Fig. 3: Restoration of cell fitness using a simplified gene set.
From: Building a eukaryotic chromosome arm by de novo design and synthesis
a Schematic diagrams of additional genes in the three neochromosomes besides the essential genes. b Fitness analysis of strains carrying assembled neochromosomes under various conditions. WT, BY4741. c Doubling times of corresponding strains in SC medium (n = 3). The average doubling time of BY4742 was set to 1.0. The data are presented as the mean and SD. Source data are provided as a Source Data file. d The logarithmic phenotype index (LPI) of BY4742 (n = 3) and yWT25 (n = 3) under MMS condition. The data are presented as the mean and SD. Unpaired t-test (two-tail) was used compare the two groups, p = 0.0155. The LPIMMS significantly greater than zero indicates the resistance phenotype of corresponding strain. Source data are provided as a Source Data file. e Cell morphology of indicated strains. WT, BY4742. Scale bars, 5 μm. Images are representative of at least three independent samples. f Lysine auxotrophy due to yll027w deletion. YLL027W is expressed in a centromeric plasmid under its native promoter and terminator. g Transcriptome-wide perturbation of yWT12 and yWT25. BY4742 was used as the control for normalization. X axis represents |log2FC|. Y axis represents the percentage of genes with |log2FC|> the value of X axis. h, i KEGG pathway enrichment analysis of the differentially expressed genes in strains, using clusterProfiler package to calculate Benjamini-Hochberg adjusted p values. All eleven terms with adjusted p value < 0.05 in yWT12 were shown in (h). All twelve terms with adjusted p value < 0.05 in yWT25 were shown in (i). Bubble size indicates the gene count and the color reflects the adjusted p value.
