The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation

Abstract

Shine-Dalgarno (SD) sequences, the core element of prokaryotic ribosome-binding sites, facilitate mRNA translation by base-pair interaction with the anti-SD (aSD) sequence of 16S rRNA. In contrast to this paradigm, an inspection of thousands of prokaryotic species unravels tremendous SD sequence diversity both within and between genomes, whereas aSD sequences remain largely static. The pattern has led many to suggest unidentified mechanisms for translation initiation. Here we review known translation-initiation pathways in prokaryotes. Moreover, we seek to understand the cause and consequence of SD diversity through surveying recent advances in biochemistry, genomics, and high-throughput genetics. These findings collectively show: (1) SD:aSD base pairing is beneficial but nonessential to translation initiation. (2) The 5' untranslated region of mRNA evolves dynamically and correlates with organismal phylogeny and ecological niches. (3) Ribosomes have evolved distinct usage of translation-initiation pathways in different species. We propose a model portraying the SD diversity shaped by optimization of gene expression, adaptation to environments and growth demands, and the species-specific prerequisite of ribosomes to initiate translation. The model highlights the coevolution of ribosomes and mRNA features, leading to functional customization of the translation apparatus in each organism.

Keywords: Shine-Dalgarno sequence; diversity; evolution; mRNA; ribosome; transcriptome; translation initiation.

Figure 1.

Architecture of prokaryotic ribosome binding sites. The 3ʹ tail sequence (1530 to 1542 nt) of E. coli 16S rRNA beyond helix 45 is shown. The illustration manifests the base-pairing interaction between the SD region of mRNA and aSD (bold text) of the 16S rRNA. IF, initiation factors; ORF, open reading frame; 5ʹUTR, 5ʹ untranslated region; RBS, ribosome binding site; D_toStart, the distance between the start codon and the 3ʹ end of 16S rRNA.[21]

Figure 2.

Translation initiation mechanisms in prokaryotes. The SD regions of mRNA able or unable to form stable base pairing with the aSD in 16S rRNA are indicated as SD(+) and SD(−), respectively. Open reading frames in mRNA are shown in grey. The 70S scanning mode is shown as the representative for translational coupling

Figure 3.

Sequence and function of the SD region in E. coli. Shown is extended analysis of a published dataset [85]. (A) The RBS contexts of three SD variant libraries. The start codon of the GFP reporter is in bold, and the 9-nt SD region is underlined. (B) Functional distribution of 4⁹ SD variants in the three RBS contexts. CA, canonical SD; 9 G, nine-guanine; 9 U, nine-uracil. (C) Functional distribution of the 1,024 5-nt motifs in the SD region under the three RBS contexts. The impact of a motif on translation initiation is computed as the mean GFP expression of all SD variants bearing this motif. The 1,024 motifs are classified and displayed in terms of the guanine content. Numbers in parentheses indicate the total amount of motifs each category. In (B) and (C), SD variants and 5-nt motifs are ranked by GFP expression and grouped into 10 equal-sized bins in the logarithmic scale. (D) Functional ranking of 5-nt motifs in the SD region under the three RBS contexts. Out of the 1,024 motifs, only the top ten and the canonical motifs are shown. Guanine residues are stressed in bold. Identical motifs present in different RBS contexts are connected by lines

Figure 4.

Distribution of SD:aSD pairing strength and D_tostart with respect to translation efficiency. Shown is extended analysis of a published dataset [85]. All SD variants in the three RBS contexts are assigned to ten groups (1–10, corresponding to low to high translation efficiency in Fig. 3B). The SD:aSD pairing strength (kcal/mol) is estimated by the ViennaRNA Package [142], and D_tostart is calculated based on a described method [21]. The distribution of these two characters is shown as density plots

Figure 5.

Coevolution model of ribosomes and transcriptomes. Pie charts illustrate the relative abundance of SD(+), SD(−), and leaderless (LS) mRNA in transcriptomes. SSU, small ribosomal subunit; LUCA, last universal common ancestor; Kz, Kozak sequence