Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle

Abstract

Sequencing of complete microbial genomes, pioneered in 1995 by J. C. Venter and colleagues, continues at an ever-increasing pace. The availability of complete genome sequences has had a major impact on the view of microbial evolution. Comparative analysis of the complete genomes of several diverse microorganisms on the basis of such properties as codon usage, open reading frame (ORF) density, and the lengths of coding regions shows many common trends in their organization. Comparison of the complete genomes of closely related bacterial species, Mycoplasma genitalium and Mycoplasma pneumoniae, showed a significant degree of synteny between these organisms. Homologous genes and their products can be classified into orthologs, related by vertical descent (e.g., speciation), and paralogs, related by duplication. Pathogenic bacteria import a variety of metabolites from their hosts, which allows them to shed genes encoding enzymes for some of the metabolic pathways. Comparative analysis of the available microbial genomes reveals both conservation of protein families and diversity of gene repertoires and gene organization among organisms that belong to diverse phylogenetic lineages. In many cases, bacterial genes seem to have substituted for the original genes of the archaeal-eukaryotic lineage, making phylogenetic reconstructions extremely complicated.