The birth of a bacterial tRNA gene by large-scale, tandem duplication events

Abstract
Data availability
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Abstract

Organisms differ in the types and numbers of tRNA genes that they carry. While the evolutionary mechanisms behind tRNA gene set evolution have been investigated theoretically and computationally, direct observations of tRNA gene set evolution remain rare. Here, we report the evolution of a tRNA gene set in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The growth defect caused by deleting the single-copy tRNA gene, serCGA, is rapidly compensated by large-scale (45-290 kb) duplications in the chromosome. Each duplication encompasses a second, compensatory tRNA gene (serTGA) and is associated with a rise in tRNA‑Ser(UGA) in the mature tRNA pool. We postulate that tRNA‑Ser(CGA) elimination increases the translational demand for tRNA‑Ser(UGA), a pressure relieved by increasing serTGA copy number. This work demonstrates that tRNA gene sets can evolve through duplication of existing tRNA genes, a phenomenon that may contribute to the presence of multiple, identical tRNA gene copies within genomes.

Data availability

Illumina whole genome sequencing data has been uploaded to NCBI SRA (accession PRJNA558233). YAMAT-seq data has been uploaded to NCBI GEO (accession GSE144791). Source data files have been provided for Figures 2B, 2C, 2D, 2F, 2G, 2H, 3B, 3C, 3D, 3E, 4C, 4D, 5A, and 5B.

The following data sets were generated

1. Jenna Gallie
(2019) Experimental evolution of a bacterial strain with a sub-optimal tRNA gene set (single-copy tRNA gene serCGA deleted)
NCBI SRA, PRJNA558233.

https://www.ncbi.nlm.nih.gov/sra/PRJNA558233
1. Gökçe Ayan
2. Jenna Gallie
(2019) YAMAT-seq of mature tRNA pools in the bacterium Pseudomonas fluorescens SBW25 and derivatives
NCBI GEO, GSE144791.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144791

Article and author information

Author details

Gökçe B Ayan

Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany

Competing interests
The authors declare that no competing interests exist.
Hye Jin Park

Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany

Competing interests
The authors declare that no competing interests exist.
Jenna Gallie

Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany

For correspondence
gallie@evolbio.mpg.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2918-0925

Funding

Max Planck Society

Gökçe B Ayan

Max Planck Society

Hye Jin Park

Max Planck Society

Jenna Gallie

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.