A bacterial homolog YciH of eukaryotic translation initiation factor eIF1 regulates stress-related gene expression and is unlikely to be involved in translation initiation fidelity

Abstract

YciH is a bacterial protein, homologous to eukaryotic translation initiation factor eIF1. Preceding evidence obtained with the aid of in vitro translation initiation system suggested that it may play a role of a translation initiation factor, ensuring selection against suboptimal initiation complexes. Here we studied the effect of Escherichia coli yciH gene inactivation on translation of model mRNAs. Neither the translation efficiency of leaderless mRNAs, nor mRNAs with non AUG start codons, was found to be affected by YciH in vivo. Comparative proteome analysis revealed that yciH gene knockout leads to a more than fold2- increase in expression of 66 genes and a more than fold2- decrease in the expression of 20 genes. Analysis of these gene sets allowed us to suggest a role of YciH as an inhibitor of translation in a stress response rather than the role of a translation initiation factor.

Keywords: initiation factor; initiation fidelity; translation; yciH.

Figure 1.

Efficiency of model monocistronic (A) CER mRNA translation relative to the control RFP mRNA translation efficiency or second cistron CER relative to control first cistron RFP in CER-RFP bicistronic (B) mRNA in the wild type strain (white bars) and ΔyciH strain (black bars). Schematic representation of mRNA CER is presented on the left panel, while translation efficiencies are shown on the right panel. All constructs' designations are indicated next to the schematic representations. Translation efficiencies of the CER reporter were normalized to the reference RFP construct. Exact values of relative translation efficiencies are shown next to the corresponding bars.

Figure 2.

Influence of yciH on E. coli growth. (A) Growth curves of the WT (gray curves) and ΔyciH (black curves) strains. Squares correspond to the growth in LB rich medium at 37°C, triangles correspond to the growth in M9 poor medium at 37°C, while circles correspond to the growth in LB rich medium at 37°C for 120 minutes followed by the substitution of LB by M9. All curves are marked on the right by the medium used. A point of LB by M9 substitution is indicated by an arrow. (B) Growth competition between the wild type and yciH knockout strains in the rich LB media. The Y-axis shows the proportion of the yciH knockout strain cells in the mixture with the wild-type calls (log scale). Each point corresponds to a 24 hour growth cycle. (C) Growth curves of the WT (light gray squares), ΔyciH (black squares) and WT with plasmid-bourne yciH (pYciH) superexpression (dark gray circles) strains in LB rich medium at 37°C. Curves are marked on the right by strain designation.

Figure 3.

Comparison of eIF1 and YciH primary (lower panel) and tertiary (upper panel) structure. Upper panel presents a superimposition of (I) 48S initiation complex containing 40S subunit, mRNA, initiator tRNA and eIF1A (not included into the presentation) (4KZZ), (II) PIC2 complex containing 40S subunit, eIF1A (not included into the presentation) and eIF1 (4KZY) and (III) the structure of E. coli YciH (1D1R). Only parts proximal to the position of eIF1 are shown. All components are designated on the picture. Position of loops 1 and 2 discussed in the text are indicated. Lower panel contains an alignment of mammalian (rabbit) eIF1 and bacterial (E. coli) YciH proteins.