involve DNA sequence repeats that alter methyltransferase expression, leading to global gene expression changes and bacterial phenotypic differentiation.
• While Type III systems are well-documented, recombination-driven switching in Streptococcal Type I R-M systems also regulates gene expression.

Purpose of the Study:

• To investigate the prevalence of simple DNA sequence repeats within the hsdRMS genes encoding Type I R-M systems.
• To determine the potential for phase variation in Type I R-M systems through these repeats.

Main Methods:

• Interrogation of the REBASE database, a comprehensive resource for R-M systems.
• Systematic searching for simple DNA sequence repeats within the hsdS, hsdM, and hsdR genes of Type I R-M systems.

Main Results:

• Simple sequence repeats capable of mediating phase variation were identified in 7.9% of hsdS genes, 2% of hsdM genes, and 4.3% of hsdR genes.
• Phase variation in hsdM and hsdS genes can lead to altered methyltransferase expression or specificity, potentially controlling phasevarions.
• Approximately 10% of surveyed Type I R-M systems show independent evolution of random switching via simple DNA sequence repeats.

Conclusions:

• Type I R-M systems, in addition to Type III systems and Streptococcal Type I R-M systems, can employ simple DNA sequence repeats for phase variation.
• This suggests a convergent evolutionary mechanism for epigenetic regulation and phenotypic diversity in bacteria.
• The findings highlight a significant, previously underappreciated mechanism of gene regulation within Type I R-M systems.