A new paper in Nature, describes how Shine-Dalgarno-like features in protein coding sequences, leads to bacterial ribosomes pausing during translation. Selection against ribosomal pausing leads to biases in codon usage and coding sequence evolution. Translational pausing represents a new level of regulatory control of gene expression.
Translation, the process by which the nucleotide sequence of mRNA transcripts is decoded and converted into amino acid sequence during protein synthesis, is carried out by ribosomes. Within the ribosome, transfer RNA molecules recognise specific trinucleotide codons on the mRNA, and add their cognate amino acids to nascent protein chains. In bacteria and archaea, ribosomes often recognise the translation start site with the help of a sequence 8 to 12 nucleotides upstream of it – the Shine-Dalgarno sequence (SD). It’s been known since the 1980s that different mRNAs are translated at different rates. The main reason for these differences was thought to be the concentration of rarer varieties of tRNA limiting the rate at which some transcripts could be decoded.
Li et al. have used a new technique, ribosome profiling, that maps ribosome occupancy along mRNAs. This has yielded high-resolution views of local translation rates on the entire protein coding transcriptome of E. coli and Bacillus subtilis. Briefly put, mRNA fragments that have been protected from nuclease digestion by ribosomal binding, are ‘deep sequenced’. The concentration of these ribosome footprints equates to the ribosome occupancy throughout the transcriptome. The local translation rate is inversely related to ribosome occupancy.
Using this technique, Li et al. found many sites where ribosomal density is ten fold or more than the mean. They sought to correlate these translational pauses with specific codons. However, there was little link between occupancy of specifc codons and the abundance of their corresponding tRNAs. Therefore, the concentration of rare tRNAs is not responsible for much translational pausing under normal growth conditions.
To try to find sequence features that were linked to ribosomal pausing, the researchers then tried to correlate any trinucleotide sequences (independently of reading frame) with ribosome occupancy. They found that 6 different trinucleotide sequences, with features resembling Shine-Dalgarno sequences, did correlate with the position of paused ribosomes. This correlation was not found in the yeast, Saccharomyces cerevisiae; in agreement with eukaryotic ribosomes not using SD- anti-SD interactions.
Li et al. went on to show definitively that internal SD-like sequences are linked to translational pausing, by introducing a mutation into one such site and showing that ribosome occupancy was reduced. They also showed that peaks of ribosome occupancy, were caused by translational pausing, rather than attempted internal translational initiation.
As translational pausing limits the amount of free ribosomes, widespread internal SD-like sequences would limit the rate of protein synthesis, and hence the potential bacterial growth rate. In line with this, SD-like sequences in protein coding genes are disfavoured. Selection pressure against SD-like sequences is therefore a major factor in determining codon usage, and more especially the usage of codon pairs (SD sequences are 6/7 nt long).
Interestingly, the authors found that patterns of ribosome occupancy were conserved between orthologous genes in E. coli and B. subtilis. This reflects two different factors; firstly, coding is obviously constrained by protein’s functionality, but secondly it’s suggestive of translational pausing being exploited for functional purposes. Li et al. suggest a number of different ways in which ribosomal pausing can regulate gene expression. It’s known that internal SD-like sequences can promote regulated shifting of reading frame. Ribosome pausing may also modulate folding of nascent protein chains. Lastly, as transcription and translation are closely coupled in bacteria, ribosome occupancy may inhibit the formation of stem-loop structures that prevent transcriptional termination. It will be exciting to work out the extents to which these potential regulatory systems are active. Eukaryotic ribosomes do not use recognition of SD sequences, instead using the 5’ mRNA cap and the less well defined Kozak sequence for translational initiation. Does ribosome pausing occur in eukaryotes? and does it have functional significance?
Li, G., Oh, E., & Weissman, J. (2012). The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria Nature, 484 (7395), 538-541 DOI: 10.1038/nature10965