A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool
| Autor: | Sivan Navon, Orna Dahan, Zohar Bloom-Ackermann, Ruth Towers, Yitzhak Pilpel, Hila Gingold |
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| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Cancer Research
lcsh:QH426-470 Genomics Yeast and Fungal Models Saccharomyces cerevisiae Biology Molecular Genetics Model Organisms Molecular cell biology RNA Transfer Stress Physiological Gene Expression Regulation Fungal Genetics Genomic library Gene Regulation Gene Networks Codon Molecular Biology Gene Genetics (clinical) Ecology Evolution Behavior and Systematics Gene Library Sequence Deletion Cellular Stress Responses Regulation of gene expression Systems Biology Robustness (evolution) RNA Gene Pool Nucleic acids lcsh:Genetics RNA processing Transfer RNA Gene pool Genetic Fitness Gene expression Transcriptome Population Genetics Research Article |
| Zdroj: | PLoS Genetics, Vol 10, Iss 1, p e1004084 (2014) PLoS Genetics |
| ISSN: | 1553-7404 1553-7390 |
| Popis: | Deciphering the architecture of the tRNA pool is a prime challenge in translation research, as tRNAs govern the efficiency and accuracy of the process. Towards this challenge, we created a systematic tRNA deletion library in Saccharomyces cerevisiae, aimed at dissecting the specific contribution of each tRNA gene to the tRNA pool and to the cell's fitness. By harnessing this resource, we observed that the majority of tRNA deletions show no appreciable phenotype in rich medium, yet under more challenging conditions, additional phenotypes were observed. Robustness to tRNA gene deletion was often facilitated through extensive backup compensation within and between tRNA families. Interestingly, we found that within tRNA families, genes carrying identical anti-codons can contribute differently to the cellular fitness, suggesting the importance of the genomic surrounding to tRNA expression. Characterization of the transcriptome response to deletions of tRNA genes exposed two disparate patterns: in single-copy families, deletions elicited a stress response; in deletions of genes from multi-copy families, expression of the translation machinery increased. Our results uncover the complex architecture of the tRNA pool and pave the way towards complete understanding of their role in cell physiology. Author Summary Transfer RNAs are an important component of the translation machinery. Despite extensive biochemical investigations, a systems-level investigation of tRNAs' functional roles in physiology, and genetic interactions among them, is lacking. We created a comprehensive tRNA deletion library in yeast and assessed the essentiality of each tRNA in multiple conditions. The majority of tRNA deletions showed no appreciable fitness defect when such strains were grown on rich medium. More challenging environmental conditions, however, revealed a richer set of specific-tRNA phenotypic defects. Co-deletion of tRNA combinations revealed that tRNAs with essential function can be compensated by members of the same or different anti-codon families. We often saw that identical tRNA gene copies contribute deferentially to fitness, suggesting that the genomic context of each gene can affect functionality. Genome-wide expression changes in response to tRNA deletions revealed two different responses. When a deleted tRNA belongs to a family which contains multiple genes with the same anti-codon, the affected cells responded by up-regulating the translation machinery, but upon deletion of singleton tRNAs, the cellular response resembled that of proteotoxic stress. Our tRNA deletion library is a unique resource that paves the way towards fully characterizing the tRNA pool and their role in cell physiology. |
| Databáze: | OpenAIRE |
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