Publicação
Elucidating the role of tRNA-modifications in adaptive evolution
| Resumo: | Transfer RNA (tRNA) is the class of small RNAs with the highest number of chemical modifications. These modifications are catalyzed by multiple enzymes and ensure tRNA stability, as well as the efficiency and fidelity of mRNA translation, potentially leading to diseases known as tRNA modopathies. In recent years, significant progress has been made in understanding the biology of tRNA modifications; however, their impact on the proteome and human diseases is still not fully understood. In this thesis, we used yeast strains with deletions in genes encoding tRNA-modifying enzymes to further investigate the biology of these modifications. These strains were phenotypically and molecularly characterized and subjected to experimental evolution studies to assess their ability to adapt to tRNA hypomodification. The molecular mechanisms underlying this adaptation were also examined, and protein aggregation induced by tRNA hypomodification was monitored using a chimeric sensor (HSP104-GFP) that binds to protein aggregates. Strains deleted for the Elp1, Elp3, Trm4, Trm9, and Slm3 genes exhibited reduced growth and extensive protein aggregation. Surprisingly, they regained growth rates during laboratory evolution, despite maintaining protein aggregation at very high levels. Genome sequencing revealed the accumulation of copy number variations (CNVs), which disappeared over the course of evolution. RNA-seq data showed that all strains responded similarly to tRNA hypomodification, with a decrease in the expression of genes involved in stress response and protein folding, and an increase in the expression of genes related to protein synthesis at generation 500 in the strains deleted for Elp1, Elp3, and Trm9. The transcriptional response of strains deleted for Trm4 and Slm3 strains present the same response at the beginning of experimental evolution. Our data provides evidence that tRNA hypomodification results in protein aggregates accumulation, decreased fitness, gene expression and genomic alterations. The data also shows that such changes can be overcome over time, creating a homeostatic condition where protein aggregation is highly tolerated and does not affect fitness. |
|---|---|
| Autores principais: | Poim, Ana Rita Teixeira |
| Assunto: | tRNA Yeast Protein aggregation Epitranscriptome tRNA modifications |
| Ano: | 2025 |
| País: | Portugal |
| Tipo de documento: | tese de doutoramento |
| Tipo de acesso: | acesso embargado |
| Instituição associada: | Universidade de Aveiro |
| Idioma: | inglês |
| Origem: | RIA - Repositório Institucional da Universidade de Aveiro |
| Resumo: | Transfer RNA (tRNA) is the class of small RNAs with the highest number of chemical modifications. These modifications are catalyzed by multiple enzymes and ensure tRNA stability, as well as the efficiency and fidelity of mRNA translation, potentially leading to diseases known as tRNA modopathies. In recent years, significant progress has been made in understanding the biology of tRNA modifications; however, their impact on the proteome and human diseases is still not fully understood. In this thesis, we used yeast strains with deletions in genes encoding tRNA-modifying enzymes to further investigate the biology of these modifications. These strains were phenotypically and molecularly characterized and subjected to experimental evolution studies to assess their ability to adapt to tRNA hypomodification. The molecular mechanisms underlying this adaptation were also examined, and protein aggregation induced by tRNA hypomodification was monitored using a chimeric sensor (HSP104-GFP) that binds to protein aggregates. Strains deleted for the Elp1, Elp3, Trm4, Trm9, and Slm3 genes exhibited reduced growth and extensive protein aggregation. Surprisingly, they regained growth rates during laboratory evolution, despite maintaining protein aggregation at very high levels. Genome sequencing revealed the accumulation of copy number variations (CNVs), which disappeared over the course of evolution. RNA-seq data showed that all strains responded similarly to tRNA hypomodification, with a decrease in the expression of genes involved in stress response and protein folding, and an increase in the expression of genes related to protein synthesis at generation 500 in the strains deleted for Elp1, Elp3, and Trm9. The transcriptional response of strains deleted for Trm4 and Slm3 strains present the same response at the beginning of experimental evolution. Our data provides evidence that tRNA hypomodification results in protein aggregates accumulation, decreased fitness, gene expression and genomic alterations. The data also shows that such changes can be overcome over time, creating a homeostatic condition where protein aggregation is highly tolerated and does not affect fitness. |
|---|