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

Khomarbaghi, Zahra; Ngan, Wing Y.; Ayan, Gökce B.; Lim, Sungbin; Dechow-Seligmann, Gunda; Nandy, Pabitra; Gallie, Jenna

doi:10.1101/2022.12.02.516541

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

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Ngan, Wing Y.
Research Group Microbial Evolutionary Dynamics (Gallie), Department Theoretical Biology (Traulsen), Max Planck Institute for Evolutionary Biology, Max Planck Society;
IMPRS for Evolutionary Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Ayan, Gökce B.
Research Group Microbial Evolutionary Dynamics (Gallie), Department Theoretical Biology (Traulsen), Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Lim, Sungbin
Research Group Microbial Evolutionary Dynamics (Gallie), Department Theoretical Biology (Traulsen), Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Dechow-Seligmann, Gunda
Research Group Microbial Evolutionary Dynamics (Gallie), Department Theoretical Biology (Traulsen), Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Nandy, Pabitra
Research Group Microbial Evolutionary Dynamics (Gallie), Department Theoretical Biology (Traulsen), Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Gallie, Jenna
Research Group Microbial Evolutionary Dynamics (Gallie), Department Theoretical Biology (Traulsen), Max Planck Institute for Evolutionary Biology, Max Planck Society;

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https://zenodo.org/records/10083944
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Citation

Khomarbaghi, Z., Ngan, W. Y., Ayan, G. B., Lim, S., Dechow-Seligmann, G., Nandy, P., et al. (2024). Large-scale duplication events underpin population-level flexibility in bacterial tRNA gene copy number. Nucleic Acids Research, 52(5), 2446-2462. doi:10.1101/2022.12.02.516541.

Cite as: https://hdl.handle.net/21.11116/0000-000D-5CAC-B

Abstract

The complement of tRNA genes within a genome is typically considered to be a (relatively) 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 high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications 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 duplications 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 by which tRNA gene set diversity can be rapidly generated, 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 high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change.