Large-scale duplication events underpin population-level flexibility in bacterial tRNA gene copy number

The complement of tRNA genes within the genome is typically regarded as a stable characteristic of an organism. Here we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the spontaneous, high-rate occurrence of large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplication fragments are up to 1 Mb in size (~15 % of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplication fragments are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism that rapidly generates tRNA gene set diversity, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then the high-rate segregation of the duplication fragment ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is selectively beneficial, the underlying duplication fragments persist and provide the raw material for further, more stable, evolutionary changes.