Distribution of potential type II restriction sites (palindromes) in prokaryotes

Restriction-modification systems are used as a defensive mechanism against inappropriate invasion of foreign DNA. The recognition sequences for the common type II restriction enzymes and their corresponding methylases are usually palindromes. In this study, we identified the most over- and underrepresented words in DNA of four bacteria: Escherichia coli, Bacillus subtilis, Clostridium perfringens, and Pseudomonas aeruginosa. Using maximum order Markov chain analysis, we found that palindromic words were most often more underrepresented than their non-palindromic counterparts. No strict rule for the intragenic palindrome content could be derived, but for three of the bacteria there was a weak correlation between codon usage bias and palindrome content. A clear drop in palindrome counts was observed in the Shine-Dalgarno region for B. subtilis and C. perfringens, but not in E. coli or P. aeruginosa. It was also shown that palindromes in eubacteria and archaebacteria seem to occur slightly more infrequently than expected on the basis of the genomic GC-content, but some exceptions to this principle exist.