Under-representation of CTAG in the Bacterial Genome

Abstract

DNA sequences in the genomes have several examples of inhomogeneities which point towards their non-random nature. One such case is under-representation of CTAG tetranucleotide in bacterial genomes. This work aims to study the reasons behind the under-representation of CTAG in bacterial genomes. A randomly selected set of 23 bacterial genomes, largely from diverse prokaryotes, showed that CTAG is under-represented (Observed / Expected value <1.0). In the majority of the selected genomes, CTAG had the lowest O/E value. It was found that TAG, a submotif of CTAG has one of the lowest O/E values in most of the bacteria. The underrepresentation effect is further enhanced by the occurrence of a cytosine at the 5’ end of TAG which makes it CTAG and explains its under-representation. CTAG distribution in the genome is also very uneven. While most of the genome has very low occurrence, there are certain short regions where CTAG is found in relatively much higher abundance. Such regions coincide with the sequence with highly uneven base composition. This study demonstrates base composition as one of the factors causing highly heterogeneous distribution of CTAGs in the bacterial genomes and indicates that CTAGs play some important biologic role in bacteria.