The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

By Gene‐Wei Li, E. Oh, Jonathan S. Weissman. Nature, 2012

652 citations recorded by the source corpus.

Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the messenger RNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling—deep sequencing of ribosome-protected mRNA fragments. This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine–Dalgarno-(SD)-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ba89d09f4da4936fc89aea8277fa79cef1fa3fe2

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Citations in the corpus

Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. (2014, methodology): “coli, there is little drop-off in ribosome density for the vast majority of genes (Li et al., 2012; Oh et al., 2011) (Figure 1A).”
Codon Bias as a Means to Fine-Tune Gene Expression (2015, methodology): “In bacteria, ribosome profiling experiments identified ribosomal pausing at Shine-Dalgarno-like sequences (Li et al., 2012).”
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction (2013, neutral): “…nutrientlimited conditions will allow for a deeper understanding of nutrient limitation-dependent effective catalytic rates, and new data sets (Li et al, 2012) and models (Tuller et al, 2010) on the processes of gene expression can help to refine model parameters and determine their…”
Recombinant protein expression in Escherichia coli: advances and challenges (2014, background): “Finally, some codon combinations can create Shine–Dalgarno-like structures that cause translational pausing by hybridization between the target mRNA and the 16S rRNA of the translating ribosome (Li et al., 2012).”
In vivo aspects of protein folding and quality control (2016, background): “The rate of translation can be manipulated by cells to optimize folding (29-34).”