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A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

Figure 1

Creation and analysis of tRNA deletion library.

(A) Schematic representation of the deletion process. 204 different tRNA strains were created using homologous recombination. In each strain, a different tRNA gene was replaced by a hygromycin B resistance marker. (B) Schematic representation of growth measurements, analysis, and scoring. For each strain, relative-growth-rate and relative-growth-yield are calculated in relation to the wild-type strain. These parameters are then projected on a distribution of the wild-type growth parameters. Sigma (σ) is calculated according to the formula and denotes the number of standard deviations from the mean of the wild-type (see also Supplemental figure S1A). The color in the histogram are areas were: σ<−3 (blue), −3<σ<−2 (cyan), 2<σ<3 (yellow) and 3<σ (red). The same color code is used to define phenotypes in the pie charts (C and D). (C–D) Distribution of phenotypes for the tRNA deletion library in rich medium, according to two growth parameters: relative growth yield (C) relative growth rate (D). Deletion strains were assigned to categories according to their σ values. Any absolute σ value larger than 2 was considered as non-normal phenotype, where negative sigma denotes impairment (worse than the wild-type) and positive sigma denotes improvement (better than the wild-type). Any absolute σ value larger than 3 was considered as a strong phenotype. Thus, highly impaired for σ<−3, impaired for −2>σ>−3, improved for 2<σ<3, and highly improved for σ>3, see also Supplemental figure S1B.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1004084.g001