Large-scale duplication events underpin population-level flexibility in tRNA gene copy number inPseudomonas fluorescensSBW25

Abstract

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 bacteriumPseudomonas fluorescensSBW25. 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.

Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes

“…There are 11 similar clusters of 4-12 tandemly repeated Group 1 and Group 3 REP sequences dispersed around the SBW25 chromosome [17, 18]. It has previously been hypothesized [17, 18] and empirically observed [14, 15] that these REP clusters can serve as recombination hot spots, resulting in large-scale genomic rearrangements.…”

“…Mutations were identified using a mixture of breseq, Geneious (version 2023.2.1), and previously published protocols [14,15] (see Supplementary Text S1, Supplementary Tables S1 and S2).…”

“…A mean coverage of 142-fold per genomic base was obtained. Mutations were identified using a mixture of breseq [23], Geneious (version 2020.1.2), and previously published protocols [14, 15] (see Supplementary Text S2, Supplementary Tables S1 and S4). Raw sequencing reads, and the updated reference genome, are available on Zenodo.…”

“…We began by testing the stability of the SBW25-Dup-IS genome rearrangement with a stability assay [15]. The stability assay involves (i) growing the duplication strain in overnight culture, (ii) plating onto agar, and (iii) examining the size of the resulting colonies.…”

Relationship between prokaryotic GC content and environmental salinity

“…It was also noticed that the correlations in tRNA and 5S rRNA genes were stronger than those in 16S rRNA and 23S rRNA genes. The tRNA genes are known for their evolutionary flexibility, as they mutate quickly and are sites of genomic instability (49)(50)(51). On the other hand, the ribosomal RNA genes are known for their conservation in evolution.…”