Periodic Reporting for period 3 - CODEKILLER (Killer plasmids as drivers of genetic code changes during yeast evolution)
Periodo di rendicontazione: 2021-10-01 al 2023-03-31
The aim of the CODEKILLER project is to discover mechanisms by which the genetic code can change during evolution. The genetic code is the set of rules that determine how the 64 different codons in mRNA are translated into the 20 different amino acids in protein molecules, for example the codon AUG is translated into methionine. In the cell, the genetic code is physically implemented by tRNA molecules, which are covalently attached to an amino acid at one end and make basepairs with codons in mRNA at the other end. The genetic code is often considered to be universal because it is the same in the nuclear genomes of most species, but in 2018 we discovered that the genetic code has changed several times during the evolution of budding yeast species. Specifically, the codon CUG, which is translated as leucine in most species, is translated as serine or alanine in some groups of yeasts. Because this change is almost the only evolutionary change in the genetic code that has ever happened during the evolution of nuclear genomes, our goal is to understand how it happened.
Our hypothesis is that the evolutionary reassignment of the codon CUG was caused by natural selection imposed by a “killer toxin”, specifically an anticodon nuclease toxin that targeted one type of tRNA molecule, tRNA-Leu(CAG). We postulate that such a toxin exists, and one of the goals of CODEKILLER is to find it. From previous research by other groups since the 1990s, toxins have been identified that target two other types of tRNA, but no toxin targeting tRNA-Leu(CAG) has been found. If we can find this toxin, we will be able to recreate the evolutionary process that eliminated tRNA-Leu(CAG) and led to the change in genetic code from CUG-Leu to CUG-Ser and CUG-Ala.
The project is of interest in evolutionary biology and genetics because it investigates how the rules governing the process of translation, which is a fundamental cellular process that was established billions of years ago, can change during evolution. For an organism to change its genetic code, it must be able to survive a drastic upheaval in the set of proteins that are made by its genes, so the evolutionary pressures that lead to a genetic code change must be strong. Understanding how the genetic code can change, and testing whether changes can be driven by a parasitic genetic element (a toxin made by a killer plasmid), will provide insight into the early evolution of life, and into the pressures experienced by unicellular organisms such as yeasts.
Our hypothesis is that the evolutionary reassignment of the codon CUG was caused by natural selection imposed by a “killer toxin”, specifically an anticodon nuclease toxin that targeted one type of tRNA molecule, tRNA-Leu(CAG). We postulate that such a toxin exists, and one of the goals of CODEKILLER is to find it. From previous research by other groups since the 1990s, toxins have been identified that target two other types of tRNA, but no toxin targeting tRNA-Leu(CAG) has been found. If we can find this toxin, we will be able to recreate the evolutionary process that eliminated tRNA-Leu(CAG) and led to the change in genetic code from CUG-Leu to CUG-Ser and CUG-Ala.
The project is of interest in evolutionary biology and genetics because it investigates how the rules governing the process of translation, which is a fundamental cellular process that was established billions of years ago, can change during evolution. For an organism to change its genetic code, it must be able to survive a drastic upheaval in the set of proteins that are made by its genes, so the evolutionary pressures that lead to a genetic code change must be strong. Understanding how the genetic code can change, and testing whether changes can be driven by a parasitic genetic element (a toxin made by a killer plasmid), will provide insight into the early evolution of life, and into the pressures experienced by unicellular organisms such as yeasts.
Using advanced bioinformatics methods, we have mined genome sequence data from yeast species to discover genes that encode potential killer toxins that act as tRNA anticodon nucleases. We have discovered a large number of new candidate toxin genes, greatly increasing the number of known toxins and the range of yeast species that they come from. The candidate toxin proteins are very diverse. Laboratory experiments to characterise their biochemical activities, and to characterise the relationship between toxin and tRNA target sequences, are underway.
The results already obtained greatly expand our knowledge of the anticodon nuclease family of killer toxins and show that this family is highly heterogeneous and evolving very rapidly. When combined with our future studies on the tRNA target specificity of each of these toxins, we will have a much clearer understanding of the ubiquity of this class of killer toxin, and its role in the evolution of the genetic code.