The evolutionary dynamics and fate of spontaneously duplicated tRNA genes in bacteria

• Applicant: Jenna Gallie, Ph.D.
• Subject Area: General Genetics and Functional Genome Biology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 466526157

Translation is the process by which genetic information is converted into proteins, the workhorses of the cell. Small molecules called transfer RNAs (“tRNAs”) play a crucial role in translation; they are the adapter molecules that match codons (the building blocks of genetic information) with amino acids (the building blocks of proteins). Organisms carry many types of tRNAs, each encoded by one or more genes (the “tRNA gene set”). Broadly speaking, the function of the tRNA gene set – to translate 61 types of codons into 20 different kinds of amino acids – is conserved across organisms. Nevertheless, tRNA gene set composition varies considerably between organisms. How and why these differences arise has been a question of long-standing interest among scientists. To date, knowledge about tRNA gene set evolution comes overwhelmingly from theoretical models and computational studies; direct observations of tRNA gene sets changing in real time remain rare. Recently, we provided such an observation, documenting the evolution of a bacterial tRNA gene set by within-genome tRNA gene duplication events. We began by removing tRNA genes from P. fluorescens SBW25, resulting in strains with fewer tRNA genes and reduced growth rates. Next, we gave the slow-growing strains the opportunity to improve their growth (i.e., adapt) during real-time evolution experiments. The strains adapted repeatedly and rapidly, by duplicating large segments (up to 15 %) of the chromosome. Each duplicated segment contains at least one compensatory tRNA gene, and alters the pool of mature, ready-to-use tRNA molecules. However, preliminary work indicates that the adaptive duplications are highly unstable; they are formed and lost – without a trace – at very high rates. Hence, while we have observed a surprising degree of adaptive flexibility in a bacterial tRNA gene set, whether the newly-formed tRNA genes persist across longer time scales remains to be seen. Here we propose experiments investigating the evolutionary fate of the large-scale duplications (and new tRNA genes). We propose to use mathematical modelling to explore factors influencing the evolutionary dynamics of the duplications. The modelling outcomes will be used to inform an extended evolution experiment, during which the evolutionary fate of the duplications will be directly observed. The evolutionary dynamics occurring in each experimental lineage will be dissected using a combination of biological assays, whole genome sequencing, Sanger sequencing, genetic engineering, and mature tRNA pool sequencing. These experiments are expected to determine whether large-scale duplications are maintained in the population, or whether they are eventually displaced by more stable adaptive solutions (e.g., small duplications, SNPs). In turn, this will shed light on whether large-scale duplications serve to generate adaptive but fleeting flexibility, or whether they may contribute to the longer-term evolution of tRNA gene sets.

• DFG Programme: Research Grants