Dynamic evolution of translation initiation mechanisms in prokaryotes

Abstract

It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5' UTR of an mRNA and the anti-SD sequence in the 3' end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5' UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution.

Fig. 1.

Highly conserved sequence in the 3′ end of 16S rRNA The sequence logo was obtained from the multiple alignment of 16S rRNAs of 277 species. Positions with information content contain a stack of nucleotide characters (A, U, G, and C). The overall height of the stack indicates the sequence conservation at that position, whereas the height of symbols within the stack indicates the relative frequency of each nucleotide at that position (Materials and Methods). An asterisk indicates the position corresponding to the 3′ end of the 16S rRNA of E. coli. See Fig. S1 for the whole alignment.

Fig. 2.

Phylogenetic trees showing dR_SD. Neighbor-joining phylogenetic trees were constructed based on the 16S ribosomal RNA sequences from eubacteria (A) and archaebacteria (B). A colored bar at the branch shows the dR_SD value for each species. The diagram at the upper left indicates the color scheme for dR_SD values. Nodes supported with high bootstrap values, which were obtained from 1,000 resamplings, are shown by a black circle (≥90%) and an open circle (≥80%). Symbols represent each taxonomic group of species.

Fig. 3.

Box plot of dR_SD depending on RPS1 function for translation initiation The box plot represents dR_SD values of each RPS1 type (I ∼ V), as described in Results. Type IV (indicated by an asterisk) does not contain Cyanobacteria species. The dR_SD values of Cyanobacteria are shown in the column indicated by the italic letter C. The middle line indicates the median and the upper and lower edges of the boxes represent the first and third quartiles, respectively. The ends of the vertical lines indicate the minimum and maximum data values, unless outliers are present, in which the lines extend to a maximum of 1.5 times the interquartile range.

Fig. 4.

Differences in the efficiencies of translation initiation between SD-containing genes and non–SD-containing genes. The mRNA folding energy (A) or codon adaptation index (B) of SD-containing genes and non–SD-containing genes are shown as black and gray bars, respectively. H, M, and L represent high SD, middle SD, and low SD groups, respectively (Results). An asterisk indicates a P value <10⁻⁵ (Wilcoxon signed-rank test with Bonferroni correction), and no mark indicates no significant differences (i.e., P > 0.05).