Are Restriction Enzymes Recognition Sites Underrepresented in the Organisms That Host Them?

Abstract: The restriction modification enzyme system is a vital bacterial defense system against invading phages. Restriction modification system consists of a restriction enzyme and a methyltransferase enzyme that work in a complementary fashion to cut foreign DNA and at the same time methylates and protects host DNA. Recognition site sequence is usually specific for each restriction enzyme. Restriction Recognition Site Representation (RRSR) principally calculates the observed frequency of occurrence of each restriction enzyme recognition site and its expected frequency of occurrence based on the abundance of the four nucleotides in the host’s whole genome sequence. A catalogue of restriction enzymes, their properties and annotation was created. The result from RRSR was statistically tested in R using Chi square goodness of fit test and the results showed that many restriction enzymes had their recognition sites underrepresented in their host genome. Adaptive bacterial ada regulon system, a system that protects bacterial genome against exogenous DNA methylation by environmental mutagens interacted with the restriction modification system and may have accounted for the bacterial restriction recognition sites underrepresentation. The dimerization state of the enzyme subunits and their gene expression, as well as the net cellular concentration for methyltransferase enzyme and cofactors; S-adenosyl-methionine, ATP and magnesium ions are vital to determine to achieve a conclusive decision about the efficiency of the restriction modification system in the host. RSRR in phage genome supported the fact that phages are bacterial specific paving a way for using phages as targeted bactericidal agents. RRSR confirmed the co-evolution of phages and bacteria.