Selection-driven gene loss in bacteria

Abstract

Gene loss by deletion is a common evolutionary process in bacteria, as exemplified by bacteria with small genomes that have evolved from bacteria with larger genomes by reductive processes. The driving force(s) for genome reduction remains unclear, and here we examined the hypothesis that gene loss is selected because carriage of superfluous genes confers a fitness cost to the bacterium. In the bacterium Salmonella enterica, we measured deletion rates at 11 chromosomal positions and the fitness effects of several spontaneous deletions. Deletion rates varied over 200-fold between different regions with the replication terminus region showing the highest rates. Approximately 25% of the examined deletions caused an increase in fitness under one or several growth conditions, and after serial passage of wild-type bacteria in rich medium for 1,000 generations we observed fixation of deletions that substantially increased bacterial fitness when reconstructed in a non-evolved bacterium. These results suggest that selection could be a significant driver of gene loss and reductive genome evolution.

Figure 1. Chromosomal locations of the Tn10 construct and deletion rates.

(A) Schematic representation of the Salmonella typhimurium LT chromosome and the structure and insertion points of the Tn10 construct used for measurements of deletion rates. Numbers and arrows outside the chromosome ring indicate the Tn10 insertion point. The relative size of the grey box and the numbers on the inside of the ring indicate the size of the deletions isolated in that specific region. When numbers are absent this indicate that the deletions were internal to the Tn10 construct. In the middle, the structure and gene content of the Tn10 construct and the resulting phenotypes of loss of the cat, moaA and lacZ genes, respectively, are shown. (B) Deletion rates at 11 different chromosomal regions. Standard errors are indicated. The normalization procedure is described in Text S1_ENREF_20. Compare with Figure S4 for a different normalization method (Text S1).

Figure 2. Relative fitness of mutants with deletion of different chromosomal regions.

(A) Relative exponential growth rates (parental strain set to 1.0) in single cultures for mutants with deletion of different chromosomal regions during growth in rich LB medium. (B) Relative exponential growth rates (parental strain set to 1.0) in single cultures for mutants with deletion of different chromosomal regions during growth in minimal (M9) glycerol medium. (C) Selection coefficients of deletion mutants obtained from competition experiments in rich LB medium with an isogenic parental control (defined as s = 0).