Molecular evolutionary studies of genome degradation in bacteria

University dissertation from Uppsala : Acta Universitatis Upsaliensis

Abstract: The genus Rickettsia belongs to the α-proteobacteria and consists of obligate intracellular bacteria, which often are pathogenic for humans. All Rickettsia have small genomes, highly adapted to an intracellular lifestyle. However, the ancestors of Rickettsia were most likely free-living organisms with substantially larger genomes, This thesis is a study of the reductive evolutionary processes by which Rickettsia has adapted to a life inside eukaryotic cells. The Rickettsia prowazekii genome sequence confirmed the close phylogenetic relationship between the genus Rickettsia and the mitochondria. In addition, 12 putative pseudogenes and an unusually large fraction of non-coding DNA (24%) were identified. Analysis of the metK genomic region in different Rickettsia species identified metK as a pseudogene in all but two lineages. The pattern of mutations indicated that the pseudogenes are no longer under purfying selection, and that metK was inactivated several times independently in different lineages. Similar patterns were found in many other Rickettsia pseudogenes, revealing an ongoing genome degradation process in the Rickettsia.Analysis of neutrally evolving pseudogenes showed that deletions dominate over insertions, and that there is a mutational bias towards A+T nucleotides, in the Rickettsia genomes. In agreement, the long intergenic regions in the R. prowazekii genome have a decreased G+C content. Several of these regions showed sequence homology to genes in orthologous positions in other Rickettsia genomes, which indicated that the long intergenic regions represent old genes that are disappearing from the genome.The ancestor of the two major Rickettsia groups may have encoded 200-300 additional genes compared to R. prowazekii. Differential loss of mostly genus specific genes during the evolution resulted in the present-day Rickettsia genomes. Currently, Rickettsia inactivates genes at a higher than they are eliminated from the genome by fixation of deletions.

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