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

Elife. 2020 Oct 30:9:e57947. doi: 10.7554/eLife.57947.

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.

Keywords: YAMAT-seq; duplication; evolution; evolutionary biology; pseudomonas fluorescens sbw25; serine; tRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Bacterial / genetics
  • Chromosomes, Bacterial / metabolism
  • DNA, Bacterial / genetics*
  • DNA, Bacterial / metabolism
  • Evolution, Molecular
  • Gene Duplication*
  • Pseudomonas fluorescens / genetics*
  • Pseudomonas fluorescens / metabolism
  • RNA, Transfer, Ser / genetics*
  • RNA, Transfer, Ser / metabolism

Substances

  • DNA, Bacterial
  • RNA, Transfer, Ser

Associated data

  • GEO/GSE144791

Grants and funding

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