Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis

1 BioInformatics Institute, Singapore 2 Human Genome Laboratory, Department of Microbiology, Faculty of Medicine, National University of Singapore, Singapore Correspondence Vincent T. K. Chow micctk{at}nus.edu.sg Obligatory intracellular parasites have undergone significant genome reduction by gene loss over time in the context of their obligate associations with the host. The flux, streamlining and elimination of genes in these genomes constitute a selective and ongoing process. Comparative analyses of five completely sequenced obligatory intracellular parasite genomes reveal that these genomes display marked similarities in patterns of protein length and frequency distribution, with substantial sharing of a ‘backbone genome’. From category distribution based on the database of cluster of orthologous groups of proteins (COG), it is clear that habitat is a major factor contributing to genome reduction. It is also observed that, in all five obligatory intracellular parasites, the reduction in number of genes/proteins is greater for proteins with lengths of 200–600 amino acids. These comparative analyses highlight that gene loss is function-dependent, but is independent of protein length. These comparisons enhance our knowledge of the forces that drive the extreme specialization of the bacteria and their association with the host. Published online ahead of print on 23 April 2004 as DOI 10.1099/ijs.0.63090-0. Bar charts showing a representation of bacterial genome sizes and gene numbers (Fig. A), the distribution of COG categories and their percentage representation in the bacterial genomes (Fig. B) and the percentage change in protein length distributions in the five obligatory intracellular parasites compared to E. coli (Fig. C), and tables listing gene numbers and genome sizes of obligatory intracellular parasites (Table A) and the percentage distribution of different COG categories (Table B) are available as supplementary material in IJSEM Online.