Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
1 Norwegian School of Veterinary Science, EpiCentre, Department of Food Safety and Infection biology, Ullevålsveien 72, Oslo, Norway
2 Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
3 Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Sciences, Ås, Norway
4 National Veterinary Institute, Ullevålsveien 68, Pb 750 Sentrum, N-0106 Oslo, Norway
5 Center for Biological Sequence Analysis, Department of Systems Biology, Comparative genomics unit, Technical University of Denmark, DK-2800 Lyngby, Denmark
BMC Genomics 2012, 13:66 doi:10.1186/1471-2164-13-66Published: 10 February 2012
We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure.
Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes.
We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.