Fig. 4: The target spectrum of EF-P and EfpL.
From: EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences
A Color code of the heat map corresponds to frequency of the motif to occur in pause site in the ribosome profiling analysis predicted with PausePred34 (From green to red = from low to high). First column: Top 29 motifs whose translation is dependent on EF-P and the control motif PAP in the ribosome profiling analysis comparing E. coli BW25113 with the efp deletion mutant (Δefp). Second column: Comparison of profiling data of Δefp and Δefp cells overexpressing efpL (Δefp +EfpL) at these motifs. B In vivo comparison of rescue efficiency of a set of stalling motifs and the control PAP. Given is the quotient of relative light units measured in Δefp and corresponding trans-complementations by EF-P (+EF-P) and EfpL (+EfpL). Motifs are sorted according to pausing strength determined with our stalling reporter (n = 12, biological replicates, mean with sd indicated as error bars). C In vitro transcription and translation of nLuc® variants nLuc_3xRIPW (IPW) and nLuc_3xRPAP (PAP). The absence (no factor) or presence of the respective translation elongation factors of E. coli (EF-P/EfpL) is shown. Translational output was determined by measuring bioluminescence in a time course of 15 min and is given in relative light units measured at the end of the reaction (RLU/min ± sd) (n ≥ 3, technical replicates). Statistically significant differences to control (no factor) according to ordinary one-way ANOVA (****P < 0.0001, ns not significant). D Left part: Venn diagram of top 388 genes, whose translation depends on EF-P and EfpL. Dependency was determined by comparing asymmetry scores from genes encompassing top 29 stalling motifs listed in (A). Right part: Enriched protein classes to which EfpL-dependent genes belong126. E Growth analysis of E. coli cells in mixture over 72 h in LB with 40 mM glucose. A ΔcadC strain without growth phenotype92 was used as the wild type. E. coli BW25113 ΔcadC was mixed with either E. coli BW25113 Δefp or ΔefpL. The share of the population was detected on LB agar plates (n = 4, biological replicates). Statistically significant differences to wild-type growth according to two-way ANOVA (***P = 0.0006, ns not significant). A–C, E Source data are provided as a Source Data file.
